diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile
index b91fdce51..414d25902 100644
--- a/.devcontainer/Dockerfile
+++ b/.devcontainer/Dockerfile
@@ -1,14 +1,16 @@
-FROM mcr.microsoft.com/devcontainers/javascript-node:1-20-bullseye
+FROM mcr.microsoft.com/devcontainers/javascript-node:24-bookworm
 
 # Install MongoDB command line tools - though mongo-database-tools not available on arm64
-ARG MONGO_TOOLS_VERSION=6.0
+ARG MONGO_TOOLS_VERSION=8.0
 RUN . /etc/os-release \
     && curl -sSL "https://www.mongodb.org/static/pgp/server-${MONGO_TOOLS_VERSION}.asc" | gpg --dearmor > /usr/share/keyrings/mongodb-archive-keyring.gpg \
     && echo "deb [arch=$(dpkg --print-architecture) signed-by=/usr/share/keyrings/mongodb-archive-keyring.gpg] http://repo.mongodb.org/apt/debian ${VERSION_CODENAME}/mongodb-org/${MONGO_TOOLS_VERSION} main" | tee /etc/apt/sources.list.d/mongodb-org-${MONGO_TOOLS_VERSION}.list \
     && apt-get update && export DEBIAN_FRONTEND=noninteractive \
     && apt-get install -y mongodb-mongosh \
     && if [ "$(dpkg --print-architecture)" = "amd64" ]; then apt-get install -y mongodb-database-tools; fi \
-    && apt-get clean -y && rm -rf /var/lib/apt/lists/*
+    && apt-get clean -y && rm -rf /var/lib/apt/lists/* \
+    && mkdir -p /data/uploads \
+    && chown -R ${USERNAME}:npm /data/uploads
 
 # [Optional] Uncomment this section to install additional OS packages.
 # RUN apt-get update && export DEBIAN_FRONTEND=noninteractive \
diff --git a/.devcontainer/docker-compose.yml b/.devcontainer/compose.yml
similarity index 90%
rename from .devcontainer/docker-compose.yml
rename to .devcontainer/compose.yml
index 4e4d52d66..d9b0868e3 100644
--- a/.devcontainer/docker-compose.yml
+++ b/.devcontainer/compose.yml
@@ -7,6 +7,9 @@ services:
       dockerfile: Dockerfile
     volumes:
       - ../..:/workspaces:cached
+      - uploads:/data/uploads
+    environment:
+      FILE_UPLOAD_FOLDER: /data/uploads
 
     # Overrides default command so things don't shut down after the process ends.
     command: sleep infinity
@@ -18,7 +21,7 @@ services:
     # (Adding the "ports" property to this file will not forward from a Codespace.)
 
   db:
-    image: mongo:latest
+    image: mongo:8
     restart: unless-stopped
     volumes:
       - mongodb-data:/data/db
@@ -34,3 +37,4 @@ services:
 
 volumes:
   mongodb-data: null
+  uploads: null
diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index 9b7b28ae8..f1778bbc3 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -3,7 +3,7 @@
 // https://github.com/devcontainers/templates/tree/main/src/javascript-node-mongo
 {
   "name": "Apollo",
-  "dockerComposeFile": "docker-compose.yml",
+  "dockerComposeFile": "compose.yml",
   "service": "app",
   "workspaceFolder": "/workspaces/${localWorkspaceFolderBasename}",
 
diff --git a/.github/workflows/cypress_debug.yml b/.github/workflows/cypress_debug.yml
index 735679470..ba595f2dc 100644
--- a/.github/workflows/cypress_debug.yml
+++ b/.github/workflows/cypress_debug.yml
@@ -9,10 +9,10 @@ jobs:
       - name: Check out
         uses: actions/checkout@v4
 
-      - name: Use Node.js 20.x
+      - name: Use Node.js 24.x
         uses: actions/setup-node@v4
         with:
-          node-version: 20
+          node-version: 24
           cache: yarn
 
       - name: Install
diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
index 5f0ab7631..89f44b2ed 100644
--- a/.github/workflows/deploy.yml
+++ b/.github/workflows/deploy.yml
@@ -20,10 +20,10 @@ jobs:
     steps:
       - name: Check out
         uses: actions/checkout@v4
-      - name: Use Node.js 20.x
+      - name: Use Node.js 24.x
         uses: actions/setup-node@v4
         with:
-          node-version: 20
+          node-version: 24
           cache: yarn
       - name: Install
         if: inputs.environment == 'staging'
@@ -31,7 +31,7 @@ jobs:
       - name: Build plugin
         if: inputs.environment == 'staging'
         run: |
-          yarn build
+          JB_NPM=false yarn build
           cp dist/jbrowse-plugin-apollo.umd.development.js dist/apollo.js
         working-directory: packages/jbrowse-plugin-apollo
       - name: Fetch plugin
diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
index aaab917fe..3e21b3048 100644
--- a/.github/workflows/pull_request.yml
+++ b/.github/workflows/pull_request.yml
@@ -12,22 +12,35 @@ jobs:
     steps:
       - name: Check out
         uses: actions/checkout@v4
-      - name: Use Node.js 20.x
+      - name: Use Node.js 24.x
         uses: actions/setup-node@v4
         with:
-          node-version: 20
+          node-version: 24
           cache: yarn
       - name: Install
         run: yarn --immutable
-        # Have to build shared before linting so type-based lint rules can
-        # run correctly
+      # Have to build shared before linting so type-based lint rules can
+      # run correctly
       - name: Build shared
         run: yarn build
         working-directory: packages/apollo-shared
       - name: Lint codebase
         run: yarn eslint --max-warnings 0
-      - name: Run Jest tests
-        run: yarn test
+
+      # apollo-shared tests
+      - name: Build shared
+        run: yarn build
+        working-directory: packages/apollo-shared
+      - name: Run apollo-shared tests
+        run: yarn run test:ci
+        working-directory: packages/apollo-shared
+
+      # jbrowse-plugin-apollo tests
+      - name: Run jbrowse-plugin-apollo tests
+        run: yarn run test:ci
+        working-directory: packages/jbrowse-plugin-apollo
+
+      # Cypress tests
       - name: Get latest JBrowse
         run: yarn run jbrowse create --nightly .jbrowse
         working-directory: packages/jbrowse-plugin-apollo
@@ -43,13 +56,16 @@ jobs:
       - name: Run Cypress tests
         run: yarn run test:e2e
         working-directory: packages/jbrowse-plugin-apollo
+
+      # CLI tests
       - name: Start apollo
         run: |
           yarn --cwd packages/apollo-shared start &
           yarn --cwd packages/apollo-collaboration-server test:cli:start &
       - name: Run CLI tests
-        run: yarn test:cli
+        run: yarn run test:ci
         working-directory: packages/apollo-cli
+
       # - name: Run docker tests
       #   working-directory: packages/apollo-cli
       #   run: python3 ./src/test/test_docker.py
diff --git a/.github/workflows/push.yml b/.github/workflows/push.yml
index d4797b503..12c944cc2 100644
--- a/.github/workflows/push.yml
+++ b/.github/workflows/push.yml
@@ -14,10 +14,10 @@ jobs:
     steps:
       - name: Check out
         uses: actions/checkout@v4
-      - name: Use Node.js 20.x
+      - name: Use Node.js 24.x
         uses: actions/setup-node@v4
         with:
-          node-version: 20
+          node-version: 24
           cache: yarn
       - name: Install
         run: yarn --immutable
@@ -25,7 +25,7 @@ jobs:
         run: yarn build
         working-directory: packages/apollo-collaboration-server
       - name: Build plugin
-        run: yarn build
+        run: JB_NPM=false yarn build
         working-directory: packages/jbrowse-plugin-apollo
   lint:
     name: Lint
@@ -33,10 +33,10 @@ jobs:
     steps:
       - name: Check out
         uses: actions/checkout@v4
-      - name: Use Node.js 20.x
+      - name: Use Node.js 24.x
         uses: actions/setup-node@v4
         with:
-          node-version: 20
+          node-version: 24
           cache: yarn
       - name: Install
         run: yarn --immutable
diff --git a/.github/workflows/website.yml b/.github/workflows/website.yml
index e23a75144..72fdb2116 100644
--- a/.github/workflows/website.yml
+++ b/.github/workflows/website.yml
@@ -11,10 +11,10 @@ jobs:
     steps:
       - name: Check out
         uses: actions/checkout@v4
-      - name: Use Node.js 20.x
+      - name: Use Node.js 24.x
         uses: actions/setup-node@v4
         with:
-          node-version: 20
+          node-version: 24
           cache: yarn
       - name: Install
         run: yarn --immutable
diff --git a/.husky/pre-commit b/.husky/pre-commit
index 5e08d62fe..508f69fa9 100755
--- a/.husky/pre-commit
+++ b/.husky/pre-commit
@@ -1,3 +1,3 @@
 #!/usr/bin/env sh
-yarn node .husky/pre-commit.js
+yarn node .husky/pre-commit.cjs
 yarn lint-staged
diff --git a/.husky/pre-commit.js b/.husky/pre-commit.cjs
similarity index 100%
rename from .husky/pre-commit.js
rename to .husky/pre-commit.cjs
diff --git a/.prettierrc.lint-staged.mjs b/.prettierrc.lint-staged.mjs
index ec3e4318e..431902430 100644
--- a/.prettierrc.lint-staged.mjs
+++ b/.prettierrc.lint-staged.mjs
@@ -13,6 +13,7 @@ const config = {
       options: { parser: 'jsonc' },
     },
   ],
+  // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment
   plugins: [packagejson],
 }
 
diff --git a/eslint.config.mjs b/eslint.config.mjs
index 2a8e98397..956fcaef0 100644
--- a/eslint.config.mjs
+++ b/eslint.config.mjs
@@ -33,18 +33,11 @@ export default [
   pluginReact.configs.flat.recommended,
   // eslint-disable-next-line @typescript-eslint/no-unsafe-member-access
   pluginJSXA11y.flatConfigs.recommended,
-  // eslint-disable-next-line @typescript-eslint/no-unsafe-member-access
   pluginCypress.configs.recommended,
   {
     languageOptions: {
       globals: { ...globals.browser, ...globals.node },
-      parserOptions: {
-        projectService: {
-          allowDefaultProject: ['packages/jbrowse-plugin-apollo/*.js'],
-        },
-        defaultProject: 'tsconfig.json',
-        tsconfigRootDir: import.meta.dirname,
-      },
+      parserOptions: { projectService: true },
     },
     settings: { react: { version: 'detect' } },
     // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment
@@ -122,6 +115,7 @@ export default [
       'packages/website/src/**/*.{jsx,tsx}',
     ],
     plugins: { 'react-hooks': pluginReactHooks },
+    // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment, @typescript-eslint/no-unsafe-member-access
     rules: { ...pluginReactHooks.configs.recommended.rules },
   },
   // Don't enforce tsdoc syntax in JS files
diff --git a/package.json b/package.json
index f05511fa6..36232a66d 100644
--- a/package.json
+++ b/package.json
@@ -2,6 +2,7 @@
   "name": "apollo3",
   "private": true,
   "description": "Monorepo containing Apollo front and back end code",
+  "type": "module",
   "workspaces": [
     "packages/*"
   ],
@@ -19,7 +20,7 @@
   "devDependencies": {
     "@eslint/js": "^9.21.0",
     "@types/cross-spawn": "^6.0.6",
-    "@types/node": "^20.19.15",
+    "@types/node": "^24.10.9",
     "@types/semver": "^7",
     "@types/yargs": "^17.0.32",
     "@typescript-eslint/parser": "^8.25.0",
diff --git a/packages/apollo-cli/README.md b/packages/apollo-cli/README.md
index 18e82a90d..0fc4741bc 100644
--- a/packages/apollo-cli/README.md
+++ b/packages/apollo-cli/README.md
@@ -16,7 +16,7 @@ $ npm install -g @apollo-annotation/cli
 $ apollo COMMAND
 running command...
 $ apollo (--version)
-@apollo-annotation/cli/0.3.11 linux-x64 node-v24.6.0
+@apollo-annotation/cli/0.3.11 linux-x64 node-v24.13.0
 $ apollo --help [COMMAND]
 USAGE
   $ apollo COMMAND
@@ -29,972 +29,7 @@ USAGE
 
 <!-- commands -->
 
-- [`apollo assembly add-from-fasta INPUT`](#apollo-assembly-add-from-fasta-input)
-- [`apollo assembly add-from-gff INPUT-FILE`](#apollo-assembly-add-from-gff-input-file)
-- [`apollo assembly check`](#apollo-assembly-check)
-- [`apollo assembly delete`](#apollo-assembly-delete)
-- [`apollo assembly get`](#apollo-assembly-get)
-- [`apollo assembly sequence`](#apollo-assembly-sequence)
-- [`apollo change get`](#apollo-change-get)
-- [`apollo config [KEY] [VALUE]`](#apollo-config-key-value)
-- [`apollo export gff3 ASSEMBLY`](#apollo-export-gff3-assembly)
-- [`apollo feature add [FEATURE-JSON]`](#apollo-feature-add-feature-json)
-- [`apollo feature add-child`](#apollo-feature-add-child)
-- [`apollo feature check`](#apollo-feature-check)
-- [`apollo feature copy`](#apollo-feature-copy)
-- [`apollo feature delete`](#apollo-feature-delete)
-- [`apollo feature edit`](#apollo-feature-edit)
-- [`apollo feature edit-attribute`](#apollo-feature-edit-attribute)
-- [`apollo feature edit-coords`](#apollo-feature-edit-coords)
-- [`apollo feature edit-type`](#apollo-feature-edit-type)
-- [`apollo feature get`](#apollo-feature-get)
-- [`apollo feature get-id`](#apollo-feature-get-id)
-- [`apollo feature get-indexed-id ID`](#apollo-feature-get-indexed-id-id)
-- [`apollo feature import INPUT-FILE`](#apollo-feature-import-input-file)
-- [`apollo feature search`](#apollo-feature-search)
-- [`apollo file delete`](#apollo-file-delete)
-- [`apollo file download`](#apollo-file-download)
-- [`apollo file get`](#apollo-file-get)
-- [`apollo file upload INPUT-FILE`](#apollo-file-upload-input-file)
 - [`apollo help [COMMANDS]`](#apollo-help-commands)
-- [`apollo jbrowse desktop JBROWSEFILE`](#apollo-jbrowse-desktop-jbrowsefile)
-- [`apollo jbrowse get-config`](#apollo-jbrowse-get-config)
-- [`apollo jbrowse set-config INPUTFILE`](#apollo-jbrowse-set-config-inputfile)
-- [`apollo login`](#apollo-login)
-- [`apollo logout`](#apollo-logout)
-- [`apollo refseq add-alias INPUT-FILE`](#apollo-refseq-add-alias-input-file)
-- [`apollo refseq get`](#apollo-refseq-get)
-- [`apollo status`](#apollo-status)
-- [`apollo user get`](#apollo-user-get)
-
-## `apollo assembly add-from-fasta INPUT`
-
-Add a new assembly from fasta input
-
-```
-USAGE
-  $ apollo assembly add-from-fasta INPUT [--profile <value>] [--config-file <value>] [-a <value>] [-f] [-e] [--fai <value>]
-    [--gzi <value>] [-z | -d]
-
-ARGUMENTS
-  INPUT  Input fasta file, local or remote, or id of a previously uploaded file. For local or remote files, it is
-         assumed the file is bgzip'd with `bgzip` and indexed with `samtools faidx`. The indexes are assumed to be at
-         <my.fasta.gz>.fai and <my.fasta.gz>.gzi unless the options --fai and --gzi are provided. A local file can be
-         uncompressed if the flag -e/--editable is set (but see below about using -e)
-
-FLAGS
-  -a, --assembly=<value>     Name for this assembly. Use the file name if omitted
-  -d, --decompressed         For local file input: Override autodetection and instruct that input is decompressed
-  -e, --editable             Instead of using indexed fasta lookup, the sequence is loaded into the Apollo database and
-                             is editable. Use with caution, as editing the sequence often has unintended side effects.
-  -f, --force                Delete existing assembly, if it exists
-  -z, --gzip                 For local file input: Override autodetection and instruct that input is gzip compressed
-      --config-file=<value>  Use this config file (mostly for testing)
-      --fai=<value>          Fasta index of the (not-editable) fasta file
-      --gzi=<value>          Gzi index of the (not-editable) fasta file
-      --profile=<value>      Use credentials from this profile
-
-DESCRIPTION
-  Add a new assembly from fasta input
-
-  Add new assembly. The input fasta may be:
-  * A local file bgzip'd and indexed. It can be uncompressed if the -e/--editable is set (but see description of -e)
-  * An external fasta file bgzip'd and indexed
-  * The id of a file previously uploaded to Apollo
-
-EXAMPLES
-  From local file assuming indexes genome.gz.fai and genome.gz.gzi are present:
-
-    $ apollo assembly add-from-fasta genome.fa.gz -a myAssembly
-
-  Local file with editable sequence does not require compression and indexing:
-
-    $ apollo assembly add-from-fasta genome.fa -a myAssembly
-
-  From external source assuming there are also indexes https://.../genome.fa.gz.fai and https://.../genome.fa.gz.gzi:
-
-    $ apollo assembly add-from-fasta https://.../genome.fa.gz -a myAssembly
-```
-
-_See code:
-[src/commands/assembly/add-from-fasta.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/assembly/add-from-fasta.ts)_
-
-## `apollo assembly add-from-gff INPUT-FILE`
-
-Add new assembly from gff or gft file
-
-```
-USAGE
-  $ apollo assembly add-from-gff INPUT-FILE [--profile <value>] [--config-file <value>] [-a <value>] [-o] [-f]
-
-ARGUMENTS
-  INPUT-FILE  Input gff file
-
-FLAGS
-  -a, --assembly=<value>     Name for this assembly. Use the file name if omitted
-  -f, --force                Delete existing assembly, if it exists
-  -o, --omit-features        Do not import features, only upload the sequences
-      --config-file=<value>  Use this config file (mostly for testing)
-      --profile=<value>      Use credentials from this profile
-
-DESCRIPTION
-  Add new assembly from gff or gft file
-
-  The gff file is expected to contain sequences as per gff specifications. Features are also imported by default.
-
-EXAMPLES
-  Import sequences and features:
-
-    $ apollo assembly add-from-gff genome.gff -a myAssembly
-
-  Import sequences only:
-
-    $ apollo assembly add-from-gff genome.gff -a myAssembly -o
-```
-
-_See code:
-[src/commands/assembly/add-from-gff.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/assembly/add-from-gff.ts)_
-
-## `apollo assembly check`
-
-Add, view, or delete checks to assembly
-
-```
-USAGE
-  $ apollo assembly check [--profile <value>] [--config-file <value>] [-a <value>] [-c <value>] [-d]
-
-FLAGS
-  -a, --assembly=<value>     Manage checks in this assembly
-  -c, --check=<value>...     Add these check names or IDs. If unset, print the checks set for assembly
-  -d, --delete               Delete (instead of adding) checks
-      --config-file=<value>  Use this config file (mostly for testing)
-      --profile=<value>      Use credentials from this profile
-
-DESCRIPTION
-  Add, view, or delete checks to assembly
-
-  Manage checks, i.e. the rules ensuring features in an assembly are plausible. This command only sets the checks to
-  apply, to retrieve features flagged by these checks use `apollo feature check`.
-
-EXAMPLES
-  View available check types:
-
-    $ apollo assembly check
-
-  View checks set for assembly hg19:
-
-    $ apollo assembly check -a hg19
-
-  Add checks to assembly:
-
-    $ apollo assembly check -a hg19 -c CDSCheck
-
-  Delete checks from assembly:
-
-    $ apollo assembly check -a hg19 -c CDSCheck --delete
-```
-
-_See code:
-[src/commands/assembly/check.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/assembly/check.ts)_
-
-## `apollo assembly delete`
-
-Delete assemblies
-
-```
-USAGE
-  $ apollo assembly delete -a <value> [--profile <value>] [--config-file <value>] [-v]
-
-FLAGS
-  -a, --assembly=<value>...  (required) Assembly names or IDs to delete
-  -v, --verbose              Print to stdout the array of assemblies deleted
-      --config-file=<value>  Use this config file (mostly for testing)
-      --profile=<value>      Use credentials from this profile
-
-DESCRIPTION
-  Delete assemblies
-
-  Assemblies to delete may be names or IDs
-
-EXAMPLES
-  Delete multiple assemblies using name or ID:
-
-    $ apollo assembly delete -a mouse 6605826fbd0eee691f83e73f
-```
-
-_See code:
-[src/commands/assembly/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/assembly/delete.ts)_
-
-## `apollo assembly get`
-
-Get available assemblies
-
-```
-USAGE
-  $ apollo assembly get [--profile <value>] [--config-file <value>] [-a <value>]
-
-FLAGS
-  -a, --assembly=<value>...  Get assemblies in this list of names or IDs
-      --config-file=<value>  Use this config file (mostly for testing)
-      --profile=<value>      Use credentials from this profile
-
-DESCRIPTION
-  Get available assemblies
-
-  Print to stdout the list of assemblies in json format
-```
-
-_See code:
-[src/commands/assembly/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/assembly/get.ts)_
-
-## `apollo assembly sequence`
-
-Get reference sequence in fasta format
-
-```
-USAGE
-  $ apollo assembly sequence [--profile <value>] [--config-file <value>] [-a <value>] [-r <value>] [-s <value>] [-e
-    <value>]
-
-FLAGS
-  -a, --assembly=<value>     Find input reference sequence in this assembly
-  -e, --end=<value>          End coordinate
-  -r, --refseq=<value>       Reference sequence. If unset, get all sequences
-  -s, --start=<value>        [default: 1] Start coordinate (1-based)
-      --config-file=<value>  Use this config file (mostly for testing)
-      --profile=<value>      Use credentials from this profile
-
-DESCRIPTION
-  Get reference sequence in fasta format
-
-  Return the reference sequence for a given assembly and coordinates
-
-EXAMPLES
-  Get all sequences in myAssembly:
-
-    $ apollo assembly sequence -a myAssembly
-
-  Get sequence in coordinates chr1:1..1000:
-
-    $ apollo assembly sequence -a myAssembly -r chr1 -s 1 -e 1000
-```
-
-_See code:
-[src/commands/assembly/sequence.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/assembly/sequence.ts)_
-
-## `apollo change get`
-
-Get list of changes
-
-```
-USAGE
-  $ apollo change get [--profile <value>] [--config-file <value>] [-a <value>]
-
-FLAGS
-  -a, --assembly=<value>...  Get changes only for these assembly names or IDs (but see description)
-      --config-file=<value>  Use this config file (mostly for testing)
-      --profile=<value>      Use credentials from this profile
-
-DESCRIPTION
-  Get list of changes
-
-  Return the change log in json format. Note that when an assembly is deleted the link between common name and ID is
-  lost (it can still be recovered by inspecting the change log but at present this task is left to the user). In such
-  cases you need to use the assembly ID.
-```
-
-_See code:
-[src/commands/change/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/change/get.ts)_
-
-## `apollo config [KEY] [VALUE]`
-
-Get or set apollo configuration options
-
-```
-USAGE
-  $ apollo config [KEY] [VALUE] [--profile <value>] [---file <value>] [--get-config-file]
-
-ARGUMENTS
-  KEY    Name of configuration parameter
-  VALUE  Parameter value
-
-FLAGS
-  --config-file=<value>  Use this config file (mostly for testing)
-  --get-config-file      Return the path to the config file and exit (this file may not exist yet)
-  --profile=<value>      Profile to create or edit
-
-DESCRIPTION
-  Get or set apollo configuration options
-
-  Use this command to create or edit a user profile with credentials to access Apollo. Configuration options are:
-
-  - address:
-  Address and port e.g http://localhost:3999
-
-  - accessType:
-  How to access Apollo. accessType is typically one of: google, microsoft, guest, root. Allowed types depend on your
-  Apollo setup
-
-  - accessToken:
-  Access token. Usually inserted by `apollo login`
-
-  - rootPassword:
-  Password for root account. Only set this for "root" access type
-
-EXAMPLES
-  Interactive setup:
-
-    $ apollo config
-
-  Setup with key/value pairs:
-
-    $ apollo config --profile admin address http://localhost:3999
-
-  Get current address for default profile:
-
-    $ apollo config address
-```
-
-_See code:
-[src/commands/config.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/config.ts)_
-
-## `apollo export gff3 ASSEMBLY`
-
-Export the annotations for an assembly to stdout as gff3
-
-```
-USAGE
-  $ apollo export gff3 ASSEMBLY [--profile <value>] [--config-file <value>] [--include-fasta]
-
-ARGUMENTS
-  ASSEMBLY  Export annotations for this assembly name or id
-
-FLAGS
-  --config-file=<value>  Use this config file (mostly for testing)
-  --include-fasta        Include fasta sequence in output
-  --profile=<value>      Use credentials from this profile
-
-DESCRIPTION
-  Export the annotations for an assembly to stdout as gff3
-
-EXAMPLES
-  Export annotations for myAssembly:
-
-    $ apollo export gff3 myAssembly > out.gff3
-```
-
-_See code:
-[src/commands/export/gff3.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/export/gff3.ts)_
-
-## `apollo feature add [FEATURE-JSON]`
-
-Add one or more features to Apollo
-
-```
-USAGE
-  $ apollo feature add [FEATURE-JSON] [--profile <value>] [--config-file <value>] [-a <value>] [-r <value> -s
-    <value> -e <value> -t <value>] [-F <value>]
-
-ARGUMENTS
-  FEATURE-JSON  Inline JSON describing the feature(s) to add. Can also be provided via stdin.
-
-FLAGS
-  -F, --feature-json-file=<value>  File with JSON describing the feature(s) to add
-  -a, --assembly=<value>           Name or ID of target assembly. Not required if refseq is unique in the database
-  -e, --max=<value>                End position in target reference sequence
-  -r, --refSeq=<value>             Name or ID of target reference sequence
-  -s, --min=<value>                Start position in target reference sequence
-  -t, --type=<value>               Type of child feature
-      --config-file=<value>        Use this config file (mostly for testing)
-      --profile=<value>            Use credentials from this profile
-
-DESCRIPTION
-  Add one or more features to Apollo
-
-  A single simple feature can be added using the --min, --max, etc. flags.
-
-  To add multiple features, features with more details, or features with children, you can pass in JSON via argument or
-  stdin or use the --feature-json-file options.
-
-
-EXAMPLES
-  Add a single feature by specifying its location and type
-
-    $ apollo feature add --assembly hg19 --refSeq chr3 --min 1000 --max 5000 --type remark
-
-  Add a single feature from inline JSON
-
-    $ apollo feature add \
-      '{"assembly":"<assemblyNameOrId>","refseq":"<refSeqNameOrId>","min":1,"max":100,"type":"<featureType>"}'
-
-  Add mutilple features from stdin JSON
-
-    echo '[{"assembly":"<assemblyNameOrId>","refseq":"<refSeqNameOrId>","min":1,"max":100,"type":"<featureType>"},{" \
-      assembly":"<assemblyNameOrId>","refseq":"<refSeqNameOrId>","min":101,"max":200,"type":"<featureType>"}]' | \
-      apollo feature add
-
-  Add a feature with children from inline JSON
-
-    $ apollo feature add '{"assembly":"<assemblyNameOrId>","refseq":"<refSeqNameOrId>","min":1,"max":100,"type":"<fe \
-      atureType>","children":[{"min":1,"max":50,"type":"<featureType>"}]}'
-```
-
-_See code:
-[src/commands/feature/add.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/add.ts)_
-
-## `apollo feature add-child`
-
-Add a child feature (e.g. add an exon to an mRNA)
-
-```
-USAGE
-  $ apollo feature add-child -s <value> -e <value> -t <value> [--profile <value>] [--config-file <value>] [-i <value>]
-
-FLAGS
-  -e, --end=<value>          (required) End coordinate of the child feature (1-based)
-  -i, --feature-id=<value>   [default: -] Add a child to this feature ID; use - to read it from stdin
-  -s, --start=<value>        (required) Start coordinate of the child feature (1-based)
-  -t, --type=<value>         (required) Type of child feature
-      --config-file=<value>  Use this config file (mostly for testing)
-      --profile=<value>      Use credentials from this profile
-
-DESCRIPTION
-  Add a child feature (e.g. add an exon to an mRNA)
-
-  See the other commands under `apollo feature` to retrive the parent ID of interest and to populate the child feature
-  with attributes.
-
-EXAMPLES
-  Add an exon at genomic coordinates 10..20 to this feature ID:
-
-    $ apollo feature add-child -i 660...73f -t exon -s 10 -e 20
-```
-
-_See code:
-[src/commands/feature/add-child.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/add-child.ts)_
-
-## `apollo feature check`
-
-Get check results
-
-```
-USAGE
-  $ apollo feature check [--profile <value>] [--config-file <value>] [-i <value>] [-a <value>]
-
-FLAGS
-  -a, --assembly=<value>       Get checks for this assembly
-  -i, --feature-id=<value>...  Get checks for these feature identifiers
-      --config-file=<value>    Use this config file (mostly for testing)
-      --profile=<value>        Use credentials from this profile
-
-DESCRIPTION
-  Get check results
-
-  Use this command to view which features fail checks along with the reason for failing.Use `apollo assembly check` for
-  managing which checks should be applied to an assembly
-
-EXAMPLES
-  Get all check results in the database:
-
-    $ apollo feature check
-
-  Get check results for assembly hg19:
-
-    $ apollo feature check -a hg19
-```
-
-_See code:
-[src/commands/feature/check.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/check.ts)_
-
-## `apollo feature copy`
-
-Copy a feature to another location
-
-```
-USAGE
-  $ apollo feature copy -r <value> -s <value> [--profile <value>] [--config-file <value>] [-i <value>] [-a <value>]
-
-FLAGS
-  -a, --assembly=<value>     Name or ID of target assembly. Not required if refseq is unique in the database
-  -i, --feature-id=<value>   [default: -] Feature ID to copy to; use - to read it from stdin
-  -r, --refseq=<value>       (required) Name or ID of target reference sequence
-  -s, --start=<value>        (required) Start position in target reference sequence
-      --config-file=<value>  Use this config file (mostly for testing)
-      --profile=<value>      Use credentials from this profile
-
-DESCRIPTION
-  Copy a feature to another location
-
-  The feature may be copied to the same or to a different assembly. The destination reference sequence may be selected
-  by name only if unique in the database or by name and assembly or by identifier.
-
-EXAMPLES
-  Copy this feature ID to chr1:100 in assembly hg38:
-
-    $ apollo feature copy -i 6605826fbd0eee691f83e73f -r chr1 -s 100 -a hg38
-```
-
-_See code:
-[src/commands/feature/copy.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/copy.ts)_
-
-## `apollo feature delete`
-
-Delete one or more features by ID
-
-```
-USAGE
-  $ apollo feature delete [--profile <value>] [--config-file <value>] [-i <value>] [-f] [-n]
-
-FLAGS
-  -f, --force                  Ignore non-existing features
-  -i, --feature-id=<value>...  [default: -] Feature IDs to delete
-  -n, --dry-run                Only show what would be delete
-      --config-file=<value>    Use this config file (mostly for testing)
-      --profile=<value>        Use credentials from this profile
-
-DESCRIPTION
-  Delete one or more features by ID
-
-  Note that deleting a child feature after deleting its parent will result in an error unless you set -f/--force.
-```
-
-_See code:
-[src/commands/feature/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/delete.ts)_
-
-## `apollo feature edit`
-
-Edit features using an appropiate json input
-
-```
-USAGE
-  $ apollo feature edit [--profile <value>] [--config-file <value>] [-j <value>]
-
-FLAGS
-  -j, --json-input=<value>   [default: -] Json string or json file or "-" to read json from stdin
-      --config-file=<value>  Use this config file (mostly for testing)
-      --profile=<value>      Use credentials from this profile
-
-DESCRIPTION
-  Edit features using an appropiate json input
-
-  Edit a feature by submitting a json input with all the required attributes for Apollo to process it. This is a very
-  low level command which most users probably do not need.
-
-  Input may be a json string or a json file and it may be an array of changes. This is an example input for editing
-  feature type:
-
-  {
-  "typeName": "TypeChange",
-  "changedIds": [
-  "6613f7d22c957525d631b1cc"
-  ],
-  "assembly": "6613f7d1360321540a11e5ed",
-  "featureId": "6613f7d22c957525d631b1cc",
-  "oldType": "BAC",
-  "newType": "G_quartet"
-  }
-
-EXAMPLES
-  Editing by passing a json to stdin:
-
-    echo '{"typeName": ... "newType": "G_quartet"}' | apollo feature edit -j -
-```
-
-_See code:
-[src/commands/feature/edit.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/edit.ts)_
-
-## `apollo feature edit-attribute`
-
-Add, edit, or view a feature attribute
-
-```
-USAGE
-  $ apollo feature edit-attribute -a <value> [--profile <value>] [--config-file <value>] [-i <value>] [-v <value>] [-d]
-
-FLAGS
-  -a, --attribute=<value>    (required) Attribute key to add or edit
-  -d, --delete               Delete this attribute
-  -i, --feature-id=<value>   [default: -] Feature ID to edit or "-" to read it from stdin
-  -v, --value=<value>...     New attribute value. Separated mutliple values by space to them as a list. If unset return
-                             current value
-      --config-file=<value>  Use this config file (mostly for testing)
-      --profile=<value>      Use credentials from this profile
-
-DESCRIPTION
-  Add, edit, or view a feature attribute
-
-  Be aware that there is no checking whether attributes names and values are valid. For example, you can create
-  non-unique ID attributes or you can set gene ontology terms to non-existing terms
-
-EXAMPLES
-  Add attribute "domains" with a list of values:
-
-    $ apollo feature edit-attribute -i 66...3f -a domains -v ABC PLD
-
-  Print values in "domains" as json array:
-
-    $ apollo feature edit-attribute -i 66...3f -a domains
-
-  Delete attribute "domains"
-
-    $ apollo feature edit-attribute -i 66...3f -a domains -d
-```
-
-_See code:
-[src/commands/feature/edit-attribute.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/edit-attribute.ts)_
-
-## `apollo feature edit-coords`
-
-Edit feature start and/or end coordinates
-
-```
-USAGE
-  $ apollo feature edit-coords [--profile <value>] [--config-file <value>] [-i <value>] [-s <value>] [-e <value>]
-
-FLAGS
-  -e, --end=<value>          New end coordinate (1-based)
-  -i, --feature-id=<value>   [default: -] Feature ID to edit or "-" to read it from stdin
-  -s, --start=<value>        New start coordinate (1-based)
-      --config-file=<value>  Use this config file (mostly for testing)
-      --profile=<value>      Use credentials from this profile
-
-DESCRIPTION
-  Edit feature start and/or end coordinates
-
-  If editing a child feature that new coordinates must be within the parent's coordinates.To get the identifier of the
-  feature to edit consider using `apollo feature get` or `apollo feature search`
-
-EXAMPLES
-  Edit start and end:
-
-    $ apollo feature edit-coords -i abc...xyz -s 10 -e 1000
-
-  Edit end and leave start as it is:
-
-    $ apollo feature edit-coords -i abc...xyz -e 2000
-```
-
-_See code:
-[src/commands/feature/edit-coords.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/edit-coords.ts)_
-
-## `apollo feature edit-type`
-
-Edit or view feature type
-
-```
-USAGE
-  $ apollo feature edit-type [--profile <value>] [--config-file <value>] [-i <value>] [-t <value>]
-
-FLAGS
-  -i, --feature-id=<value>   [default: -] Feature ID to edit or "-" to read it from stdin
-  -t, --type=<value>         Assign feature to this type. If unset return the current type
-      --config-file=<value>  Use this config file (mostly for testing)
-      --profile=<value>      Use credentials from this profile
-
-DESCRIPTION
-  Edit or view feature type
-
-  Feature type is column 3 in gff format.It must be a valid sequence ontology term although but the valifdity of the new
-  term is not checked.
-```
-
-_See code:
-[src/commands/feature/edit-type.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/edit-type.ts)_
-
-## `apollo feature get`
-
-Get features in assembly, reference sequence or genomic window
-
-```
-USAGE
-  $ apollo feature get [--profile <value>] [--config-file <value>] [-a <value>] [-r <value>] [-s <value>] [-e
-    <value>]
-
-FLAGS
-  -a, --assembly=<value>     Find input reference sequence in this assembly
-  -e, --end=<value>          End coordinate
-  -r, --refseq=<value>       Reference sequence. If unset, query all sequences
-  -s, --start=<value>        [default: 1] Start coordinate (1-based)
-      --config-file=<value>  Use this config file (mostly for testing)
-      --profile=<value>      Use credentials from this profile
-
-DESCRIPTION
-  Get features in assembly, reference sequence or genomic window
-
-EXAMPLES
-  Get all features in myAssembly:
-
-    $ apollo feature get -a myAssembly
-
-  Get features intersecting chr1:1..1000. You can omit the assembly name if there are no other reference sequences
-  named chr1:
-
-    $ apollo feature get -a myAssembly -r chr1 -s 1 -e 1000
-```
-
-_See code:
-[src/commands/feature/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/get.ts)_
-
-## `apollo feature get-id`
-
-Get features given their identifiers
-
-```
-USAGE
-  $ apollo feature get-id [--profile <value>] [--config-file <value>] [-i <value>]
-
-FLAGS
-  -i, --feature-id=<value>...  [default: -] Retrieves feature with these IDs. Use "-" to read IDs from stdin (one per
-                               line)
-      --config-file=<value>    Use this config file (mostly for testing)
-      --profile=<value>        Use credentials from this profile
-
-DESCRIPTION
-  Get features given their identifiers
-
-  Invalid identifiers or identifiers not found in the database will be silently ignored
-
-EXAMPLES
-  Get features for these identifiers:
-
-    $ apollo feature get-id -i abc...zyz def...foo
-```
-
-_See code:
-[src/commands/feature/get-id.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/get-id.ts)_
-
-## `apollo feature get-indexed-id ID`
-
-Get features given an indexed identifier
-
-```
-USAGE
-  $ apollo feature get-indexed-id ID [--profile <value>] [--config-file <value>] [-a <value>] [--topLevel]
-
-ARGUMENTS
-  ID  Indexed identifier to search for
-
-FLAGS
-  -a, --assembly=<value>...  Assembly names or IDs to search; use "-" to read it from stdin. If omitted search all
-                             assemblies
-      --config-file=<value>  Use this config file (mostly for testing)
-      --profile=<value>      Use credentials from this profile
-      --topLevel             Return the top-level parent of the feature instead of the feature itself
-
-DESCRIPTION
-  Get features given an indexed identifier
-
-  Get features that match a given indexed identifier, such as the ID of a feature from an imported GFF3 file
-
-EXAMPLES
-  Get features for this indexed identifier:
-
-    $ apollo feature get-indexed-id -i abc...zyz def...foo
-```
-
-_See code:
-[src/commands/feature/get-indexed-id.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/get-indexed-id.ts)_
-
-## `apollo feature import INPUT-FILE`
-
-Import features from local gff file
-
-```
-USAGE
-  $ apollo feature import INPUT-FILE -a <value> [--profile <value>] [--config-file <value>] [-d]
-
-ARGUMENTS
-  INPUT-FILE  Input gff file
-
-FLAGS
-  -a, --assembly=<value>     (required) Import into this assembly name or assembly ID
-  -d, --delete-existing      Delete existing features before importing
-      --config-file=<value>  Use this config file (mostly for testing)
-      --profile=<value>      Use credentials from this profile
-
-DESCRIPTION
-  Import features from local gff file
-
-  By default, features are added to the existing ones.
-
-EXAMPLES
-  Delete features in myAssembly and then import features.gff3:
-
-    $ apollo feature import features.gff3 -d -a myAssembly
-```
-
-_See code:
-[src/commands/feature/import.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/import.ts)_
-
-## `apollo feature search`
-
-Free text search for feature in one or more assemblies
-
-```
-USAGE
-  $ apollo feature search -t <value> [--profile <value>] [--config-file <value>] [-a <value>]
-
-FLAGS
-  -a, --assembly=<value>...  Assembly names or IDs to search; use "-" to read it from stdin. If omitted search all
-                             assemblies
-  -t, --text=<value>         (required) Search for this text query
-      --config-file=<value>  Use this config file (mostly for testing)
-      --profile=<value>      Use credentials from this profile
-
-DESCRIPTION
-  Free text search for feature in one or more assemblies
-
-  Return features matching a query string. This command searches only in:
-
-  - Attribute *values* (not attribute names)
-  - Source field (which in fact is stored as an attribute)
-  - Feature type
-
-  The search mode is:
-
-  - Case insensitive
-  - Match only full words, but not necessarily the full value
-  - Common words are ignored. E.g. "the", "with"
-
-  For example, given this feature:
-
-  chr1 example SNP 10 30 0.987 . . "someKey=Fingerprint BAC with reads"
-
-  Queries "bac" or "mRNA" return the feature. Instead these queries will NOT match:
-
-  - "someKey"
-  - "with"
-  - "Finger"
-  - "chr1"
-  - "0.987"
-
-EXAMPLES
-  Search "bac" in these assemblies:
-
-    $ apollo feature search -a mm9 mm10 -t bac
-```
-
-_See code:
-[src/commands/feature/search.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/feature/search.ts)_
-
-## `apollo file delete`
-
-Delete files from the Apollo server
-
-```
-USAGE
-  $ apollo file delete [--profile <value>] [--config-file <value>] [-i <value>]
-
-FLAGS
-  -i, --file-id=<value>...   [default: -] IDs of the files to delete
-      --config-file=<value>  Use this config file (mostly for testing)
-      --profile=<value>      Use credentials from this profile
-
-DESCRIPTION
-  Delete files from the Apollo server
-
-  Deleted files are printed to stdout. See also `apollo file get` to list the files on the server
-
-EXAMPLES
-  Delete file multiple files:
-
-    $ apollo file delete -i 123...abc xyz...789
-```
-
-_See code:
-[src/commands/file/delete.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/file/delete.ts)_
-
-## `apollo file download`
-
-Download a file from the Apollo server
-
-```
-USAGE
-  $ apollo file download [--profile <value>] [--config-file <value>] [-i <value>] [-o <value>]
-
-FLAGS
-  -i, --file-id=<value>      [default: -] ID of the file to download
-  -o, --output=<value>       Write output to this file or "-" for stdout. Default to the name of the uploaded file.
-      --config-file=<value>  Use this config file (mostly for testing)
-      --profile=<value>      Use credentials from this profile
-
-DESCRIPTION
-  Download a file from the Apollo server
-
-  See also `apollo file get` to list the files on the server
-
-EXAMPLES
-  Download file with id xyz
-
-    $ apollo file download -i xyz -o genome.fa
-```
-
-_See code:
-[src/commands/file/download.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/file/download.ts)_
-
-## `apollo file get`
-
-Get list of files uploaded to the Apollo server
-
-```
-USAGE
-  $ apollo file get [--profile <value>] [--config-file <value>] [-i <value>]
-
-FLAGS
-  -i, --file-id=<value>...   Get files matching this IDs
-      --config-file=<value>  Use this config file (mostly for testing)
-      --profile=<value>      Use credentials from this profile
-
-DESCRIPTION
-  Get list of files uploaded to the Apollo server
-
-  Print to stdout the list of files in json format
-
-EXAMPLES
-  Get files by id:
-
-    $ apollo file get -i xyz abc
-```
-
-_See code:
-[src/commands/file/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/file/get.ts)_
-
-## `apollo file upload INPUT-FILE`
-
-Upload a local file to the Apollo server
-
-```
-USAGE
-  $ apollo file upload INPUT-FILE [--profile <value>] [--config-file <value>] [-t
-    text/x-fasta|text/x-gff3|application/x-bgzip-fasta|text/x-fai|application/x-gzi] [-z | -d]
-
-ARGUMENTS
-  INPUT-FILE  Local file to upload
-
-FLAGS
-  -d, --decompressed         Override autodetection and instruct that input is decompressed
-  -t, --type=<option>        Set file type or autodetected it if not set.
-                             NB: There is no check for whether the file complies to this type
-                             <options: text/x-fasta|text/x-gff3|application/x-bgzip-fasta|text/x-fai|application/x-gzi>
-  -z, --gzip                 Override autodetection and instruct that input is gzip compressed
-      --config-file=<value>  Use this config file (mostly for testing)
-      --profile=<value>      Use credentials from this profile
-
-DESCRIPTION
-  Upload a local file to the Apollo server
-
-  This command only uploads a file and returns the corresponding file id.
-  To add an assembly based on this file or to upload & add an assembly in a single pass   see `apollo assembly
-  add-from-fasta` and `add-from-gff`
-
-EXAMPLES
-  Upload local file, type auto-detected:
-
-    $ apollo file upload genome.fa > file.json
-```
-
-_See code:
-[src/commands/file/upload.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/file/upload.ts)_
 
 ## `apollo help [COMMANDS]`
 
@@ -1017,294 +52,4 @@ DESCRIPTION
 _See code:
 [@oclif/plugin-help](https://github.com/oclif/plugin-help/blob/v6.0.8/src/commands/help.ts)_
 
-## `apollo jbrowse desktop JBROWSEFILE`
-
-Generate JBrowse file for use with desktop client
-
-```
-USAGE
-  $ apollo jbrowse desktop JBROWSEFILE [--profile <value>] [--config-file <value>] [-o | -w <value>] [-f <value>]
-
-ARGUMENTS
-  JBROWSEFILE  Generated JBrowse file
-
-FLAGS
-  -f, --gff3-file=<value>    generated session will open the specified file
-  -o, --open                 open generated file
-  -w, --open-with=<value>    open generated file with specified application
-      --config-file=<value>  Use this config file (mostly for testing)
-      --profile=<value>      Use credentials from this profile
-
-DESCRIPTION
-  Generate JBrowse file for use with desktop client
-
-  Generates a file that can be opened with JBrowse Desktop. This file has Apollo already configured and, optionally, a
-  GFF3 for local editing configured as well.
-
-EXAMPLES
-  Generate JBrowse file:
-
-    $ apollo jbrowse desktop apollo.jbrowse
-
-  Generate JBrowse file and open with default handler:
-
-    $ apollo jbrowse desktop apollo.jbrowse --open
-
-  Generate JBrowse file and open with specified application:
-
-    $ apollo jbrowse desktop apollo.jbrowse --open-with=path/to/jbrowse.AppImage
-
-  Generate JBrowse file opening specified gff3 file:
-
-    $ apollo jbrowse desktop apollo.jbrowse --gff3-file=path/to/file.gff3
-```
-
-_See code:
-[src/commands/jbrowse/desktop.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/jbrowse/desktop.ts)_
-
-## `apollo jbrowse get-config`
-
-Get JBrowse configuration from Apollo
-
-```
-USAGE
-  $ apollo jbrowse get-config [--profile <value>] [--config-file <value>]
-
-FLAGS
-  --config-file=<value>  Use this config file (mostly for testing)
-  --profile=<value>      Use credentials from this profile
-
-DESCRIPTION
-  Get JBrowse configuration from Apollo
-
-  Print to stdout the JBrowse configuration from Apollo in JSON format
-
-EXAMPLES
-  Get JBrowse configuration:
-
-    $ apollo jbrowse get-config > config.json
-```
-
-_See code:
-[src/commands/jbrowse/get-config.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/jbrowse/get-config.ts)_
-
-## `apollo jbrowse set-config INPUTFILE`
-
-Set JBrowse configuration
-
-```
-USAGE
-  $ apollo jbrowse set-config INPUTFILE [--profile <value>] [--config-file <value>]
-
-ARGUMENTS
-  INPUTFILE  JBrowse configuration file
-
-FLAGS
-  --config-file=<value>  Use this config file (mostly for testing)
-  --profile=<value>      Use credentials from this profile
-
-DESCRIPTION
-  Set JBrowse configuration
-
-  Set JBrowse configuration in Apollo collaboration server
-
-EXAMPLES
-  Add JBrowse configuration:
-
-    $ apollo jbrowse set-config config.json
-```
-
-_See code:
-[src/commands/jbrowse/set-config.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/jbrowse/set-config.ts)_
-
-## `apollo login`
-
-Login to Apollo
-
-```
-USAGE
-  $ apollo login [--profile <value>] [--config-file <value>] [-a <value>] [-u <value>] [-p <value>] [-f]
-    [--port <value>]
-
-FLAGS
-  -a, --address=<value>      Address of Apollo server
-  -f, --force                Force re-authentication even if user is already logged in
-  -p, --password=<value>     Password for <username>
-  -u, --username=<value>     Username for root login
-      --config-file=<value>  Use this config file (mostly for testing)
-      --port=<value>         [default: 3000] Get token by listening to this port number (usually this is >= 1024 and <
-                             65536)
-      --profile=<value>      Use credentials from this profile
-
-DESCRIPTION
-  Login to Apollo
-
-  Use the provided credentials to obtain and save the token to access Apollo. Once the token for the given profile has
-  been saved in the configuration file, users do not normally need to execute this command again unless the token has
-  expired. To setup a new profile use "apollo config"
-
-EXAMPLES
-  The most basic and probably most typical usage is to login using the default profile in configuration file:
-
-    $ apollo login
-
-  Login with a different profile:
-
-    $ apollo login --profile my-profile
-```
-
-_See code:
-[src/commands/login.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/login.ts)_
-
-## `apollo logout`
-
-Logout of Apollo
-
-```
-USAGE
-  $ apollo logout [--profile <value>] [--config-file <value>]
-
-FLAGS
-  --config-file=<value>  Use this config file (mostly for testing)
-  --profile=<value>      Use credentials from this profile
-
-DESCRIPTION
-  Logout of Apollo
-
-  Logout by removing the access token from the selected profile
-
-EXAMPLES
-  Logout default profile:
-
-    $ apollo logout
-
-  Logout selected profile
-
-    $ apollo logout --profile my-profile
-```
-
-_See code:
-[src/commands/logout.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/logout.ts)_
-
-## `apollo refseq add-alias INPUT-FILE`
-
-Add reference name aliases from a file
-
-```
-USAGE
-  $ apollo refseq add-alias INPUT-FILE -a <value> [--profile <value>] [--config-file <value>]
-
-ARGUMENTS
-  INPUT-FILE  Input refname alias file
-
-FLAGS
-  -a, --assembly=<value>     (required) Name for this assembly.
-      --config-file=<value>  Use this config file (mostly for testing)
-      --profile=<value>      Use credentials from this profile
-
-DESCRIPTION
-  Add reference name aliases from a file
-
-  Reference name aliasing is a process to make chromosomes that are named slightly differently but which refer to the
-  same thing render properly. This command reads a file with reference name aliases and adds them to the database.
-
-EXAMPLES
-  Add reference name aliases:
-
-    $ apollo refseq add-alias alias.txt -a myAssembly
-```
-
-_See code:
-[src/commands/refseq/add-alias.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/refseq/add-alias.ts)_
-
-## `apollo refseq get`
-
-Get reference sequences
-
-```
-USAGE
-  $ apollo refseq get [--profile <value>] [--config-file <value>] [-a <value>]
-
-FLAGS
-  -a, --assembly=<value>...  Get reference sequences for these assembly names or IDs; use - to read it from stdin
-      --config-file=<value>  Use this config file (mostly for testing)
-      --profile=<value>      Use credentials from this profile
-
-DESCRIPTION
-  Get reference sequences
-
-  Output the reference sequences in one or more assemblies in json format. This command returns the sequence
-  characteristics (e.g., name, ID, etc), not the DNA sequences. Use `assembly sequence` for that.
-
-EXAMPLES
-  All sequences in the database:
-
-    $ apollo refseq get
-
-  Only sequences for these assemblies:
-
-    $ apollo refseq get -a mm9 mm10
-```
-
-_See code:
-[src/commands/refseq/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/refseq/get.ts)_
-
-## `apollo status`
-
-View authentication status
-
-```
-USAGE
-  $ apollo status [--profile <value>] [--config-file <value>]
-
-FLAGS
-  --config-file=<value>  Use this config file (mostly for testing)
-  --profile=<value>      Use credentials from this profile
-
-DESCRIPTION
-  View authentication status
-
-  This command returns "<profile>: Logged in" if the selected profile has an access token and "<profile>: Logged out"
-  otherwise.Note that this command does not check the validity of the access token.
-```
-
-_See code:
-[src/commands/status.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/status.ts)_
-
-## `apollo user get`
-
-Get list of users
-
-```
-USAGE
-  $ apollo user get [--profile <value>] [--config-file <value>] [-u <value>] [-r <value>]
-
-FLAGS
-  -r, --role=<value>         Get users with this role
-  -u, --username=<value>     Find this username
-      --config-file=<value>  Use this config file (mostly for testing)
-      --profile=<value>      Use credentials from this profile
-
-DESCRIPTION
-  Get list of users
-
-  If set, filters username and role must be both satisfied to return an entry
-
-EXAMPLES
-  By username:
-
-    $ apollo user get -u Guest
-
-  By role:
-
-    $ apollo user get -r admin
-
-  Use jq for more control:
-
-    $ apollo user get | jq '.[] | select(.createdAt > "2024-03-18")'
-```
-
-_See code:
-[src/commands/user/get.ts](https://github.com/GMOD/Apollo3/blob/v0.3.11/packages/apollo-cli/src/commands/user/get.ts)_
-
 <!-- commandsstop -->
diff --git a/packages/apollo-cli/package.json b/packages/apollo-cli/package.json
index 5b4d42be4..71f2cf6fb 100644
--- a/packages/apollo-cli/package.json
+++ b/packages/apollo-cli/package.json
@@ -10,7 +10,6 @@
   "author": "Apollo Team",
   "type": "module",
   "exports": "./dist/index.js",
-  "main": "",
   "types": "dist/index.d.ts",
   "bin": {
     "apollo": "./bin/run.js"
@@ -26,10 +25,8 @@
     "prepack": "yarn build && oclif manifest && oclif readme && prettier --write README.md",
     "postpack": "shx rm -f oclif.manifest.json",
     "prepare": "yarn build",
-    "test": "mocha --require src/test/fixtures.ts 'src/**/*.test.ts'",
-    "posttest": "yarn lint",
-    "test:ci": "nyc mocha 'src/**/*.test.ts'",
-    "test:cli": "yarn tsx src/test/test.ts",
+    "test": "yarn tsx src/test/test.ts",
+    "test:ci": "yarn tsx src/test/test.ts",
     "version": "oclif readme --multi --dir ../website/docs/03-guides/04-cli/ && oclif readme && git add README.md"
   },
   "oclif": {
@@ -98,11 +95,9 @@
     "@types/cli-progress": "^3",
     "@types/cross-spawn": "^6.0.6",
     "@types/inquirer": "^9.0.7",
-    "@types/mocha": "^10",
-    "@types/node": "^20.19.15",
+    "@types/node": "^24.10.9",
     "babel-plugin-istanbul": "^6.1.1",
     "cross-spawn": "^7.0.3",
-    "mocha": "^10.2.0",
     "mongodb": "^4.7.0",
     "nyc": "^15.1.0",
     "oclif": "^4.4.2",
@@ -116,7 +111,7 @@
     "typescript": "^5.5.3"
   },
   "engines": {
-    "node": ">=18.0.0"
+    "node": ">=20.0.0"
   },
   "publishConfig": {
     "access": "public"
diff --git a/packages/apollo-cli/src/commands/assembly/get.test.ts b/packages/apollo-cli/src/commands/assembly/get.test.ts
deleted file mode 100644
index d9aafbefe..000000000
--- a/packages/apollo-cli/src/commands/assembly/get.test.ts
+++ /dev/null
@@ -1,68 +0,0 @@
-import fs from 'node:fs'
-import path from 'node:path'
-import { fileURLToPath } from 'node:url'
-
-import { expect, test } from '@oclif/test'
-
-import {
-  CONFIG_FILE,
-  TEST_DATA_DIR,
-  VERBOSE,
-  copyFile,
-} from '../../test/fixtures.js'
-
-// import nock from 'nock'
-
-const __dirname = fileURLToPath(new URL('.', import.meta.url))
-
-describe.skip('apollo assembly get: Fail without token', () => {
-  before(() => {
-    copyFile(`${TEST_DATA_DIR}/guest.yml`, CONFIG_FILE, VERBOSE)
-  })
-  after(() => {
-    fs.rmSync(CONFIG_FILE)
-  })
-
-  const cmd = ['assembly:get']
-  test
-    .stderr()
-    .command(cmd, { root: path.dirname(path.dirname(__dirname)) })
-    .exit(1)
-    .do((output) =>
-      expect(output.stderr).to.contain('Profile "default" has no access token'),
-    )
-    .do((output) => expect(output.stderr).to.not.contain(' at async ')) // Don't print error stack
-    .it(cmd.join(' '))
-})
-
-// TODO: Need valid token
-describe.skip('apollo assembly get: Get assemblies as YAML string', () => {
-  before(() => {
-    copyFile(`${TEST_DATA_DIR}/complete_config.yml`, CONFIG_FILE, VERBOSE)
-  })
-  after(() => {
-    fs.rmSync(CONFIG_FILE)
-  })
-
-  const cmd = ['assembly:get']
-  test
-    .stdout()
-    .command(cmd, { root: path.dirname(path.dirname(__dirname)) })
-    .it(cmd.join(' '), (output) => {
-      JSON.parse(output.stdout)
-    })
-})
-
-describe.skip('apollo assembly get: Test nock', () => {
-  const cmd = ['assembly:get', '--config-file', 'tmp.yml']
-  test
-    .stdout()
-    .nock('http://127.0.0.1:3999', (api) =>
-      api.persist().get('/assemblies').reply(200, { stuff: 'foo' }),
-    )
-    .command(cmd, { root: path.dirname(path.dirname(__dirname)) })
-    .it(cmd.join(' '), (output) => {
-      console.error(output.stdout)
-      // const out = JSON.parse(output.stdout)
-    })
-})
diff --git a/packages/apollo-cli/src/commands/change/get.test.ts b/packages/apollo-cli/src/commands/change/get.test.ts
deleted file mode 100644
index 0ab56eccd..000000000
--- a/packages/apollo-cli/src/commands/change/get.test.ts
+++ /dev/null
@@ -1,32 +0,0 @@
-import fs from 'node:fs'
-import path from 'node:path'
-import { fileURLToPath } from 'node:url'
-
-import { test } from '@oclif/test'
-
-import {
-  CONFIG_FILE,
-  TEST_DATA_DIR,
-  VERBOSE,
-  copyFile,
-} from '../../test/fixtures.js'
-
-const __dirname = fileURLToPath(new URL('.', import.meta.url))
-
-// TODO: Need valid token
-describe.skip('apollo change get: Get changes as YAML string', () => {
-  before(() => {
-    copyFile(`${TEST_DATA_DIR}/complete_config.yml`, CONFIG_FILE, VERBOSE)
-  })
-  after(() => {
-    fs.rmSync(CONFIG_FILE)
-  })
-
-  const cmd = ['change:get']
-  test
-    .stdout()
-    .command(cmd, { root: path.dirname(path.dirname(__dirname)) })
-    .it(cmd.join(' '), (output) => {
-      JSON.parse(output.stdout)
-    })
-})
diff --git a/packages/apollo-cli/src/commands/user/get.test.ts b/packages/apollo-cli/src/commands/user/get.test.ts
deleted file mode 100644
index ebff4eeaa..000000000
--- a/packages/apollo-cli/src/commands/user/get.test.ts
+++ /dev/null
@@ -1,33 +0,0 @@
-import fs from 'node:fs'
-import path from 'node:path'
-import { fileURLToPath } from 'node:url'
-
-import { expect, test } from '@oclif/test'
-
-import {
-  CONFIG_FILE,
-  TEST_DATA_DIR,
-  VERBOSE,
-  copyFile,
-} from '../../test/fixtures.js'
-
-const __dirname = fileURLToPath(new URL('.', import.meta.url))
-
-// TODO: Need valid token
-describe.skip('apollo user get: Get users as YAML string', () => {
-  before(() => {
-    copyFile(`${TEST_DATA_DIR}/complete_config.yml`, CONFIG_FILE, VERBOSE)
-  })
-  after(() => {
-    fs.rmSync(CONFIG_FILE)
-  })
-
-  const cmd = ['user:get']
-  test
-    .stdout()
-    .command(cmd, { root: path.dirname(path.dirname(__dirname)) })
-    .it(cmd.join(' '), (output) => {
-      const str: string = JSON.stringify(JSON.parse(output.stdout))
-      expect(str).contain('username')
-    })
-})
diff --git a/packages/apollo-cli/src/test/fixtures.ts b/packages/apollo-cli/src/test/fixtures.ts
deleted file mode 100644
index 7c3e1aa50..000000000
--- a/packages/apollo-cli/src/test/fixtures.ts
+++ /dev/null
@@ -1,44 +0,0 @@
-import fs from 'node:fs'
-import os from 'node:os'
-import path from 'node:path'
-
-export const TEST_DATA_DIR = path.resolve('test_data')
-export const VERBOSE = false
-export const CONFIG_DIR = path.join(os.homedir(), '.config', 'apollo-cli')
-export const CONFIG_FILE = path.join(CONFIG_DIR, 'config.yml')
-const CONFIG_BAK = path.join(TEST_DATA_DIR, 'original.config.yml.bak')
-
-function renameFile(src: string, dest: string, verbose = true) {
-  if (fs.existsSync(dest)) {
-    throw new Error(`File ${dest} already exists`)
-  }
-  let msg = ''
-  if (fs.existsSync(src)) {
-    fs.renameSync(src, dest)
-    msg = `mv ${src} ${dest}`
-  } else {
-    msg = `${src} does not exist`
-  }
-  if (verbose) {
-    process.stdout.write(`${msg}\n`)
-  }
-}
-
-export function copyFile(src: string, dest: string, verbose: boolean) {
-  fs.mkdirSync(path.dirname(dest), { recursive: true })
-  fs.copyFileSync(src, dest)
-  if (verbose) {
-    const msg = `cp ${src} ${dest}`
-    process.stdout.write(`${msg} # Copied: ${fs.existsSync(dest)}\n`)
-  }
-}
-
-export function mochaGlobalSetup() {
-  process.stdout.write(`Temporarily remove config file ${CONFIG_FILE} if any`)
-  renameFile(CONFIG_FILE, CONFIG_BAK, VERBOSE)
-}
-
-export function mochaGlobalTeardown() {
-  process.stdout.write(`Putting back config file ${CONFIG_FILE} if any\n`)
-  renameFile(CONFIG_BAK, CONFIG_FILE, VERBOSE)
-}
diff --git a/packages/apollo-cli/tsconfig.eslint.json b/packages/apollo-cli/tsconfig.eslint.json
deleted file mode 100644
index d22466d83..000000000
--- a/packages/apollo-cli/tsconfig.eslint.json
+++ /dev/null
@@ -1,4 +0,0 @@
-{
-  "extends": "../../tsconfig.json",
-  "include": ["jest.config.cjs, babel.config.js"],
-}
diff --git a/packages/apollo-cli/tsconfig.json b/packages/apollo-cli/tsconfig.json
index 759b80a1f..62c85accd 100644
--- a/packages/apollo-cli/tsconfig.json
+++ b/packages/apollo-cli/tsconfig.json
@@ -1,13 +1,12 @@
 {
+  "extends": "../../tsconfig",
   "compilerOptions": {
-    "declaration": true,
-    "module": "Node16",
     "outDir": "./dist",
     "rootDir": "./src",
-    "strict": true,
-    "target": "es2022",
-    "moduleResolution": "node16",
-    "skipLibCheck": true,
+    // For Node.js >=20: https://github.com/microsoft/TypeScript/wiki/Node-Target-Mapping
+    "target": "es2023",
+    "lib": ["es2023"],
+    "types": ["node"],
   },
   "include": ["./src"],
   "references": [{ "path": "../apollo-mst" }, { "path": "../apollo-shared" }],
diff --git a/packages/apollo-collaboration-server/package.json b/packages/apollo-collaboration-server/package.json
index 8523372f8..8e8de3039 100644
--- a/packages/apollo-collaboration-server/package.json
+++ b/packages/apollo-collaboration-server/package.json
@@ -4,6 +4,7 @@
   "description": "",
   "license": "Apache-2.0",
   "author": "",
+  "type": "module",
   "scripts": {
     "build": "yarn build:shared && rimraf dist && nest build",
     "cypress:start": "GUEST_USER_ROLE=admin MONGODB_URI=\"mongodb://localhost:27017/apolloTestDb?directConnection=true\" LOG_LEVELS=error,warn yarn start",
@@ -45,8 +46,9 @@
     "@emotion/styled": "^11.10.6",
     "@gmod/gff": "^2.0.0",
     "@gmod/indexedfasta": "^2.0.4",
-    "@jbrowse/core": "^3.6.5",
-    "@mui/material": "^7.0.0",
+    "@jbrowse/core": "^4.1.1",
+    "@jbrowse/mobx-state-tree": "^5.5.0",
+    "@mui/material": "^7.3.7",
     "@nestjs/common": "^10.1.0",
     "@nestjs/config": "^3.0.0",
     "@nestjs/core": "^10.1.0",
@@ -68,11 +70,9 @@
     "material-ui-popup-state": "^5.0.4",
     "mobx": "^6.6.1",
     "mobx-react": "^7.2.1",
-    "mobx-state-tree": "^5.4.0",
     "mongoose": "^6.12.0",
     "mongoose-id-validator": "^0.6.0",
-    "multer": "^1.4.5-lts.1",
-    "node-fetch": "^2.6.7",
+    "multer": "^2.0.2",
     "passport": "^0.5.0",
     "passport-google-oauth20": "^2.0.0",
     "passport-jwt": "^4.0.0",
@@ -96,10 +96,9 @@
     "@nestjs/testing": "^10.1.0",
     "@types/express": "^4.17.13",
     "@types/express-session": "^1",
-    "@types/jest": "^27.0.1",
-    "@types/multer": "^1.4.7",
-    "@types/node": "^20.19.15",
-    "@types/node-fetch": "^2.6.2",
+    "@types/jest": "^30.0.0",
+    "@types/multer": "^2.0.0",
+    "@types/node": "^24.10.9",
     "@types/passport-google-oauth20": "^2.0.11",
     "@types/passport-jwt": "^3.0.6",
     "@types/passport-local": "^1.0.34",
@@ -113,7 +112,7 @@
     "serve": "^14.0.1",
     "source-map-support": "^0.5.20",
     "supertest": "^6.1.3",
-    "ts-jest": "^29.1.1",
+    "ts-jest": "^29.4.6",
     "ts-loader": "^9.2.3",
     "ts-node": "^10.3.0",
     "ts-node-dev": "^1.1.8",
diff --git a/packages/apollo-collaboration-server/src/app.module.ts b/packages/apollo-collaboration-server/src/app.module.ts
index 8455137fc..7d586612f 100644
--- a/packages/apollo-collaboration-server/src/app.module.ts
+++ b/packages/apollo-collaboration-server/src/app.module.ts
@@ -3,29 +3,32 @@ import fs from 'node:fs/promises'
 import { Module } from '@nestjs/common'
 import { ConfigModule, ConfigService } from '@nestjs/config'
 import { APP_GUARD } from '@nestjs/core'
-import { MongooseModule, MongooseModuleFactoryOptions } from '@nestjs/mongoose'
+import {
+  MongooseModule,
+  type MongooseModuleFactoryOptions,
+} from '@nestjs/mongoose'
 import Joi from 'joi'
-import { Connection } from 'mongoose'
+import { type Connection } from 'mongoose'
 
-import { AssembliesModule } from './assemblies/assemblies.module'
-import { AuthenticationModule } from './authentication/authentication.module'
-import { ChangesModule } from './changes/changes.module'
-import { ChecksModule } from './checks/checks.module'
-import { CountersModule } from './counters/counters.module'
-import { ExportModule } from './export/export.module'
-import { FeaturesModule } from './features/features.module'
-import { FilesModule } from './files/files.module'
-import { HealthModule } from './health/health.module'
-import { JBrowseModule } from './jbrowse/jbrowse.module'
-import { MessagesModule } from './messages/messages.module'
-import { OperationsModule } from './operations/operations.module'
-import { PluginsModule } from './plugins/plugins.module'
-import { RefSeqChunksModule } from './refSeqChunks/refSeqChunks.module'
-import { RefSeqsModule } from './refSeqs/refSeqs.module'
-import { SequenceModule } from './sequence/sequence.module'
-import { UsersModule } from './users/users.module'
-import { JwtAuthGuard } from './utils/jwt-auth.guard'
-import { ValidationGuard } from './utils/validation/validation.guards'
+import { AssembliesModule } from './assemblies/assemblies.module.js'
+import { AuthenticationModule } from './authentication/authentication.module.js'
+import { ChangesModule } from './changes/changes.module.js'
+import { ChecksModule } from './checks/checks.module.js'
+import { CountersModule } from './counters/counters.module.js'
+import { ExportModule } from './export/export.module.js'
+import { FeaturesModule } from './features/features.module.js'
+import { FilesModule } from './files/files.module.js'
+import { HealthModule } from './health/health.module.js'
+import { JBrowseModule } from './jbrowse/jbrowse.module.js'
+import { MessagesModule } from './messages/messages.module.js'
+import { OperationsModule } from './operations/operations.module.js'
+import { PluginsModule } from './plugins/plugins.module.js'
+import { RefSeqChunksModule } from './refSeqChunks/refSeqChunks.module.js'
+import { RefSeqsModule } from './refSeqs/refSeqs.module.js'
+import { SequenceModule } from './sequence/sequence.module.js'
+import { UsersModule } from './users/users.module.js'
+import { JwtAuthGuard } from './utils/jwt-auth.guard.js'
+import { ValidationGuard } from './utils/validation/validation.guards.js'
 
 interface MongoDBURIConfig {
   MONGODB_URI?: string
diff --git a/packages/apollo-collaboration-server/src/assemblies/assemblies.controller.spec.ts b/packages/apollo-collaboration-server/src/assemblies/assemblies.controller.spec.ts
index 4b4ae9a85..bada2b819 100644
--- a/packages/apollo-collaboration-server/src/assemblies/assemblies.controller.spec.ts
+++ b/packages/apollo-collaboration-server/src/assemblies/assemblies.controller.spec.ts
@@ -1,6 +1,6 @@
 import { Test, type TestingModule } from '@nestjs/testing'
 
-import { AssembliesController } from './assemblies.controller'
+import { AssembliesController } from './assemblies.controller.js'
 
 describe('AssembliesController', () => {
   let controller: AssembliesController
diff --git a/packages/apollo-collaboration-server/src/assemblies/assemblies.controller.ts b/packages/apollo-collaboration-server/src/assemblies/assemblies.controller.ts
index 05d15e933..bc2abdd2a 100644
--- a/packages/apollo-collaboration-server/src/assemblies/assemblies.controller.ts
+++ b/packages/apollo-collaboration-server/src/assemblies/assemblies.controller.ts
@@ -8,10 +8,10 @@ import {
   Post,
 } from '@nestjs/common'
 
-import { Role } from '../utils/role/role.enum'
-import { Validations } from '../utils/validation/validatation.decorator'
+import { Role } from '../utils/role/role.enum.js'
+import { Validations } from '../utils/validation/validatation.decorator.js'
 
-import { AssembliesService } from './assemblies.service'
+import { AssembliesService } from './assemblies.service.js'
 
 interface AssemblyDocument {
   _id: string
diff --git a/packages/apollo-collaboration-server/src/assemblies/assemblies.module.ts b/packages/apollo-collaboration-server/src/assemblies/assemblies.module.ts
index 183a2170e..db1f783f6 100644
--- a/packages/apollo-collaboration-server/src/assemblies/assemblies.module.ts
+++ b/packages/apollo-collaboration-server/src/assemblies/assemblies.module.ts
@@ -1,14 +1,14 @@
 import { Assembly, AssemblySchema } from '@apollo-annotation/schemas'
 import { Module } from '@nestjs/common'
 import { MongooseModule } from '@nestjs/mongoose'
-import { FeaturesModule } from 'src/features/features.module'
-import { RefSeqsModule } from 'src/refSeqs/refSeqs.module'
 
-import { ChecksModule } from '../checks/checks.module'
-import { OperationsModule } from '../operations/operations.module'
+import { ChecksModule } from '../checks/checks.module.js'
+import { FeaturesModule } from '../features/features.module.js'
+import { OperationsModule } from '../operations/operations.module.js'
+import { RefSeqsModule } from '../refSeqs/refSeqs.module.js'
 
-import { AssembliesController } from './assemblies.controller'
-import { AssembliesService } from './assemblies.service'
+import { AssembliesController } from './assemblies.controller.js'
+import { AssembliesService } from './assemblies.service.js'
 
 @Module({
   controllers: [AssembliesController],
diff --git a/packages/apollo-collaboration-server/src/assemblies/assemblies.service.spec.ts b/packages/apollo-collaboration-server/src/assemblies/assemblies.service.spec.ts
index 11226216c..76a241fa2 100644
--- a/packages/apollo-collaboration-server/src/assemblies/assemblies.service.spec.ts
+++ b/packages/apollo-collaboration-server/src/assemblies/assemblies.service.spec.ts
@@ -1,6 +1,6 @@
 import { Test, type TestingModule } from '@nestjs/testing'
 
-import { AssembliesService } from './assemblies.service'
+import { AssembliesService } from './assemblies.service.js'
 
 describe('AssembliesService', () => {
   let service: AssembliesService
diff --git a/packages/apollo-collaboration-server/src/assemblies/assemblies.service.ts b/packages/apollo-collaboration-server/src/assemblies/assemblies.service.ts
index aa13146e5..ce731b2c3 100644
--- a/packages/apollo-collaboration-server/src/assemblies/assemblies.service.ts
+++ b/packages/apollo-collaboration-server/src/assemblies/assemblies.service.ts
@@ -1,8 +1,8 @@
 import {
   Assembly,
-  AssemblyDocument,
+  type AssemblyDocument,
   Check,
-  CheckDocument,
+  type CheckDocument,
 } from '@apollo-annotation/schemas'
 import { GetAssembliesOperation } from '@apollo-annotation/shared'
 import {
@@ -13,14 +13,14 @@ import {
 } from '@nestjs/common'
 import { InjectModel } from '@nestjs/mongoose'
 import { Model } from 'mongoose'
-import { FeaturesService } from 'src/features/features.service'
-import { RefSeqsService } from 'src/refSeqs/refSeqs.service'
 
-import { ChecksService } from '../checks/checks.service'
-import { OperationsService } from '../operations/operations.service'
+import { ChecksService } from '../checks/checks.service.js'
+import { FeaturesService } from '../features/features.service.js'
+import { OperationsService } from '../operations/operations.service.js'
+import { RefSeqsService } from '../refSeqs/refSeqs.service.js'
 
-import { CreateAssemblyDto } from './dto/create-assembly.dto'
-import { UpdateAssemblyDto } from './dto/update-assembly.dto'
+import { CreateAssemblyDto } from './dto/create-assembly.dto.js'
+import { UpdateAssemblyDto } from './dto/update-assembly.dto.js'
 
 @Injectable()
 export class AssembliesService {
diff --git a/packages/apollo-collaboration-server/src/assemblies/dto/update-assembly.dto.ts b/packages/apollo-collaboration-server/src/assemblies/dto/update-assembly.dto.ts
index 914118edc..b7393e908 100644
--- a/packages/apollo-collaboration-server/src/assemblies/dto/update-assembly.dto.ts
+++ b/packages/apollo-collaboration-server/src/assemblies/dto/update-assembly.dto.ts
@@ -1,5 +1,5 @@
 import { PartialType } from '@nestjs/mapped-types'
 
-import { CreateAssemblyDto } from './create-assembly.dto'
+import { CreateAssemblyDto } from './create-assembly.dto.js'
 
 export class UpdateAssemblyDto extends PartialType(CreateAssemblyDto) {}
diff --git a/packages/apollo-collaboration-server/src/authentication/authentication.controller.spec.ts b/packages/apollo-collaboration-server/src/authentication/authentication.controller.spec.ts
index ac3321521..ed12ca658 100644
--- a/packages/apollo-collaboration-server/src/authentication/authentication.controller.spec.ts
+++ b/packages/apollo-collaboration-server/src/authentication/authentication.controller.spec.ts
@@ -1,6 +1,6 @@
 import { Test, type TestingModule } from '@nestjs/testing'
 
-import { AuthenticationController } from './authentication.controller'
+import { AuthenticationController } from './authentication.controller.js'
 
 describe('AuthenticationController', () => {
   let controller: AuthenticationController
diff --git a/packages/apollo-collaboration-server/src/authentication/authentication.controller.ts b/packages/apollo-collaboration-server/src/authentication/authentication.controller.ts
index dec75d049..a73a6e608 100644
--- a/packages/apollo-collaboration-server/src/authentication/authentication.controller.ts
+++ b/packages/apollo-collaboration-server/src/authentication/authentication.controller.ts
@@ -12,15 +12,15 @@ import {
   UseGuards,
 } from '@nestjs/common'
 
-import { GoogleAuthGuard } from '../utils/google.guard'
-import { MicrosoftAuthGuard } from '../utils/microsoft.guard'
-import { Role } from '../utils/role/role.enum'
-import { Validations } from '../utils/validation/validatation.decorator'
+import { GoogleAuthGuard } from '../utils/google.guard.js'
+import { MicrosoftAuthGuard } from '../utils/microsoft.guard.js'
+import { Role } from '../utils/role/role.enum.js'
+import { Validations } from '../utils/validation/validatation.decorator.js'
 
 import {
   AuthenticationService,
-  RequestWithUserToken,
-} from './authentication.service'
+  type RequestWithUserToken,
+} from './authentication.service.js'
 
 @Validations(Role.None)
 @Controller('auth')
diff --git a/packages/apollo-collaboration-server/src/authentication/authentication.module.ts b/packages/apollo-collaboration-server/src/authentication/authentication.module.ts
index 1e67d4f36..7fa66c985 100644
--- a/packages/apollo-collaboration-server/src/authentication/authentication.module.ts
+++ b/packages/apollo-collaboration-server/src/authentication/authentication.module.ts
@@ -2,16 +2,16 @@ import fs from 'node:fs/promises'
 
 import { Module } from '@nestjs/common'
 import { ConfigModule, ConfigService } from '@nestjs/config'
-import { JwtModule, JwtModuleOptions } from '@nestjs/jwt'
+import { JwtModule, type JwtModuleOptions } from '@nestjs/jwt'
 import { PassportModule } from '@nestjs/passport'
 
-import { UsersModule } from '../users/users.module'
-import { GoogleStrategy } from '../utils/strategies/google.strategy'
-import { JwtStrategy } from '../utils/strategies/jwt.strategy'
-import { MicrosoftStrategy } from '../utils/strategies/microsoft.strategy'
+import { UsersModule } from '../users/users.module.js'
+import { GoogleStrategy } from '../utils/strategies/google.strategy.js'
+import { JwtStrategy } from '../utils/strategies/jwt.strategy.js'
+import { MicrosoftStrategy } from '../utils/strategies/microsoft.strategy.js'
 
-import { AuthenticationController } from './authentication.controller'
-import { AuthenticationService } from './authentication.service'
+import { AuthenticationController } from './authentication.controller.js'
+import { AuthenticationService } from './authentication.service.js'
 
 interface JWTSecretConfig {
   JWT_SECRET?: string
diff --git a/packages/apollo-collaboration-server/src/authentication/authentication.service.spec.ts b/packages/apollo-collaboration-server/src/authentication/authentication.service.spec.ts
index e79c50ed5..51023256a 100644
--- a/packages/apollo-collaboration-server/src/authentication/authentication.service.spec.ts
+++ b/packages/apollo-collaboration-server/src/authentication/authentication.service.spec.ts
@@ -1,6 +1,6 @@
 import { Test, type TestingModule } from '@nestjs/testing'
 
-import { AuthenticationService } from './authentication.service'
+import { AuthenticationService } from './authentication.service.js'
 
 describe('AuthenticationService', () => {
   let service: AuthenticationService
diff --git a/packages/apollo-collaboration-server/src/authentication/authentication.service.ts b/packages/apollo-collaboration-server/src/authentication/authentication.service.ts
index c696f3a64..4cabf5822 100644
--- a/packages/apollo-collaboration-server/src/authentication/authentication.service.ts
+++ b/packages/apollo-collaboration-server/src/authentication/authentication.service.ts
@@ -2,7 +2,7 @@
 /* eslint-disable @typescript-eslint/no-unsafe-assignment */
 import fs from 'node:fs/promises'
 
-import { JWTPayload } from '@apollo-annotation/shared'
+import { type JWTPayload } from '@apollo-annotation/shared'
 import {
   BadRequestException,
   Injectable,
@@ -11,18 +11,18 @@ import {
 } from '@nestjs/common'
 import { ConfigService } from '@nestjs/config'
 import { JwtService } from '@nestjs/jwt'
-import { Request } from 'express'
-import { Profile as GoogleProfile } from 'passport-google-oauth20'
+import { type Request } from 'express'
+import { type Profile as GoogleProfile } from 'passport-google-oauth20'
 
-import { CreateUserDto } from '../users/dto/create-user.dto'
-import { UsersService } from '../users/users.service'
+import { CreateUserDto } from '../users/dto/create-user.dto.js'
+import { UsersService } from '../users/users.service.js'
 import {
   GUEST_USER_EMAIL,
   GUEST_USER_NAME,
   ROOT_USER_EMAIL,
-} from '../utils/constants'
-import { Role } from '../utils/role/role.enum'
-import { Profile as MicrosoftProfile } from '../utils/strategies/microsoft.strategy'
+} from '../utils/constants.js'
+import { Role } from '../utils/role/role.enum.js'
+import { type Profile as MicrosoftProfile } from '../utils/strategies/microsoft.strategy.js'
 
 export interface RequestWithUserToken extends Request {
   user: { token: string }
diff --git a/packages/apollo-collaboration-server/src/changes/changes.controller.spec.ts b/packages/apollo-collaboration-server/src/changes/changes.controller.spec.ts
index e3567320b..03c474760 100644
--- a/packages/apollo-collaboration-server/src/changes/changes.controller.spec.ts
+++ b/packages/apollo-collaboration-server/src/changes/changes.controller.spec.ts
@@ -1,7 +1,7 @@
 import { Test, type TestingModule } from '@nestjs/testing'
 
-import { ChangesController } from './changes.controller'
-import { ChangesService } from './changes.service'
+import { ChangesController } from './changes.controller.js'
+import { ChangesService } from './changes.service.js'
 
 describe('ChangesController', () => {
   let controller: ChangesController
diff --git a/packages/apollo-collaboration-server/src/changes/changes.controller.ts b/packages/apollo-collaboration-server/src/changes/changes.controller.ts
index 43aa3403d..4906f607a 100644
--- a/packages/apollo-collaboration-server/src/changes/changes.controller.ts
+++ b/packages/apollo-collaboration-server/src/changes/changes.controller.ts
@@ -1,15 +1,15 @@
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 import { Change } from '@apollo-annotation/common'
-import { DecodedJWT } from '@apollo-annotation/shared'
+import { type DecodedJWT } from '@apollo-annotation/shared'
 import { Body, Controller, Get, Logger, Post, Query, Req } from '@nestjs/common'
-import { Request } from 'express'
+import { type Request } from 'express'
 
-import { ParseChangePipe } from '../utils/parse-change.pipe'
-import { Role } from '../utils/role/role.enum'
-import { Validations } from '../utils/validation/validatation.decorator'
+import { ParseChangePipe } from '../utils/parse-change.pipe.js'
+import { Role } from '../utils/role/role.enum.js'
+import { Validations } from '../utils/validation/validatation.decorator.js'
 
-import { ChangesService } from './changes.service'
-import { FindChangeDto } from './dto/find-change.dto'
+import { ChangesService } from './changes.service.js'
+import { FindChangeDto } from './dto/find-change.dto.js'
 
 @Validations(Role.ReadOnly)
 @Controller('changes')
diff --git a/packages/apollo-collaboration-server/src/changes/changes.module.ts b/packages/apollo-collaboration-server/src/changes/changes.module.ts
index 74e43c844..73ae3864e 100644
--- a/packages/apollo-collaboration-server/src/changes/changes.module.ts
+++ b/packages/apollo-collaboration-server/src/changes/changes.module.ts
@@ -4,19 +4,19 @@ import { Module } from '@nestjs/common'
 import { MongooseModule, getConnectionToken } from '@nestjs/mongoose'
 import idValidator from 'mongoose-id-validator'
 
-import { AssembliesModule } from '../assemblies/assemblies.module'
-import { ChecksModule } from '../checks/checks.module'
-import { CountersModule } from '../counters/counters.module'
-import { FeaturesModule } from '../features/features.module'
-import { FilesModule } from '../files/files.module'
-import { JBrowseModule } from '../jbrowse/jbrowse.module'
-import { MessagesModule } from '../messages/messages.module'
-import { RefSeqChunksModule } from '../refSeqChunks/refSeqChunks.module'
-import { RefSeqsModule } from '../refSeqs/refSeqs.module'
-import { UsersModule } from '../users/users.module'
+import { AssembliesModule } from '../assemblies/assemblies.module.js'
+import { ChecksModule } from '../checks/checks.module.js'
+import { CountersModule } from '../counters/counters.module.js'
+import { FeaturesModule } from '../features/features.module.js'
+import { FilesModule } from '../files/files.module.js'
+import { JBrowseModule } from '../jbrowse/jbrowse.module.js'
+import { MessagesModule } from '../messages/messages.module.js'
+import { RefSeqChunksModule } from '../refSeqChunks/refSeqChunks.module.js'
+import { RefSeqsModule } from '../refSeqs/refSeqs.module.js'
+import { UsersModule } from '../users/users.module.js'
 
-import { ChangesController } from './changes.controller'
-import { ChangesService } from './changes.service'
+import { ChangesController } from './changes.controller.js'
+import { ChangesService } from './changes.service.js'
 
 @Module({
   controllers: [ChangesController],
diff --git a/packages/apollo-collaboration-server/src/changes/changes.service.spec.ts b/packages/apollo-collaboration-server/src/changes/changes.service.spec.ts
index 1a7c66967..334bea9d3 100644
--- a/packages/apollo-collaboration-server/src/changes/changes.service.spec.ts
+++ b/packages/apollo-collaboration-server/src/changes/changes.service.spec.ts
@@ -1,6 +1,6 @@
 import { Test, type TestingModule } from '@nestjs/testing'
 
-import { ChangesService } from './changes.service'
+import { ChangesService } from './changes.service.js'
 
 describe('ChangesService', () => {
   let service: ChangesService
diff --git a/packages/apollo-collaboration-server/src/changes/changes.service.ts b/packages/apollo-collaboration-server/src/changes/changes.service.ts
index b1173f20d..201644fe5 100644
--- a/packages/apollo-collaboration-server/src/changes/changes.service.ts
+++ b/packages/apollo-collaboration-server/src/changes/changes.service.ts
@@ -6,29 +6,29 @@ import {
 } from '@apollo-annotation/common'
 import {
   Assembly,
-  AssemblyDocument,
+  type AssemblyDocument,
   Change,
-  ChangeDocument,
+  type ChangeDocument,
   Check,
-  CheckDocument,
+  type CheckDocument,
   Feature,
-  FeatureDocument,
+  type FeatureDocument,
   File,
-  FileDocument,
+  type FileDocument,
   JBrowseConfig,
-  JBrowseConfigDocument,
+  type JBrowseConfigDocument,
   RefSeq,
   RefSeqChunk,
-  RefSeqChunkDocument,
-  RefSeqDocument,
+  type RefSeqChunkDocument,
+  type RefSeqDocument,
   User,
-  UserDocument,
+  type UserDocument,
 } from '@apollo-annotation/schemas'
 import {
   AddFeatureChange,
-  AddFeatureChangeDetails,
-  ChangeMessage,
-  DecodedJWT,
+  type AddFeatureChangeDetails,
+  type ChangeMessage,
+  type DecodedJWT,
   makeUserSessionId,
   validationRegistry,
 } from '@apollo-annotation/shared'
@@ -38,14 +38,14 @@ import {
   UnprocessableEntityException,
 } from '@nestjs/common'
 import { InjectModel } from '@nestjs/mongoose'
-import { FilterQuery, Model } from 'mongoose'
+import { type FilterQuery, Model } from 'mongoose'
 
-import { CountersService } from '../counters/counters.service'
-import { FilesService } from '../files/files.service'
-import { MessagesGateway } from '../messages/messages.gateway'
-import { PluginsService } from '../plugins/plugins.service'
+import { CountersService } from '../counters/counters.service.js'
+import { FilesService } from '../files/files.service.js'
+import { MessagesGateway } from '../messages/messages.gateway.js'
+import { PluginsService } from '../plugins/plugins.service.js'
 
-import { FindChangeDto } from './dto/find-change.dto'
+import { FindChangeDto } from './dto/find-change.dto.js'
 
 const STATUS_ZERO_CHANGE_TYPES = new Set([
   'AddAssemblyAndFeaturesFromFileChange',
diff --git a/packages/apollo-collaboration-server/src/changes/dto/update-change.dto.ts b/packages/apollo-collaboration-server/src/changes/dto/update-change.dto.ts
index 1b18c2c28..e9ce8fb9b 100644
--- a/packages/apollo-collaboration-server/src/changes/dto/update-change.dto.ts
+++ b/packages/apollo-collaboration-server/src/changes/dto/update-change.dto.ts
@@ -1,5 +1,5 @@
 import { PartialType } from '@nestjs/mapped-types'
 
-import { CreateChangeDto } from './create-change.dto'
+import { CreateChangeDto } from './create-change.dto.js'
 
 export class UpdateChangeDto extends PartialType(CreateChangeDto) {}
diff --git a/packages/apollo-collaboration-server/src/checks/checks.controller.spec.ts b/packages/apollo-collaboration-server/src/checks/checks.controller.spec.ts
index 241b52f9c..819463ffa 100644
--- a/packages/apollo-collaboration-server/src/checks/checks.controller.spec.ts
+++ b/packages/apollo-collaboration-server/src/checks/checks.controller.spec.ts
@@ -1,6 +1,6 @@
 import { Test, type TestingModule } from '@nestjs/testing'
 
-import { ChecksController } from './checks.controller'
+import { ChecksController } from './checks.controller.js'
 
 describe('ChecksController', () => {
   let controller: ChecksController
diff --git a/packages/apollo-collaboration-server/src/checks/checks.controller.ts b/packages/apollo-collaboration-server/src/checks/checks.controller.ts
index 45ce9ed8e..a1b5944eb 100644
--- a/packages/apollo-collaboration-server/src/checks/checks.controller.ts
+++ b/packages/apollo-collaboration-server/src/checks/checks.controller.ts
@@ -1,10 +1,10 @@
 import { Controller, Get, Logger, Param, Query } from '@nestjs/common'
 
-import { FeatureRangeSearchDto } from '../entity/gff3Object.dto'
-import { Role } from '../utils/role/role.enum'
-import { Validations } from '../utils/validation/validatation.decorator'
+import { type FeatureRangeSearchDto } from '../entity/gff3Object.dto.js'
+import { Role } from '../utils/role/role.enum.js'
+import { Validations } from '../utils/validation/validatation.decorator.js'
 
-import { ChecksService } from './checks.service'
+import { ChecksService } from './checks.service.js'
 
 @Validations(Role.ReadOnly)
 @Controller('checks')
diff --git a/packages/apollo-collaboration-server/src/checks/checks.module.ts b/packages/apollo-collaboration-server/src/checks/checks.module.ts
index 78d22b854..2f9ed0598 100644
--- a/packages/apollo-collaboration-server/src/checks/checks.module.ts
+++ b/packages/apollo-collaboration-server/src/checks/checks.module.ts
@@ -1,25 +1,25 @@
 /* eslint-disable @typescript-eslint/no-unsafe-assignment */
 /* eslint-disable @typescript-eslint/no-unsafe-argument */
-import { CheckResultSnapshot } from '@apollo-annotation/mst'
+import { type CheckResultSnapshot } from '@apollo-annotation/mst'
 import {
   Check,
   CheckResult,
-  CheckResultDocument,
+  type CheckResultDocument,
   CheckResultSchema,
   CheckSchema,
 } from '@apollo-annotation/schemas'
-import { CheckResultUpdate } from '@apollo-annotation/shared'
+import { type CheckResultUpdate } from '@apollo-annotation/shared'
 import { Module, forwardRef } from '@nestjs/common'
 import { MongooseModule, getConnectionToken } from '@nestjs/mongoose'
 import idValidator from 'mongoose-id-validator'
 
-import { MessagesGateway } from '../messages/messages.gateway'
-import { MessagesModule } from '../messages/messages.module'
-import { RefSeqsModule } from '../refSeqs/refSeqs.module'
-import { SequenceModule } from '../sequence/sequence.module'
+import { MessagesGateway } from '../messages/messages.gateway.js'
+import { MessagesModule } from '../messages/messages.module.js'
+import { RefSeqsModule } from '../refSeqs/refSeqs.module.js'
+import { SequenceModule } from '../sequence/sequence.module.js'
 
-import { ChecksController } from './checks.controller'
-import { ChecksService } from './checks.service'
+import { ChecksController } from './checks.controller.js'
+import { ChecksService } from './checks.service.js'
 
 @Module({
   providers: [ChecksService],
diff --git a/packages/apollo-collaboration-server/src/checks/checks.service.spec.ts b/packages/apollo-collaboration-server/src/checks/checks.service.spec.ts
index 8ec52e0f6..536f16fc2 100644
--- a/packages/apollo-collaboration-server/src/checks/checks.service.spec.ts
+++ b/packages/apollo-collaboration-server/src/checks/checks.service.spec.ts
@@ -1,6 +1,6 @@
 import { Test, type TestingModule } from '@nestjs/testing'
 
-import { ChecksService } from './checks.service'
+import { ChecksService } from './checks.service.js'
 
 describe('ChecksService', () => {
   let service: ChecksService
diff --git a/packages/apollo-collaboration-server/src/checks/checks.service.ts b/packages/apollo-collaboration-server/src/checks/checks.service.ts
index 061001621..f6f8b2c30 100644
--- a/packages/apollo-collaboration-server/src/checks/checks.service.ts
+++ b/packages/apollo-collaboration-server/src/checks/checks.service.ts
@@ -3,26 +3,26 @@
 /* eslint-disable @typescript-eslint/restrict-template-expressions */
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 import { checkRegistry } from '@apollo-annotation/common'
-import { AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
+import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
 import {
   Assembly,
-  AssemblyDocument,
+  type AssemblyDocument,
   Check,
-  CheckDocument,
+  type CheckDocument,
   CheckResult,
-  CheckResultDocument,
-  FeatureDocument,
+  type CheckResultDocument,
+  type FeatureDocument,
   RefSeq,
-  RefSeqDocument,
+  type RefSeqDocument,
 } from '@apollo-annotation/schemas'
 import { Inject, Injectable, Logger, forwardRef } from '@nestjs/common'
 import { InjectModel } from '@nestjs/mongoose'
 import { ObjectId } from 'mongodb'
 import { Model } from 'mongoose'
 
-import { FeatureRangeSearchDto } from '../entity/gff3Object.dto'
-import { RefSeqsService } from '../refSeqs/refSeqs.service'
-import { SequenceService } from '../sequence/sequence.service'
+import { type FeatureRangeSearchDto } from '../entity/gff3Object.dto.js'
+import { RefSeqsService } from '../refSeqs/refSeqs.service.js'
+import { SequenceService } from '../sequence/sequence.service.js'
 
 @Injectable()
 export class ChecksService {
@@ -31,7 +31,7 @@ export class ChecksService {
     private readonly checkResultModel: Model<CheckResultDocument>,
     private readonly refSeqsService: RefSeqsService,
     @Inject(forwardRef(() => SequenceService))
-    private readonly sequenceService: SequenceService,
+    private readonly sequenceService: Readonly<SequenceService>,
     @InjectModel(Check.name)
     private readonly checkModel: Model<CheckDocument>,
   ) {}
diff --git a/packages/apollo-collaboration-server/src/counters/counters.module.ts b/packages/apollo-collaboration-server/src/counters/counters.module.ts
index 0c4b2f52a..fb1940e79 100644
--- a/packages/apollo-collaboration-server/src/counters/counters.module.ts
+++ b/packages/apollo-collaboration-server/src/counters/counters.module.ts
@@ -2,7 +2,7 @@ import { Counter, CounterSchema } from '@apollo-annotation/schemas'
 import { Module } from '@nestjs/common'
 import { MongooseModule } from '@nestjs/mongoose'
 
-import { CountersService } from './counters.service'
+import { CountersService } from './counters.service.js'
 
 @Module({
   // controllers: [CountersController],
diff --git a/packages/apollo-collaboration-server/src/counters/counters.service.ts b/packages/apollo-collaboration-server/src/counters/counters.service.ts
index a9177597a..2d7a9eeb2 100644
--- a/packages/apollo-collaboration-server/src/counters/counters.service.ts
+++ b/packages/apollo-collaboration-server/src/counters/counters.service.ts
@@ -1,5 +1,5 @@
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
-import { Counter, CounterDocument } from '@apollo-annotation/schemas'
+import { Counter, type CounterDocument } from '@apollo-annotation/schemas'
 import { Injectable, Logger, NotFoundException } from '@nestjs/common'
 import { InjectModel } from '@nestjs/mongoose'
 import { Model } from 'mongoose'
diff --git a/packages/apollo-collaboration-server/src/export/export.controller.spec.ts b/packages/apollo-collaboration-server/src/export/export.controller.spec.ts
index db427787d..7eb989ab8 100644
--- a/packages/apollo-collaboration-server/src/export/export.controller.spec.ts
+++ b/packages/apollo-collaboration-server/src/export/export.controller.spec.ts
@@ -1,6 +1,6 @@
 import { Test, type TestingModule } from '@nestjs/testing'
 
-import { ExportController } from './export.controller'
+import { ExportController } from './export.controller.js'
 
 describe('ExportController', () => {
   let controller: ExportController
diff --git a/packages/apollo-collaboration-server/src/export/export.controller.ts b/packages/apollo-collaboration-server/src/export/export.controller.ts
index 7caf73f22..a9c319990 100644
--- a/packages/apollo-collaboration-server/src/export/export.controller.ts
+++ b/packages/apollo-collaboration-server/src/export/export.controller.ts
@@ -10,12 +10,12 @@ import {
   Response,
   StreamableFile,
 } from '@nestjs/common'
-import { Response as ExpressResponse } from 'express'
+import { type Response as ExpressResponse } from 'express'
 
-import { Role } from '../utils/role/role.enum'
-import { Validations } from '../utils/validation/validatation.decorator'
+import { Role } from '../utils/role/role.enum.js'
+import { Validations } from '../utils/validation/validatation.decorator.js'
 
-import { ExportService } from './export.service'
+import { ExportService } from './export.service.js'
 
 @Controller('export')
 export class ExportController {
diff --git a/packages/apollo-collaboration-server/src/export/export.module.ts b/packages/apollo-collaboration-server/src/export/export.module.ts
index 18549ea30..2dea9ee62 100644
--- a/packages/apollo-collaboration-server/src/export/export.module.ts
+++ b/packages/apollo-collaboration-server/src/export/export.module.ts
@@ -2,14 +2,14 @@ import { Export, ExportSchema } from '@apollo-annotation/schemas'
 import { Module } from '@nestjs/common'
 import { MongooseModule } from '@nestjs/mongoose'
 
-import { AssembliesModule } from '../assemblies/assemblies.module'
-import { FeaturesModule } from '../features/features.module'
-import { FilesModule } from '../files/files.module'
-import { RefSeqChunksModule } from '../refSeqChunks/refSeqChunks.module'
-import { RefSeqsModule } from '../refSeqs/refSeqs.module'
+import { AssembliesModule } from '../assemblies/assemblies.module.js'
+import { FeaturesModule } from '../features/features.module.js'
+import { FilesModule } from '../files/files.module.js'
+import { RefSeqChunksModule } from '../refSeqChunks/refSeqChunks.module.js'
+import { RefSeqsModule } from '../refSeqs/refSeqs.module.js'
 
-import { ExportController } from './export.controller'
-import { ExportService } from './export.service'
+import { ExportController } from './export.controller.js'
+import { ExportService } from './export.service.js'
 
 @Module({
   imports: [
diff --git a/packages/apollo-collaboration-server/src/export/export.service.spec.ts b/packages/apollo-collaboration-server/src/export/export.service.spec.ts
index f9271464f..2432fcdb1 100644
--- a/packages/apollo-collaboration-server/src/export/export.service.spec.ts
+++ b/packages/apollo-collaboration-server/src/export/export.service.spec.ts
@@ -1,6 +1,6 @@
 import { Test, type TestingModule } from '@nestjs/testing'
 
-import { ExportService } from './export.service'
+import { ExportService } from './export.service.js'
 
 describe('ExportService', () => {
   let service: ExportService
diff --git a/packages/apollo-collaboration-server/src/export/export.service.ts b/packages/apollo-collaboration-server/src/export/export.service.ts
index 6fc9de2e6..c12cc004c 100644
--- a/packages/apollo-collaboration-server/src/export/export.service.ts
+++ b/packages/apollo-collaboration-server/src/export/export.service.ts
@@ -6,29 +6,29 @@ import { ReadableStream, TransformStream } from 'node:stream/web'
 
 import {
   Assembly,
-  AssemblyDocument,
+  type AssemblyDocument,
   Export,
-  ExportDocument,
+  type ExportDocument,
   Feature,
-  FeatureDocument,
+  type FeatureDocument,
   File,
-  FileDocument,
+  type FileDocument,
   RefSeq,
   RefSeqChunk,
-  RefSeqDocument,
+  type RefSeqDocument,
 } from '@apollo-annotation/schemas'
 import { GFFFormattingTransformer } from '@gmod/gff'
 import { Injectable, Logger, NotFoundException } from '@nestjs/common'
 import { ConfigService } from '@nestjs/config'
 import { InjectModel } from '@nestjs/mongoose'
-import { FilterQuery, Model } from 'mongoose'
+import { type FilterQuery, Model } from 'mongoose'
 import StreamConcat from 'stream-concat'
 
 import {
   FeatureDocToGFF3FeatureStream,
   RefSeqChunkDocToFASTAStream,
   RefSeqDocToGFF3HeaderStream,
-} from './transforms'
+} from './transforms.js'
 
 @Injectable()
 export class ExportService {
@@ -108,7 +108,6 @@ export class ExportService {
         sequenceStreams = await this.streamFromLocalFasta(
           assemblyDoc.fileIds.fa,
         )
-        // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
       } else if (assemblyDoc.externalLocation) {
         sequenceStreams = await this.streamFromRemoteFasta(
           assemblyDoc.externalLocation.fa,
diff --git a/packages/apollo-collaboration-server/src/features/dto/update-feature.dto.ts b/packages/apollo-collaboration-server/src/features/dto/update-feature.dto.ts
index fae8322d4..d5018d2f3 100644
--- a/packages/apollo-collaboration-server/src/features/dto/update-feature.dto.ts
+++ b/packages/apollo-collaboration-server/src/features/dto/update-feature.dto.ts
@@ -1,5 +1,5 @@
 import { PartialType } from '@nestjs/mapped-types'
 
-import { CreateFeatureDto } from './create-feature.dto'
+import { CreateFeatureDto } from './create-feature.dto.js'
 
 export class UpdateFeatureDto extends PartialType(CreateFeatureDto) {}
diff --git a/packages/apollo-collaboration-server/src/features/features.controller.spec.ts b/packages/apollo-collaboration-server/src/features/features.controller.spec.ts
index 2336fa863..d447a8e90 100644
--- a/packages/apollo-collaboration-server/src/features/features.controller.spec.ts
+++ b/packages/apollo-collaboration-server/src/features/features.controller.spec.ts
@@ -1,7 +1,7 @@
 import { Test, type TestingModule } from '@nestjs/testing'
 
-import { FeaturesController } from './features.controller'
-import { FeaturesService } from './features.service'
+import { FeaturesController } from './features.controller.js'
+import { FeaturesService } from './features.service.js'
 
 describe('FeaturesController', () => {
   let controller: FeaturesController
diff --git a/packages/apollo-collaboration-server/src/features/features.controller.ts b/packages/apollo-collaboration-server/src/features/features.controller.ts
index 22006282f..949f4bb40 100644
--- a/packages/apollo-collaboration-server/src/features/features.controller.ts
+++ b/packages/apollo-collaboration-server/src/features/features.controller.ts
@@ -10,14 +10,17 @@ import {
 } from '@nestjs/common'
 
 import {
-  FeatureIdsSearchDto,
-  FeatureRangeSearchDto,
-} from '../entity/gff3Object.dto'
-import { Role } from '../utils/role/role.enum'
-import { Validations } from '../utils/validation/validatation.decorator'
+  type FeatureIdsSearchDto,
+  type FeatureRangeSearchDto,
+} from '../entity/gff3Object.dto.js'
+import { Role } from '../utils/role/role.enum.js'
+import { Validations } from '../utils/validation/validatation.decorator.js'
 
-import { FeatureCountRequest, GetByIndexedIdRequest } from './dto/feature.dto'
-import { FeaturesService } from './features.service'
+import {
+  type FeatureCountRequest,
+  type GetByIndexedIdRequest,
+} from './dto/feature.dto.js'
+import { FeaturesService } from './features.service.js'
 
 @Validations(Role.ReadOnly)
 @Controller('features')
diff --git a/packages/apollo-collaboration-server/src/features/features.module.ts b/packages/apollo-collaboration-server/src/features/features.module.ts
index 23126647a..9c4a098f5 100644
--- a/packages/apollo-collaboration-server/src/features/features.module.ts
+++ b/packages/apollo-collaboration-server/src/features/features.module.ts
@@ -1,21 +1,21 @@
 import {
   Feature,
-  FeatureDocument,
+  type FeatureDocument,
   FeatureSchema,
 } from '@apollo-annotation/schemas'
 import { Module, forwardRef } from '@nestjs/common'
 import { MongooseModule, getConnectionToken } from '@nestjs/mongoose'
-import { Connection } from 'mongoose'
+import { type Connection } from 'mongoose'
 import idValidator from 'mongoose-id-validator'
 
-import { ChecksModule } from '../checks/checks.module'
-import { ChecksService } from '../checks/checks.service'
-import { OperationsModule } from '../operations/operations.module'
-import { RefSeqsModule } from '../refSeqs/refSeqs.module'
-import { SequenceModule } from '../sequence/sequence.module'
+import { ChecksModule } from '../checks/checks.module.js'
+import { ChecksService } from '../checks/checks.service.js'
+import { OperationsModule } from '../operations/operations.module.js'
+import { RefSeqsModule } from '../refSeqs/refSeqs.module.js'
+import { SequenceModule } from '../sequence/sequence.module.js'
 
-import { FeaturesController } from './features.controller'
-import { FeaturesService } from './features.service'
+import { FeaturesController } from './features.controller.js'
+import { FeaturesService } from './features.service.js'
 
 @Module({
   controllers: [FeaturesController],
diff --git a/packages/apollo-collaboration-server/src/features/features.service.spec.ts b/packages/apollo-collaboration-server/src/features/features.service.spec.ts
index 3b073b7fd..4349c3747 100644
--- a/packages/apollo-collaboration-server/src/features/features.service.spec.ts
+++ b/packages/apollo-collaboration-server/src/features/features.service.spec.ts
@@ -1,6 +1,6 @@
 import { Test, type TestingModule } from '@nestjs/testing'
 
-import { FeaturesService } from './features.service'
+import { FeaturesService } from './features.service.js'
 
 describe('FeaturesService', () => {
   let service: FeaturesService
diff --git a/packages/apollo-collaboration-server/src/features/features.service.ts b/packages/apollo-collaboration-server/src/features/features.service.ts
index 87f078048..14e04ca1d 100644
--- a/packages/apollo-collaboration-server/src/features/features.service.ts
+++ b/packages/apollo-collaboration-server/src/features/features.service.ts
@@ -2,20 +2,23 @@
 /* eslint-disable @typescript-eslint/no-unsafe-argument */
 import {
   Feature,
-  FeatureDocument,
+  type FeatureDocument,
   RefSeq,
-  RefSeqDocument,
+  type RefSeqDocument,
 } from '@apollo-annotation/schemas'
 import { GetFeaturesOperation } from '@apollo-annotation/shared'
 import { Injectable, Logger, NotFoundException } from '@nestjs/common'
 import { InjectModel } from '@nestjs/mongoose'
 import { Model } from 'mongoose'
 
-import { ChecksService } from '../checks/checks.service'
-import { FeatureRangeSearchDto } from '../entity/gff3Object.dto'
-import { OperationsService } from '../operations/operations.service'
+import { ChecksService } from '../checks/checks.service.js'
+import { type FeatureRangeSearchDto } from '../entity/gff3Object.dto.js'
+import { OperationsService } from '../operations/operations.service.js'
 
-import { FeatureCountRequest, GetByIndexedIdRequest } from './dto/feature.dto'
+import {
+  type FeatureCountRequest,
+  type GetByIndexedIdRequest,
+} from './dto/feature.dto.js'
 
 @Injectable()
 export class FeaturesService {
diff --git a/packages/apollo-collaboration-server/src/files/FileStorageEngine.ts b/packages/apollo-collaboration-server/src/files/FileStorageEngine.ts
index 3262455cf..f428ab353 100644
--- a/packages/apollo-collaboration-server/src/files/FileStorageEngine.ts
+++ b/packages/apollo-collaboration-server/src/files/FileStorageEngine.ts
@@ -3,9 +3,9 @@ import {
   InternalServerErrorException,
   Logger,
 } from '@nestjs/common'
-import { StorageEngine } from 'multer'
+import { type StorageEngine } from 'multer'
 
-import { writeFileAndCalculateHash } from './filesUtil'
+import { writeFileAndCalculateHash } from './filesUtil.js'
 
 export interface UploadedFile extends Express.Multer.File {
   checksum: string
diff --git a/packages/apollo-collaboration-server/src/files/files.controller.spec.ts b/packages/apollo-collaboration-server/src/files/files.controller.spec.ts
index 1578d990e..313f0c83b 100644
--- a/packages/apollo-collaboration-server/src/files/files.controller.spec.ts
+++ b/packages/apollo-collaboration-server/src/files/files.controller.spec.ts
@@ -1,6 +1,6 @@
 import { Test, type TestingModule } from '@nestjs/testing'
 
-import { FilesController } from './files.controller'
+import { FilesController } from './files.controller.js'
 
 describe('FilesController', () => {
   let controller: FilesController
diff --git a/packages/apollo-collaboration-server/src/files/files.controller.ts b/packages/apollo-collaboration-server/src/files/files.controller.ts
index bf7834ed3..88b01fd41 100644
--- a/packages/apollo-collaboration-server/src/files/files.controller.ts
+++ b/packages/apollo-collaboration-server/src/files/files.controller.ts
@@ -1,4 +1,3 @@
-/* eslint-disable @typescript-eslint/no-unnecessary-condition */
 import { Readable } from 'node:stream'
 
 import {
@@ -13,17 +12,16 @@ import {
   Req,
   Res,
   StreamableFile,
-  UnprocessableEntityException,
   UploadedFile,
   UseInterceptors,
 } from '@nestjs/common'
-import { FileInterceptor } from '@nestjs/platform-express/multer'
-import { Request, Response } from 'express'
+import { FileInterceptor } from '@nestjs/platform-express'
+import { type Request, type Response } from 'express'
 
-import { FileStorageEngine } from './FileStorageEngine'
-import { FilesInterceptor as StreamingFileInterceptor } from './files.interceptor'
-import { FilesService } from './files.service'
-import { UploadedFile as UploadedApolloFile } from './filesUtil'
+import { FileStorageEngine } from './FileStorageEngine.js'
+import { FilesInterceptor as StreamingFileInterceptor } from './files.interceptor.js'
+import { FilesService } from './files.service.js'
+import { type UploadedFile as UploadedApolloFile } from './filesUtil.js'
 
 @Controller('files')
 export class FilesController {
@@ -55,9 +53,6 @@ export class FilesController {
     @UploadedFile() file: UploadedApolloFile,
     @Query('type') type: 'text/x-gff3' | 'text/x-fasta',
   ) {
-    if (!file) {
-      throw new UnprocessableEntityException('No "file" found in request')
-    }
     this.logger.debug(
       `Upload file "${file.originalname}", checksum "${file.checksum}"`,
     )
diff --git a/packages/apollo-collaboration-server/src/files/files.interceptor.ts b/packages/apollo-collaboration-server/src/files/files.interceptor.ts
index df7f27cd3..73d63ce1a 100644
--- a/packages/apollo-collaboration-server/src/files/files.interceptor.ts
+++ b/packages/apollo-collaboration-server/src/files/files.interceptor.ts
@@ -1,13 +1,13 @@
 import {
-  CallHandler,
-  ExecutionContext,
+  type CallHandler,
+  type ExecutionContext,
   Injectable,
-  NestInterceptor,
+  type NestInterceptor,
 } from '@nestjs/common'
 import { Observable } from 'rxjs'
 
-import { FilesService } from './files.service'
-import { FileRequest } from './filesUtil'
+import { FilesService } from './files.service.js'
+import { type FileRequest } from './filesUtil.js'
 
 @Injectable()
 export class FilesInterceptor<T> implements NestInterceptor<T, T> {
diff --git a/packages/apollo-collaboration-server/src/files/files.module.ts b/packages/apollo-collaboration-server/src/files/files.module.ts
index 4bbbc9780..f39dbdf75 100644
--- a/packages/apollo-collaboration-server/src/files/files.module.ts
+++ b/packages/apollo-collaboration-server/src/files/files.module.ts
@@ -2,8 +2,8 @@ import { File, FileSchema } from '@apollo-annotation/schemas'
 import { Module } from '@nestjs/common'
 import { MongooseModule } from '@nestjs/mongoose'
 
-import { FilesController } from './files.controller'
-import { FilesService } from './files.service'
+import { FilesController } from './files.controller.js'
+import { FilesService } from './files.service.js'
 
 @Module({
   controllers: [FilesController],
diff --git a/packages/apollo-collaboration-server/src/files/files.service.spec.ts b/packages/apollo-collaboration-server/src/files/files.service.spec.ts
index 93b35bf46..fc4af042e 100644
--- a/packages/apollo-collaboration-server/src/files/files.service.spec.ts
+++ b/packages/apollo-collaboration-server/src/files/files.service.spec.ts
@@ -1,6 +1,6 @@
 import { Test, type TestingModule } from '@nestjs/testing'
 
-import { FilesService } from './files.service'
+import { FilesService } from './files.service.js'
 
 describe('FilesService', () => {
   let service: FilesService
diff --git a/packages/apollo-collaboration-server/src/files/files.service.ts b/packages/apollo-collaboration-server/src/files/files.service.ts
index c079c6c69..56aa161a2 100644
--- a/packages/apollo-collaboration-server/src/files/files.service.ts
+++ b/packages/apollo-collaboration-server/src/files/files.service.ts
@@ -4,7 +4,7 @@ import path from 'node:path'
 import { Readable } from 'node:stream'
 import { ReadableStream, TransformStream } from 'node:stream/web'
 
-import { File, FileDocument } from '@apollo-annotation/schemas'
+import { File, type FileDocument } from '@apollo-annotation/schemas'
 import { type GFF3Feature, GFFTransformer } from '@gmod/gff'
 import {
   Injectable,
@@ -14,15 +14,15 @@ import {
 } from '@nestjs/common'
 import { ConfigService } from '@nestjs/config'
 import { InjectModel } from '@nestjs/mongoose'
-import { GenericFilehandle, LocalFile } from 'generic-filehandle'
+import { type GenericFilehandle, LocalFile } from 'generic-filehandle'
 import { Model } from 'mongoose'
 
-import { CreateFileDto } from './dto/create-file.dto'
+import { CreateFileDto } from './dto/create-file.dto.js'
 import {
-  FileRequest,
+  type FileRequest,
   LocalFileGzip,
   writeFileAndCalculateHash,
-} from './filesUtil'
+} from './filesUtil.js'
 
 @Injectable()
 export class FilesService {
diff --git a/packages/apollo-collaboration-server/src/global-exceptions.filter.ts b/packages/apollo-collaboration-server/src/global-exceptions.filter.ts
index 9571c201f..858ef10b1 100644
--- a/packages/apollo-collaboration-server/src/global-exceptions.filter.ts
+++ b/packages/apollo-collaboration-server/src/global-exceptions.filter.ts
@@ -1,4 +1,4 @@
-import { ArgumentsHost, Catch, Logger } from '@nestjs/common'
+import { type ArgumentsHost, Catch, Logger } from '@nestjs/common'
 import { BaseExceptionFilter } from '@nestjs/core'
 
 @Catch()
diff --git a/packages/apollo-collaboration-server/src/health/health.controller.spec.ts b/packages/apollo-collaboration-server/src/health/health.controller.spec.ts
index a59708669..0faaaa988 100644
--- a/packages/apollo-collaboration-server/src/health/health.controller.spec.ts
+++ b/packages/apollo-collaboration-server/src/health/health.controller.spec.ts
@@ -1,6 +1,6 @@
 import { Test, type TestingModule } from '@nestjs/testing'
 
-import { HealthController } from './health.controller'
+import { HealthController } from './health.controller.js'
 
 describe('HealthController', () => {
   let controller: HealthController
diff --git a/packages/apollo-collaboration-server/src/health/health.controller.ts b/packages/apollo-collaboration-server/src/health/health.controller.ts
index 66d52d83f..083e93ae1 100644
--- a/packages/apollo-collaboration-server/src/health/health.controller.ts
+++ b/packages/apollo-collaboration-server/src/health/health.controller.ts
@@ -1,8 +1,8 @@
 import { Controller, Get } from '@nestjs/common'
 import { HealthCheck, HealthCheckService } from '@nestjs/terminus'
 
-import { Role } from '../utils/role/role.enum'
-import { Validations } from '../utils/validation/validatation.decorator'
+import { Role } from '../utils/role/role.enum.js'
+import { Validations } from '../utils/validation/validatation.decorator.js'
 
 @Controller('health')
 export class HealthController {
diff --git a/packages/apollo-collaboration-server/src/health/health.module.ts b/packages/apollo-collaboration-server/src/health/health.module.ts
index fc31f9424..634d6e5d2 100644
--- a/packages/apollo-collaboration-server/src/health/health.module.ts
+++ b/packages/apollo-collaboration-server/src/health/health.module.ts
@@ -1,7 +1,7 @@
 import { Module } from '@nestjs/common'
 import { TerminusModule } from '@nestjs/terminus'
 
-import { HealthController } from './health.controller'
+import { HealthController } from './health.controller.js'
 
 @Module({
   imports: [TerminusModule],
diff --git a/packages/apollo-collaboration-server/src/jbrowse/jbrowse.controller.spec.ts b/packages/apollo-collaboration-server/src/jbrowse/jbrowse.controller.spec.ts
index 5e3bae5d1..0fb828de9 100644
--- a/packages/apollo-collaboration-server/src/jbrowse/jbrowse.controller.spec.ts
+++ b/packages/apollo-collaboration-server/src/jbrowse/jbrowse.controller.spec.ts
@@ -1,6 +1,6 @@
 import { Test, type TestingModule } from '@nestjs/testing'
 
-import { JBrowseController } from './jbrowse.controller'
+import { JBrowseController } from './jbrowse.controller.js'
 
 describe('JBrowseController', () => {
   let controller: JBrowseController
diff --git a/packages/apollo-collaboration-server/src/jbrowse/jbrowse.controller.ts b/packages/apollo-collaboration-server/src/jbrowse/jbrowse.controller.ts
index 8aa382004..c2520e6a9 100644
--- a/packages/apollo-collaboration-server/src/jbrowse/jbrowse.controller.ts
+++ b/packages/apollo-collaboration-server/src/jbrowse/jbrowse.controller.ts
@@ -1,10 +1,10 @@
 import { Controller, Get, Logger, Req } from '@nestjs/common'
-import { Request } from 'express'
+import { type Request } from 'express'
 
-import { Role } from '../utils/role/role.enum'
-import { Validations } from '../utils/validation/validatation.decorator'
+import { Role } from '../utils/role/role.enum.js'
+import { Validations } from '../utils/validation/validatation.decorator.js'
 
-import { JBrowseService } from './jbrowse.service'
+import { JBrowseService } from './jbrowse.service.js'
 
 export interface RequestWithUser extends Request {
   user?: { role: Role; id?: string }
diff --git a/packages/apollo-collaboration-server/src/jbrowse/jbrowse.module.ts b/packages/apollo-collaboration-server/src/jbrowse/jbrowse.module.ts
index 8fd22308d..7a33230df 100644
--- a/packages/apollo-collaboration-server/src/jbrowse/jbrowse.module.ts
+++ b/packages/apollo-collaboration-server/src/jbrowse/jbrowse.module.ts
@@ -4,11 +4,11 @@ import { Module, forwardRef } from '@nestjs/common'
 import { MongooseModule, getConnectionToken } from '@nestjs/mongoose'
 import idValidator from 'mongoose-id-validator'
 
-import { AssembliesModule } from '../assemblies/assemblies.module'
-import { RefSeqsModule } from '../refSeqs/refSeqs.module'
+import { AssembliesModule } from '../assemblies/assemblies.module.js'
+import { RefSeqsModule } from '../refSeqs/refSeqs.module.js'
 
-import { JBrowseController } from './jbrowse.controller'
-import { JBrowseService } from './jbrowse.service'
+import { JBrowseController } from './jbrowse.controller.js'
+import { JBrowseService } from './jbrowse.service.js'
 
 @Module({
   controllers: [JBrowseController],
diff --git a/packages/apollo-collaboration-server/src/jbrowse/jbrowse.service.spec.ts b/packages/apollo-collaboration-server/src/jbrowse/jbrowse.service.spec.ts
index 35ed1ff9c..71eed0411 100644
--- a/packages/apollo-collaboration-server/src/jbrowse/jbrowse.service.spec.ts
+++ b/packages/apollo-collaboration-server/src/jbrowse/jbrowse.service.spec.ts
@@ -1,6 +1,6 @@
 import { Test, type TestingModule } from '@nestjs/testing'
 
-import { JBrowseService } from './jbrowse.service'
+import { JBrowseService } from './jbrowse.service.js'
 
 describe('JBrowseService', () => {
   let service: JBrowseService
diff --git a/packages/apollo-collaboration-server/src/jbrowse/jbrowse.service.ts b/packages/apollo-collaboration-server/src/jbrowse/jbrowse.service.ts
index 48fe59d37..641d261a9 100644
--- a/packages/apollo-collaboration-server/src/jbrowse/jbrowse.service.ts
+++ b/packages/apollo-collaboration-server/src/jbrowse/jbrowse.service.ts
@@ -1,6 +1,6 @@
 import {
   JBrowseConfig,
-  JBrowseConfigDocument,
+  type JBrowseConfigDocument,
 } from '@apollo-annotation/schemas'
 import { Injectable, Logger } from '@nestjs/common'
 import { ConfigService } from '@nestjs/config'
@@ -8,9 +8,9 @@ import { InjectModel } from '@nestjs/mongoose'
 import merge from 'deepmerge'
 import { Model } from 'mongoose'
 
-import { AssembliesService } from '../assemblies/assemblies.service'
-import { RefSeqsService } from '../refSeqs/refSeqs.service'
-import { Role } from '../utils/role/role.enum'
+import { AssembliesService } from '../assemblies/assemblies.service.js'
+import { RefSeqsService } from '../refSeqs/refSeqs.service.js'
+import { Role } from '../utils/role/role.enum.js'
 
 @Injectable()
 export class JBrowseService {
diff --git a/packages/apollo-collaboration-server/src/main.ts b/packages/apollo-collaboration-server/src/main.ts
index 67acca501..854371d62 100644
--- a/packages/apollo-collaboration-server/src/main.ts
+++ b/packages/apollo-collaboration-server/src/main.ts
@@ -26,9 +26,9 @@ import { json, urlencoded } from 'express'
 import session from 'express-session'
 import mongoose from 'mongoose'
 
-import { AppModule } from './app.module'
-import { GlobalExceptionsFilter } from './global-exceptions.filter'
-import { AuthorizationValidation } from './utils/validation/AuthorizationValidation'
+import { AppModule } from './app.module.js'
+import { GlobalExceptionsFilter } from './global-exceptions.filter.js'
+import { AuthorizationValidation } from './utils/validation/AuthorizationValidation.js'
 
 const MongoDBStore = connectMongoDBSession(session)
 
@@ -123,14 +123,15 @@ async function bootstrap() {
   const ChecksModel = mongoose.model('checks', CheckSchema)
   for (const [key, check] of checksMap.entries()) {
     const checkByName = await ChecksModel.find({ name: key }).exec()
-    if (checkByName.length > 0) {
+    const firstCheck = checkByName.at(0)
+    if (firstCheck) {
       const checkByNameAndVersion = await ChecksModel.find({
         name: key,
         version: check.version,
       }).exec()
       if (checkByNameAndVersion.length === 0) {
-        checkByName[0].version = check.version
-        await checkByName[0].save()
+        firstCheck.version = check.version
+        await firstCheck.save()
       }
     } else {
       await ChecksModel.create(check)
diff --git a/packages/apollo-collaboration-server/src/messages/dto/update-message.dto.ts b/packages/apollo-collaboration-server/src/messages/dto/update-message.dto.ts
index 19614e8f6..871ec6618 100644
--- a/packages/apollo-collaboration-server/src/messages/dto/update-message.dto.ts
+++ b/packages/apollo-collaboration-server/src/messages/dto/update-message.dto.ts
@@ -1,6 +1,6 @@
 import { PartialType } from '@nestjs/mapped-types'
 
-import { CreateMessageDto } from './create-message.dto'
+import { CreateMessageDto } from './create-message.dto.js'
 
 export class UpdateMessageDto extends PartialType(CreateMessageDto) {
   id: number
diff --git a/packages/apollo-collaboration-server/src/messages/messages.gateway.spec.ts b/packages/apollo-collaboration-server/src/messages/messages.gateway.spec.ts
index d40bd95eb..dc706bb41 100644
--- a/packages/apollo-collaboration-server/src/messages/messages.gateway.spec.ts
+++ b/packages/apollo-collaboration-server/src/messages/messages.gateway.spec.ts
@@ -1,7 +1,7 @@
 import { Test, type TestingModule } from '@nestjs/testing'
 
-import { MessagesGateway } from './messages.gateway'
-import { MessagesService } from './messages.service'
+import { MessagesGateway } from './messages.gateway.js'
+import { MessagesService } from './messages.service.js'
 
 describe('MessagesGateway', () => {
   let gateway: MessagesGateway
diff --git a/packages/apollo-collaboration-server/src/messages/messages.gateway.ts b/packages/apollo-collaboration-server/src/messages/messages.gateway.ts
index 86c8b6cd8..6469262db 100644
--- a/packages/apollo-collaboration-server/src/messages/messages.gateway.ts
+++ b/packages/apollo-collaboration-server/src/messages/messages.gateway.ts
@@ -7,8 +7,7 @@ import {
 } from '@nestjs/websockets'
 import { Server } from 'socket.io'
 
-import { CreateMessageDto } from './dto/create-message.dto'
-import { MessagesService } from './messages.service'
+import { CreateMessageDto } from './dto/create-message.dto.js'
 
 @WebSocketGateway({ cors: { origin: '*' } })
 @Injectable()
@@ -16,8 +15,6 @@ export class MessagesGateway {
   @WebSocketServer()
   server: Server
 
-  constructor(private readonly messagesService: MessagesService) {}
-
   @SubscribeMessage('createMessage')
   async create(eventName: string, createMessageDto: CreateMessageDto) {
     this.server.emit(eventName, createMessageDto)
diff --git a/packages/apollo-collaboration-server/src/messages/messages.module.ts b/packages/apollo-collaboration-server/src/messages/messages.module.ts
index 64b58df49..d5cfc00bf 100644
--- a/packages/apollo-collaboration-server/src/messages/messages.module.ts
+++ b/packages/apollo-collaboration-server/src/messages/messages.module.ts
@@ -1,7 +1,7 @@
 import { Module } from '@nestjs/common'
 
-import { MessagesGateway } from './messages.gateway'
-import { MessagesService } from './messages.service'
+import { MessagesGateway } from './messages.gateway.js'
+import { MessagesService } from './messages.service.js'
 
 @Module({
   providers: [MessagesGateway, MessagesService],
diff --git a/packages/apollo-collaboration-server/src/messages/messages.service.spec.ts b/packages/apollo-collaboration-server/src/messages/messages.service.spec.ts
index 74480a9d1..05fe4b7ff 100644
--- a/packages/apollo-collaboration-server/src/messages/messages.service.spec.ts
+++ b/packages/apollo-collaboration-server/src/messages/messages.service.spec.ts
@@ -1,6 +1,6 @@
 import { Test, type TestingModule } from '@nestjs/testing'
 
-import { MessagesService } from './messages.service'
+import { MessagesService } from './messages.service.js'
 
 describe('MessagesService', () => {
   let service: MessagesService
diff --git a/packages/apollo-collaboration-server/src/operations/operations.module.ts b/packages/apollo-collaboration-server/src/operations/operations.module.ts
index 367ce74a1..9756aa44c 100644
--- a/packages/apollo-collaboration-server/src/operations/operations.module.ts
+++ b/packages/apollo-collaboration-server/src/operations/operations.module.ts
@@ -1,17 +1,17 @@
 import { Module, forwardRef } from '@nestjs/common'
 
-import { AssembliesModule } from '../assemblies/assemblies.module'
-import { ChecksModule } from '../checks/checks.module'
-import { CountersModule } from '../counters/counters.module'
-import { FeaturesModule } from '../features/features.module'
-import { FilesModule } from '../files/files.module'
-import { JBrowseModule } from '../jbrowse/jbrowse.module'
-import { MessagesModule } from '../messages/messages.module'
-import { RefSeqChunksModule } from '../refSeqChunks/refSeqChunks.module'
-import { RefSeqsModule } from '../refSeqs/refSeqs.module'
-import { UsersModule } from '../users/users.module'
+import { AssembliesModule } from '../assemblies/assemblies.module.js'
+import { ChecksModule } from '../checks/checks.module.js'
+import { CountersModule } from '../counters/counters.module.js'
+import { FeaturesModule } from '../features/features.module.js'
+import { FilesModule } from '../files/files.module.js'
+import { JBrowseModule } from '../jbrowse/jbrowse.module.js'
+import { MessagesModule } from '../messages/messages.module.js'
+import { RefSeqChunksModule } from '../refSeqChunks/refSeqChunks.module.js'
+import { RefSeqsModule } from '../refSeqs/refSeqs.module.js'
+import { UsersModule } from '../users/users.module.js'
 
-import { OperationsService } from './operations.service'
+import { OperationsService } from './operations.service.js'
 
 @Module({
   imports: [
diff --git a/packages/apollo-collaboration-server/src/operations/operations.service.spec.ts b/packages/apollo-collaboration-server/src/operations/operations.service.spec.ts
index 8a007d2c2..9f66b9a1d 100644
--- a/packages/apollo-collaboration-server/src/operations/operations.service.spec.ts
+++ b/packages/apollo-collaboration-server/src/operations/operations.service.spec.ts
@@ -1,6 +1,6 @@
 import { Test, type TestingModule } from '@nestjs/testing'
 
-import { OperationsService } from './operations.service'
+import { OperationsService } from './operations.service.js'
 
 describe('OperationsService', () => {
   let service: OperationsService
diff --git a/packages/apollo-collaboration-server/src/operations/operations.service.ts b/packages/apollo-collaboration-server/src/operations/operations.service.ts
index a7332e5b7..99ca5aadc 100644
--- a/packages/apollo-collaboration-server/src/operations/operations.service.ts
+++ b/packages/apollo-collaboration-server/src/operations/operations.service.ts
@@ -1,29 +1,29 @@
 import { Operation, operationRegistry } from '@apollo-annotation/common'
 import {
   Assembly,
-  AssemblyDocument,
+  type AssemblyDocument,
   Check,
-  CheckDocument,
+  type CheckDocument,
   Feature,
-  FeatureDocument,
+  type FeatureDocument,
   File,
-  FileDocument,
+  type FileDocument,
   JBrowseConfig,
-  JBrowseConfigDocument,
+  type JBrowseConfigDocument,
   RefSeq,
   RefSeqChunk,
-  RefSeqChunkDocument,
-  RefSeqDocument,
+  type RefSeqChunkDocument,
+  type RefSeqDocument,
   User,
-  UserDocument,
+  type UserDocument,
 } from '@apollo-annotation/schemas'
 import { Injectable, Logger } from '@nestjs/common'
 import { InjectConnection, InjectModel } from '@nestjs/mongoose'
-import { Connection, Model } from 'mongoose'
+import { type Connection, type Model } from 'mongoose'
 
-import { CountersService } from '../counters/counters.service'
-import { FilesService } from '../files/files.service'
-import { PluginsService } from '../plugins/plugins.service'
+import { CountersService } from '../counters/counters.service.js'
+import { FilesService } from '../files/files.service.js'
+import { PluginsService } from '../plugins/plugins.service.js'
 
 @Injectable()
 export class OperationsService {
diff --git a/packages/apollo-collaboration-server/src/plugins/plugins.module.ts b/packages/apollo-collaboration-server/src/plugins/plugins.module.ts
index 849aee804..a6187b8ab 100644
--- a/packages/apollo-collaboration-server/src/plugins/plugins.module.ts
+++ b/packages/apollo-collaboration-server/src/plugins/plugins.module.ts
@@ -1,22 +1,23 @@
-/* eslint-disable @typescript-eslint/prefer-promise-reject-errors */
-/* eslint-disable @typescript-eslint/use-unknown-in-catch-callback-variable */
-/* eslint-disable @typescript-eslint/no-confusing-void-expression */
-/* eslint-disable @typescript-eslint/no-unnecessary-condition */
 /* eslint-disable @typescript-eslint/no-unsafe-assignment */
 import fs from 'node:fs'
 import fsPromises from 'node:fs/promises'
 import path from 'node:path'
+import { Writable } from 'node:stream'
 
 import {
   ApolloPlugin,
-  ApolloPluginConstructor,
+  type ApolloPluginConstructor,
 } from '@apollo-annotation/common'
-import { DynamicModule, Logger, Module, Provider } from '@nestjs/common'
-import fetch from 'node-fetch'
+import {
+  type DynamicModule,
+  Logger,
+  Module,
+  type Provider,
+} from '@nestjs/common'
 import sanitize from 'sanitize-filename'
 
-import { APOLLO_PLUGINS } from './plugins.constants'
-import { PluginsService } from './plugins.service'
+import { APOLLO_PLUGINS } from './plugins.constants.js'
+import { PluginsService } from './plugins.service.js'
 
 @Module({})
 export class PluginsModule {
@@ -61,25 +62,18 @@ export class PluginsModule {
           __dirname,
           pluginLocation,
         )}`
-        await new Promise<void>((resolve, reject) => {
-          const file = fs.createWriteStream(pluginLocation)
-          fetch(url)
-            .then((response) => {
-              if (!response.body) {
-                return reject('fetch failed')
-              }
-              response.body.pipe(file)
-              file.on('finish', resolve)
-              file.on('error', (err) => {
-                fs.unlinkSync(pluginLocation)
-                reject(err)
-              })
-            })
-            .catch((error) => {
-              console.error(error)
-              throw error
-            })
-        })
+        const file = Writable.toWeb(fs.createWriteStream(pluginLocation))
+        const response = await fetch(url)
+        if (!response.body) {
+          throw new Error('fetch failed')
+        }
+        try {
+          await response.body.pipeTo(file)
+        } catch (error) {
+          fs.unlinkSync(pluginLocation)
+          console.error(error)
+          throw error
+        }
         plugin = await import(pluginLocationRelative)
       } finally {
         await fsPromises.rm(tmpDir, { recursive: true })
diff --git a/packages/apollo-collaboration-server/src/plugins/plugins.service.spec.ts b/packages/apollo-collaboration-server/src/plugins/plugins.service.spec.ts
index 27e2e2863..3dc57e259 100644
--- a/packages/apollo-collaboration-server/src/plugins/plugins.service.spec.ts
+++ b/packages/apollo-collaboration-server/src/plugins/plugins.service.spec.ts
@@ -1,6 +1,6 @@
 import { Test, type TestingModule } from '@nestjs/testing'
 
-import { PluginsService } from './plugins.service'
+import { PluginsService } from './plugins.service.js'
 
 describe('PluginsService', () => {
   let service: PluginsService
diff --git a/packages/apollo-collaboration-server/src/plugins/plugins.service.ts b/packages/apollo-collaboration-server/src/plugins/plugins.service.ts
index 53c5f5da8..d86a338d4 100644
--- a/packages/apollo-collaboration-server/src/plugins/plugins.service.ts
+++ b/packages/apollo-collaboration-server/src/plugins/plugins.service.ts
@@ -2,7 +2,7 @@
 import { ApolloPlugin } from '@apollo-annotation/common'
 import { Inject, Injectable } from '@nestjs/common'
 
-import { APOLLO_PLUGINS } from './plugins.constants'
+import { APOLLO_PLUGINS } from './plugins.constants.js'
 
 @Injectable()
 export class PluginsService {
diff --git a/packages/apollo-collaboration-server/src/refSeqChunks/dto/update-refSeqChunk.dto.ts b/packages/apollo-collaboration-server/src/refSeqChunks/dto/update-refSeqChunk.dto.ts
index a5f9ea264..f0248e9cd 100644
--- a/packages/apollo-collaboration-server/src/refSeqChunks/dto/update-refSeqChunk.dto.ts
+++ b/packages/apollo-collaboration-server/src/refSeqChunks/dto/update-refSeqChunk.dto.ts
@@ -1,5 +1,5 @@
 import { PartialType } from '@nestjs/mapped-types'
 
-import { CreateRefSeqChunkDto } from './create-refSeqChunk.dto'
+import { CreateRefSeqChunkDto } from './create-refSeqChunk.dto.js'
 
 export class UpdateRefSeqChunkDto extends PartialType(CreateRefSeqChunkDto) {}
diff --git a/packages/apollo-collaboration-server/src/refSeqs/dto/update-refSeq.dto.ts b/packages/apollo-collaboration-server/src/refSeqs/dto/update-refSeq.dto.ts
index 77c0766ca..a73c615be 100644
--- a/packages/apollo-collaboration-server/src/refSeqs/dto/update-refSeq.dto.ts
+++ b/packages/apollo-collaboration-server/src/refSeqs/dto/update-refSeq.dto.ts
@@ -1,5 +1,5 @@
 import { PartialType } from '@nestjs/mapped-types'
 
-import { CreateRefSeqDto } from './create-refSeq.dto'
+import { CreateRefSeqDto } from './create-refSeq.dto.js'
 
 export class UpdateRefSeqDto extends PartialType(CreateRefSeqDto) {}
diff --git a/packages/apollo-collaboration-server/src/refSeqs/refSeqs.controller.spec.ts b/packages/apollo-collaboration-server/src/refSeqs/refSeqs.controller.spec.ts
index 2afc80770..089b152b1 100644
--- a/packages/apollo-collaboration-server/src/refSeqs/refSeqs.controller.spec.ts
+++ b/packages/apollo-collaboration-server/src/refSeqs/refSeqs.controller.spec.ts
@@ -1,7 +1,7 @@
 import { Test, type TestingModule } from '@nestjs/testing'
 
-import { RefSeqsController } from './refSeqs.controller'
-import { RefSeqsService } from './refSeqs.service'
+import { RefSeqsController } from './refSeqs.controller.js'
+import { RefSeqsService } from './refSeqs.service.js'
 
 describe('RefSeqsController', () => {
   let controller: RefSeqsController
diff --git a/packages/apollo-collaboration-server/src/refSeqs/refSeqs.controller.ts b/packages/apollo-collaboration-server/src/refSeqs/refSeqs.controller.ts
index a549d1f15..2f24e5f40 100644
--- a/packages/apollo-collaboration-server/src/refSeqs/refSeqs.controller.ts
+++ b/packages/apollo-collaboration-server/src/refSeqs/refSeqs.controller.ts
@@ -1,10 +1,10 @@
 import { Controller, Get, Logger, Param, Query } from '@nestjs/common'
 
-import { Role } from '../utils/role/role.enum'
-import { Validations } from '../utils/validation/validatation.decorator'
+import { Role } from '../utils/role/role.enum.js'
+import { Validations } from '../utils/validation/validatation.decorator.js'
 
-import { FindRefSeqDto } from './dto/find-refSeq.dto'
-import { RefSeqsService } from './refSeqs.service'
+import { FindRefSeqDto } from './dto/find-refSeq.dto.js'
+import { RefSeqsService } from './refSeqs.service.js'
 
 @Validations(Role.ReadOnly)
 @Controller('refSeqs')
diff --git a/packages/apollo-collaboration-server/src/refSeqs/refSeqs.module.ts b/packages/apollo-collaboration-server/src/refSeqs/refSeqs.module.ts
index d25c2c912..77b25560a 100644
--- a/packages/apollo-collaboration-server/src/refSeqs/refSeqs.module.ts
+++ b/packages/apollo-collaboration-server/src/refSeqs/refSeqs.module.ts
@@ -4,8 +4,8 @@ import { Module } from '@nestjs/common'
 import { MongooseModule, getConnectionToken } from '@nestjs/mongoose'
 import idValidator from 'mongoose-id-validator'
 
-import { RefSeqsController } from './refSeqs.controller'
-import { RefSeqsService } from './refSeqs.service'
+import { RefSeqsController } from './refSeqs.controller.js'
+import { RefSeqsService } from './refSeqs.service.js'
 
 @Module({
   imports: [
diff --git a/packages/apollo-collaboration-server/src/refSeqs/refSeqs.service.spec.ts b/packages/apollo-collaboration-server/src/refSeqs/refSeqs.service.spec.ts
index 23cc4121f..deff4ba90 100644
--- a/packages/apollo-collaboration-server/src/refSeqs/refSeqs.service.spec.ts
+++ b/packages/apollo-collaboration-server/src/refSeqs/refSeqs.service.spec.ts
@@ -1,6 +1,6 @@
 import { Test, type TestingModule } from '@nestjs/testing'
 
-import { RefSeqsService } from './refSeqs.service'
+import { RefSeqsService } from './refSeqs.service.js'
 
 describe('RefSeqsService', () => {
   let service: RefSeqsService
diff --git a/packages/apollo-collaboration-server/src/refSeqs/refSeqs.service.ts b/packages/apollo-collaboration-server/src/refSeqs/refSeqs.service.ts
index d5471e1be..c24cca74b 100644
--- a/packages/apollo-collaboration-server/src/refSeqs/refSeqs.service.ts
+++ b/packages/apollo-collaboration-server/src/refSeqs/refSeqs.service.ts
@@ -1,11 +1,11 @@
-import { RefSeq, RefSeqDocument } from '@apollo-annotation/schemas'
+import { RefSeq, type RefSeqDocument } from '@apollo-annotation/schemas'
 import { Injectable, Logger, NotFoundException } from '@nestjs/common'
 import { InjectModel } from '@nestjs/mongoose'
 import { Model } from 'mongoose'
 
-import { CreateRefSeqDto } from './dto/create-refSeq.dto'
-import { FindRefSeqDto } from './dto/find-refSeq.dto'
-import { UpdateRefSeqDto } from './dto/update-refSeq.dto'
+import { CreateRefSeqDto } from './dto/create-refSeq.dto.js'
+import { FindRefSeqDto } from './dto/find-refSeq.dto.js'
+import { UpdateRefSeqDto } from './dto/update-refSeq.dto.js'
 
 @Injectable()
 export class RefSeqsService {
diff --git a/packages/apollo-collaboration-server/src/sequence/sequence.controller.spec.ts b/packages/apollo-collaboration-server/src/sequence/sequence.controller.spec.ts
index 771e820fb..72695b5e0 100644
--- a/packages/apollo-collaboration-server/src/sequence/sequence.controller.spec.ts
+++ b/packages/apollo-collaboration-server/src/sequence/sequence.controller.spec.ts
@@ -1,6 +1,6 @@
 import { Test, type TestingModule } from '@nestjs/testing'
 
-import { SequenceController } from './sequence.controller'
+import { SequenceController } from './sequence.controller.js'
 
 describe('SequenceController', () => {
   let controller: SequenceController
diff --git a/packages/apollo-collaboration-server/src/sequence/sequence.controller.ts b/packages/apollo-collaboration-server/src/sequence/sequence.controller.ts
index 4a35570ba..8829cba8a 100644
--- a/packages/apollo-collaboration-server/src/sequence/sequence.controller.ts
+++ b/packages/apollo-collaboration-server/src/sequence/sequence.controller.ts
@@ -1,10 +1,10 @@
 import { Controller, Get, Logger, Query } from '@nestjs/common'
 
-import { Role } from '../utils/role/role.enum'
-import { Validations } from '../utils/validation/validatation.decorator'
+import { Role } from '../utils/role/role.enum.js'
+import { Validations } from '../utils/validation/validatation.decorator.js'
 
-import { GetSequenceDto } from './dto/get-sequence.dto'
-import { SequenceService } from './sequence.service'
+import { GetSequenceDto } from './dto/get-sequence.dto.js'
+import { SequenceService } from './sequence.service.js'
 
 @Validations(Role.ReadOnly)
 @Controller('sequence')
diff --git a/packages/apollo-collaboration-server/src/sequence/sequence.module.ts b/packages/apollo-collaboration-server/src/sequence/sequence.module.ts
index d3950f1f5..a200d01d4 100644
--- a/packages/apollo-collaboration-server/src/sequence/sequence.module.ts
+++ b/packages/apollo-collaboration-server/src/sequence/sequence.module.ts
@@ -1,12 +1,12 @@
 import { Module, forwardRef } from '@nestjs/common'
 
-import { AssembliesModule } from '../assemblies/assemblies.module'
-import { FilesModule } from '../files/files.module'
-import { RefSeqChunksModule } from '../refSeqChunks/refSeqChunks.module'
-import { RefSeqsModule } from '../refSeqs/refSeqs.module'
+import { AssembliesModule } from '../assemblies/assemblies.module.js'
+import { FilesModule } from '../files/files.module.js'
+import { RefSeqChunksModule } from '../refSeqChunks/refSeqChunks.module.js'
+import { RefSeqsModule } from '../refSeqs/refSeqs.module.js'
 
-import { SequenceController } from './sequence.controller'
-import { SequenceService } from './sequence.service'
+import { SequenceController } from './sequence.controller.js'
+import { SequenceService } from './sequence.service.js'
 
 @Module({
   imports: [
diff --git a/packages/apollo-collaboration-server/src/sequence/sequence.service.spec.ts b/packages/apollo-collaboration-server/src/sequence/sequence.service.spec.ts
index fbd178434..fdffbad17 100644
--- a/packages/apollo-collaboration-server/src/sequence/sequence.service.spec.ts
+++ b/packages/apollo-collaboration-server/src/sequence/sequence.service.spec.ts
@@ -1,6 +1,6 @@
 import { Test, type TestingModule } from '@nestjs/testing'
 
-import { SequenceService } from './sequence.service'
+import { SequenceService } from './sequence.service.js'
 
 describe('SequenceService', () => {
   let service: SequenceService
diff --git a/packages/apollo-collaboration-server/src/sequence/sequence.service.ts b/packages/apollo-collaboration-server/src/sequence/sequence.service.ts
index c6f0cdd63..334fa6adc 100644
--- a/packages/apollo-collaboration-server/src/sequence/sequence.service.ts
+++ b/packages/apollo-collaboration-server/src/sequence/sequence.service.ts
@@ -1,12 +1,12 @@
 /* eslint-disable @typescript-eslint/no-base-to-string */
-/* eslint-disable @typescript-eslint/no-unnecessary-condition */
+
 import {
   File,
-  FileDocument,
+  type FileDocument,
   RefSeq,
   RefSeqChunk,
-  RefSeqChunkDocument,
-  RefSeqDocument,
+  type RefSeqChunkDocument,
+  type RefSeqDocument,
 } from '@apollo-annotation/schemas'
 import { BgzipIndexedFasta, IndexedFasta } from '@gmod/indexedfasta'
 import { Injectable, Logger } from '@nestjs/common'
@@ -14,10 +14,10 @@ import { InjectModel } from '@nestjs/mongoose'
 import { RemoteFile } from 'generic-filehandle'
 import { Model } from 'mongoose'
 
-import { AssembliesService } from '../assemblies/assemblies.service'
-import { FilesService } from '../files/files.service'
+import { AssembliesService } from '../assemblies/assemblies.service.js'
+import { FilesService } from '../files/files.service.js'
 
-import { GetSequenceDto } from './dto/get-sequence.dto'
+import { GetSequenceDto } from './dto/get-sequence.dto.js'
 
 @Injectable()
 export class SequenceService {
@@ -45,7 +45,7 @@ export class SequenceService {
       assembly.toString(),
     )
 
-    if (assemblyDoc?.externalLocation) {
+    if (assemblyDoc.externalLocation) {
       const { fa, fai, gzi } = assemblyDoc.externalLocation
 
       const sequenceAdapter = gzi
@@ -65,7 +65,7 @@ export class SequenceService {
       return sequence
     }
 
-    if (assemblyDoc?.fileIds?.fai) {
+    if (assemblyDoc.fileIds?.fai) {
       const { fa: faId, fai: faiId, gzi: gziId } = assemblyDoc.fileIds
       const faDoc = await this.fileModel.findById(faId)
       if (!faDoc) {
diff --git a/packages/apollo-collaboration-server/src/users/dto/create-user.dto.ts b/packages/apollo-collaboration-server/src/users/dto/create-user.dto.ts
index f36dccefc..3608687d7 100644
--- a/packages/apollo-collaboration-server/src/users/dto/create-user.dto.ts
+++ b/packages/apollo-collaboration-server/src/users/dto/create-user.dto.ts
@@ -1,4 +1,4 @@
-import { type Role } from '../../utils/role/role.enum'
+import { type Role } from '../../utils/role/role.enum.js'
 
 export class CreateUserDto {
   readonly email: string
diff --git a/packages/apollo-collaboration-server/src/users/dto/update-user.dto.ts b/packages/apollo-collaboration-server/src/users/dto/update-user.dto.ts
index 1543f739a..cf5387306 100644
--- a/packages/apollo-collaboration-server/src/users/dto/update-user.dto.ts
+++ b/packages/apollo-collaboration-server/src/users/dto/update-user.dto.ts
@@ -1,5 +1,5 @@
 import { PartialType } from '@nestjs/mapped-types'
 
-import { CreateUserDto } from './create-user.dto'
+import { CreateUserDto } from './create-user.dto.js'
 
 export class UpdateUserDto extends PartialType(CreateUserDto) {}
diff --git a/packages/apollo-collaboration-server/src/users/users.controller.spec.ts b/packages/apollo-collaboration-server/src/users/users.controller.spec.ts
index 25c13ec8c..4e5302c0a 100644
--- a/packages/apollo-collaboration-server/src/users/users.controller.spec.ts
+++ b/packages/apollo-collaboration-server/src/users/users.controller.spec.ts
@@ -1,7 +1,7 @@
 import { Test, type TestingModule } from '@nestjs/testing'
 
-import { UsersController } from './users.controller'
-import { UsersService } from './users.service'
+import { UsersController } from './users.controller.js'
+import { UsersService } from './users.service.js'
 
 describe('UsersController', () => {
   let controller: UsersController
diff --git a/packages/apollo-collaboration-server/src/users/users.controller.ts b/packages/apollo-collaboration-server/src/users/users.controller.ts
index c71afe8dc..5c3adadf0 100644
--- a/packages/apollo-collaboration-server/src/users/users.controller.ts
+++ b/packages/apollo-collaboration-server/src/users/users.controller.ts
@@ -1,14 +1,14 @@
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 /* eslint-disable @typescript-eslint/no-unsafe-assignment */
-import { DecodedJWT } from '@apollo-annotation/shared'
+import { type DecodedJWT } from '@apollo-annotation/shared'
 import { Body, Controller, Get, Logger, Param, Post, Req } from '@nestjs/common'
-import { Request } from 'express'
+import { type Request } from 'express'
 
-import { Role } from '../utils/role/role.enum'
-import { Validations } from '../utils/validation/validatation.decorator'
+import { Role } from '../utils/role/role.enum.js'
+import { Validations } from '../utils/validation/validatation.decorator.js'
 
-import { UserLocationDto } from './dto/create-user.dto'
-import { UsersService } from './users.service'
+import { UserLocationDto } from './dto/create-user.dto.js'
+import { UsersService } from './users.service.js'
 
 @Controller('users')
 export class UsersController {
diff --git a/packages/apollo-collaboration-server/src/users/users.module.ts b/packages/apollo-collaboration-server/src/users/users.module.ts
index 5842d7717..a3a088c00 100644
--- a/packages/apollo-collaboration-server/src/users/users.module.ts
+++ b/packages/apollo-collaboration-server/src/users/users.module.ts
@@ -1,11 +1,11 @@
 import { User, UserSchema } from '@apollo-annotation/schemas'
-import { Module, OnApplicationBootstrap } from '@nestjs/common'
+import { Module, type OnApplicationBootstrap } from '@nestjs/common'
 import { MongooseModule } from '@nestjs/mongoose'
 
-import { MessagesModule } from '../messages/messages.module'
+import { MessagesModule } from '../messages/messages.module.js'
 
-import { UsersController } from './users.controller'
-import { UsersService } from './users.service'
+import { UsersController } from './users.controller.js'
+import { UsersService } from './users.service.js'
 
 @Module({
   controllers: [UsersController],
diff --git a/packages/apollo-collaboration-server/src/users/users.service.spec.ts b/packages/apollo-collaboration-server/src/users/users.service.spec.ts
index 8f05f289d..b8fb5dacf 100644
--- a/packages/apollo-collaboration-server/src/users/users.service.spec.ts
+++ b/packages/apollo-collaboration-server/src/users/users.service.spec.ts
@@ -1,6 +1,6 @@
 import { Test, type TestingModule } from '@nestjs/testing'
 
-import { UsersService } from './users.service'
+import { UsersService } from './users.service.js'
 
 describe('UsersService', () => {
   let service: UsersService
diff --git a/packages/apollo-collaboration-server/src/users/users.service.ts b/packages/apollo-collaboration-server/src/users/users.service.ts
index 59040377e..afe364b11 100644
--- a/packages/apollo-collaboration-server/src/users/users.service.ts
+++ b/packages/apollo-collaboration-server/src/users/users.service.ts
@@ -1,8 +1,11 @@
-import { User as UserSchema, UserDocument } from '@apollo-annotation/schemas'
 import {
-  DecodedJWT,
-  RequestUserInformationMessage,
-  UserLocationMessage,
+  User as UserSchema,
+  type UserDocument,
+} from '@apollo-annotation/schemas'
+import {
+  type DecodedJWT,
+  type RequestUserInformationMessage,
+  type UserLocationMessage,
   makeUserSessionId,
 } from '@apollo-annotation/shared'
 import { Injectable, Logger } from '@nestjs/common'
@@ -10,11 +13,11 @@ import { ConfigService } from '@nestjs/config'
 import { InjectModel } from '@nestjs/mongoose'
 import { Model } from 'mongoose'
 
-import { MessagesGateway } from '../messages/messages.gateway'
-import { GUEST_USER_EMAIL, GUEST_USER_NAME } from '../utils/constants'
-import { Role } from '../utils/role/role.enum'
+import { MessagesGateway } from '../messages/messages.gateway.js'
+import { GUEST_USER_EMAIL, GUEST_USER_NAME } from '../utils/constants.js'
+import { Role } from '../utils/role/role.enum.js'
 
-import { CreateUserDto, UserLocationDto } from './dto/create-user.dto'
+import { CreateUserDto, UserLocationDto } from './dto/create-user.dto.js'
 
 export interface User {
   email: string
diff --git a/packages/apollo-collaboration-server/src/utils/google.guard.ts b/packages/apollo-collaboration-server/src/utils/google.guard.ts
index f8cfc0a66..2859d8250 100644
--- a/packages/apollo-collaboration-server/src/utils/google.guard.ts
+++ b/packages/apollo-collaboration-server/src/utils/google.guard.ts
@@ -1,7 +1,7 @@
 /* eslint-disable @typescript-eslint/no-unsafe-assignment */
 /* eslint-disable @typescript-eslint/no-unsafe-member-access */
-import { ExecutionContext, Injectable } from '@nestjs/common'
-import { AuthGuard, IAuthModuleOptions } from '@nestjs/passport'
+import { type ExecutionContext, Injectable } from '@nestjs/common'
+import { AuthGuard, type IAuthModuleOptions } from '@nestjs/passport'
 
 @Injectable()
 export class GoogleAuthGuard extends AuthGuard('google') {
diff --git a/packages/apollo-collaboration-server/src/utils/jwt-auth.guard.ts b/packages/apollo-collaboration-server/src/utils/jwt-auth.guard.ts
index 4d48dec0b..0c016c7bc 100644
--- a/packages/apollo-collaboration-server/src/utils/jwt-auth.guard.ts
+++ b/packages/apollo-collaboration-server/src/utils/jwt-auth.guard.ts
@@ -1,9 +1,9 @@
 /* eslint-disable @typescript-eslint/no-unsafe-return */
-import { JWTPayload } from '@apollo-annotation/shared'
-import { ExecutionContext, Injectable } from '@nestjs/common'
+import { type JWTPayload } from '@apollo-annotation/shared'
+import { type ExecutionContext, Injectable } from '@nestjs/common'
 import { AuthGuard } from '@nestjs/passport'
 
-import { Role } from './role/role.enum'
+import { Role } from './role/role.enum.js'
 
 export const IS_PUBLIC_KEY = 'isPublic'
 @Injectable()
diff --git a/packages/apollo-collaboration-server/src/utils/microsoft.guard.ts b/packages/apollo-collaboration-server/src/utils/microsoft.guard.ts
index 4f80f26c8..3c1450c31 100644
--- a/packages/apollo-collaboration-server/src/utils/microsoft.guard.ts
+++ b/packages/apollo-collaboration-server/src/utils/microsoft.guard.ts
@@ -1,7 +1,7 @@
 /* eslint-disable @typescript-eslint/no-unsafe-assignment */
 /* eslint-disable @typescript-eslint/no-unsafe-member-access */
-import { ExecutionContext, Injectable } from '@nestjs/common'
-import { AuthGuard, IAuthModuleOptions } from '@nestjs/passport'
+import { type ExecutionContext, Injectable } from '@nestjs/common'
+import { AuthGuard, type IAuthModuleOptions } from '@nestjs/passport'
 
 @Injectable()
 export class MicrosoftAuthGuard extends AuthGuard('microsoft') {
diff --git a/packages/apollo-collaboration-server/src/utils/parse-change.pipe.ts b/packages/apollo-collaboration-server/src/utils/parse-change.pipe.ts
index 3caacce4e..02e310e54 100644
--- a/packages/apollo-collaboration-server/src/utils/parse-change.pipe.ts
+++ b/packages/apollo-collaboration-server/src/utils/parse-change.pipe.ts
@@ -1,10 +1,10 @@
-import { Change, SerializedChange } from '@apollo-annotation/common'
+import { Change, type SerializedChange } from '@apollo-annotation/common'
 import {
-  ArgumentMetadata,
+  type ArgumentMetadata,
   BadRequestException,
   Injectable,
   Logger,
-  PipeTransform,
+  type PipeTransform,
 } from '@nestjs/common'
 
 @Injectable()
diff --git a/packages/apollo-collaboration-server/src/utils/strategies/google.strategy.ts b/packages/apollo-collaboration-server/src/utils/strategies/google.strategy.ts
index accb13786..ffe41286b 100644
--- a/packages/apollo-collaboration-server/src/utils/strategies/google.strategy.ts
+++ b/packages/apollo-collaboration-server/src/utils/strategies/google.strategy.ts
@@ -4,9 +4,9 @@ import { Injectable, Logger } from '@nestjs/common'
 import { ConfigService } from '@nestjs/config'
 import { PassportStrategy } from '@nestjs/passport'
 import { HttpsProxyAgent } from 'https-proxy-agent'
-import { Profile, Strategy } from 'passport-google-oauth20'
+import { type Profile, Strategy } from 'passport-google-oauth20'
 
-import { AuthenticationService } from '../../authentication/authentication.service'
+import { AuthenticationService } from '../../authentication/authentication.service.js'
 
 interface ConfigValues {
   GOOGLE_CLIENT_ID?: string
diff --git a/packages/apollo-collaboration-server/src/utils/strategies/jwt.strategy.ts b/packages/apollo-collaboration-server/src/utils/strategies/jwt.strategy.ts
index 5be8d1ea3..ce3239a38 100644
--- a/packages/apollo-collaboration-server/src/utils/strategies/jwt.strategy.ts
+++ b/packages/apollo-collaboration-server/src/utils/strategies/jwt.strategy.ts
@@ -1,6 +1,6 @@
 import fs from 'node:fs'
 
-import { DecodedJWT } from '@apollo-annotation/shared'
+import { type DecodedJWT } from '@apollo-annotation/shared'
 import { Injectable, Logger } from '@nestjs/common'
 import { ConfigService } from '@nestjs/config'
 import { PassportStrategy } from '@nestjs/passport'
diff --git a/packages/apollo-collaboration-server/src/utils/strategies/microsoft.strategy.ts b/packages/apollo-collaboration-server/src/utils/strategies/microsoft.strategy.ts
index 489567aee..f12c8b842 100644
--- a/packages/apollo-collaboration-server/src/utils/strategies/microsoft.strategy.ts
+++ b/packages/apollo-collaboration-server/src/utils/strategies/microsoft.strategy.ts
@@ -1,12 +1,12 @@
 import fs from 'node:fs'
 
-import { Injectable, Logger } from '@nestjs/common'
+import { Inject, Injectable, Logger, forwardRef } from '@nestjs/common'
 import { ConfigService } from '@nestjs/config'
 import { PassportStrategy } from '@nestjs/passport'
 import { HttpsProxyAgent } from 'https-proxy-agent'
 import { Strategy } from 'passport-microsoft'
 
-import { AuthenticationService } from '../../authentication/authentication.service'
+import { AuthenticationService } from '../../authentication/authentication.service.js'
 
 export interface Profile {
   provider: 'microsoft'
@@ -31,7 +31,8 @@ export class MicrosoftStrategy extends PassportStrategy(Strategy) {
   private readonly logger = new Logger(MicrosoftStrategy.name)
 
   constructor(
-    private readonly authService: AuthenticationService,
+    @Inject(forwardRef(() => AuthenticationService))
+    private readonly authService: Readonly<AuthenticationService>,
     configService: ConfigService<ConfigValues, true>,
   ) {
     let clientID = configService.get('MICROSOFT_CLIENT_ID', { infer: true })
diff --git a/packages/apollo-collaboration-server/src/utils/validation/AuthorizationValidation.ts b/packages/apollo-collaboration-server/src/utils/validation/AuthorizationValidation.ts
index bf6931bc9..c9125dcf8 100644
--- a/packages/apollo-collaboration-server/src/utils/validation/AuthorizationValidation.ts
+++ b/packages/apollo-collaboration-server/src/utils/validation/AuthorizationValidation.ts
@@ -12,10 +12,10 @@ import {
 import { Logger } from '@nestjs/common'
 import { type Request } from 'express'
 
-import { Role, RoleInheritance } from '../role/role.enum'
+import { Role, RoleInheritance } from '../role/role.enum.js'
 
-import { getRequiredRoleForChange } from './validatation.changeTypePermissions'
-import { ROLE_KEY } from './validatation.decorator'
+import { getRequiredRoleForChange } from './validatation.changeTypePermissions.js'
+import { ROLE_KEY } from './validatation.decorator.js'
 
 export class AuthorizationValidation extends Validation {
   name = 'Authorization' as const
diff --git a/packages/apollo-collaboration-server/src/utils/validation/validatation.changeTypePermissions.ts b/packages/apollo-collaboration-server/src/utils/validation/validatation.changeTypePermissions.ts
index df874dfed..6e9884f5e 100644
--- a/packages/apollo-collaboration-server/src/utils/validation/validatation.changeTypePermissions.ts
+++ b/packages/apollo-collaboration-server/src/utils/validation/validatation.changeTypePermissions.ts
@@ -1,4 +1,4 @@
-import { Role } from '../role/role.enum'
+import { Role } from '../role/role.enum.js'
 
 export function getRequiredRoleForChange(changeName: string) {
   if (
diff --git a/packages/apollo-collaboration-server/src/utils/validation/validatation.decorator.ts b/packages/apollo-collaboration-server/src/utils/validation/validatation.decorator.ts
index f8120d122..7d1260660 100644
--- a/packages/apollo-collaboration-server/src/utils/validation/validatation.decorator.ts
+++ b/packages/apollo-collaboration-server/src/utils/validation/validatation.decorator.ts
@@ -1,6 +1,6 @@
 import { SetMetadata } from '@nestjs/common'
 
-import { type Role } from '../role/role.enum'
+import { type Role } from '../role/role.enum.js'
 
 export const ROLE_KEY = 'role'
 export const Validations = (role: Role) => SetMetadata(ROLE_KEY, role)
diff --git a/packages/apollo-collaboration-server/src/utils/validation/validation.guards.ts b/packages/apollo-collaboration-server/src/utils/validation/validation.guards.ts
index 720f51ce0..03b8b4bbf 100644
--- a/packages/apollo-collaboration-server/src/utils/validation/validation.guards.ts
+++ b/packages/apollo-collaboration-server/src/utils/validation/validation.guards.ts
@@ -1,7 +1,7 @@
 import { validationRegistry } from '@apollo-annotation/shared'
 import {
-  CanActivate,
-  ExecutionContext,
+  type CanActivate,
+  type ExecutionContext,
   Injectable,
   Logger,
   UnprocessableEntityException,
diff --git a/packages/apollo-collaboration-server/test/app/app.e2e-spec.ts b/packages/apollo-collaboration-server/test/app/app.e2e-spec.ts
deleted file mode 100644
index ff3d2f1a9..000000000
--- a/packages/apollo-collaboration-server/test/app/app.e2e-spec.ts
+++ /dev/null
@@ -1,40 +0,0 @@
-/* eslint-disable @typescript-eslint/no-unsafe-assignment */
-/* eslint-disable @typescript-eslint/no-unsafe-member-access */
-/* eslint-disable @typescript-eslint/no-unsafe-call */
-/* eslint-disable @typescript-eslint/no-unsafe-return */
-import { type INestApplication } from '@nestjs/common'
-import { Test } from '@nestjs/testing'
-import * as request from 'supertest'
-
-import { AppModule } from '../../src/app.module'
-
-describe('E2E JWT Sample', () => {
-  let app: INestApplication
-
-  beforeAll(async () => {
-    const modRef = await Test.createTestingModule({
-      imports: [AppModule],
-    }).compile()
-
-    app = modRef.createNestApplication()
-    await app.init()
-  })
-
-  it('should get a JWT then successfully make a call', async () => {
-    const loginReq = await request(app.getHttpServer())
-      .post('/auth/login')
-      .send({ username: 'john', password: 'changeme' })
-      .expect(201)
-
-    const token = loginReq.body.access_token
-    return request(app.getHttpServer())
-      .get('/profile')
-      .set('Authorization', `Bearer ${token}`)
-      .expect(200)
-      .expect({ userId: 1, username: 'john' })
-  })
-
-  afterAll(async () => {
-    await app.close()
-  })
-})
diff --git a/packages/apollo-collaboration-server/tsconfig.json b/packages/apollo-collaboration-server/tsconfig.json
index fda356433..fd3b451eb 100644
--- a/packages/apollo-collaboration-server/tsconfig.json
+++ b/packages/apollo-collaboration-server/tsconfig.json
@@ -1,22 +1,20 @@
 {
-  "extends": "../../tsconfig-base.json",
+  "extends": "../../tsconfig",
   "compilerOptions": {
-    "module": "commonjs",
-    "lib": ["esnext"],
-    "removeComments": true,
+    "outDir": "./dist",
+    "rootDir": "./src",
     "emitDecoratorMetadata": true,
     "experimentalDecorators": true,
-    "allowSyntheticDefaultImports": true,
-    "target": "es2017",
-    "outDir": "./dist",
-    "baseUrl": "./",
-    "incremental": true,
     "strictPropertyInitialization": false,
-    "forceConsistentCasingInFileNames": false,
-    "sourceMap": true,
+    // For Node.js >=20: https://github.com/microsoft/TypeScript/wiki/Node-Target-Mapping
+    "target": "es2023",
+    "lib": ["es2023"],
+    "types": ["jest", "node"],
   },
+  "include": ["./src"],
   "references": [
     { "path": "../apollo-common" },
+    { "path": "../apollo-mst" },
     { "path": "../apollo-schemas" },
     { "path": "../apollo-shared" },
   ],
diff --git a/packages/apollo-common/package.json b/packages/apollo-common/package.json
index 43182fca3..980f79117 100644
--- a/packages/apollo-common/package.json
+++ b/packages/apollo-common/package.json
@@ -6,13 +6,15 @@
     "url": "https://github.com/GMOD/Apollo3.git",
     "directory": "packages/apollo-common"
   },
-  "main": "./dist/index.js",
+  "sideEffects": false,
+  "type": "module",
+  "exports": "./dist/index.js",
   "scripts": {
-    "build": "tsc"
+    "build": "tsc --build"
   },
   "dependencies": {
     "@apollo-annotation/schemas": "workspace:^",
-    "@jbrowse/core": "^3.6.5",
+    "@jbrowse/core": "^4.1.1",
     "bson-objectid": "^2.0.4",
     "tslib": "^2.3.1"
   },
@@ -21,20 +23,21 @@
     "@gmod/gff": "^2.0.0",
     "@nestjs/common": "^10.1.0",
     "@nestjs/core": "^10.1.0",
-    "@types/node": "^20.19.15",
+    "@types/node": "^24.10.9",
     "generic-filehandle": "^3.0.0",
     "mongoose": "^6.12.0",
     "typescript": "^5.5.3"
   },
   "peerDependencies": {
-    "@mui/material": "^7.0.0",
+    "@jbrowse/mobx-state-tree": "^5.5.0",
+    "@mui/material": "^7.3.7",
     "@mui/x-data-grid": "^8.0.0",
     "mobx": "^6.6.1",
     "mobx-react": "^7.2.1",
-    "mobx-state-tree": "^5.4.0",
     "prop-types": "^15.8.1",
     "react": "^18.2.0",
     "react-dom": "^18.2.0",
+    "reflect-metadata": "^0.1.13",
     "rxjs": "^7.4.0",
     "tss-react": "^4.6.1"
   },
diff --git a/packages/apollo-common/src/AssemblySpecificChange.ts b/packages/apollo-common/src/AssemblySpecificChange.ts
index a167d95f6..4bb8b3437 100644
--- a/packages/apollo-common/src/AssemblySpecificChange.ts
+++ b/packages/apollo-common/src/AssemblySpecificChange.ts
@@ -7,7 +7,7 @@ import {
   type ChangeOptions,
   type SerializedChange,
   isChange,
-} from './Change'
+} from './Change.js'
 
 export interface SerializedAssemblySpecificChange extends SerializedChange {
   assembly: string
@@ -42,7 +42,7 @@ export abstract class AssemblySpecificChange extends Change {
         attributes instanceof Map
           ? attributes.get(additionalId)
           : attributes?.[additionalId]
-      if (idValue) {
+      if (idValue?.[0]) {
         indexedIds.push(idValue[0])
       }
     }
diff --git a/packages/apollo-common/src/Change.ts b/packages/apollo-common/src/Change.ts
index 7dbdfe76f..22037625a 100644
--- a/packages/apollo-common/src/Change.ts
+++ b/packages/apollo-common/src/Change.ts
@@ -10,13 +10,13 @@ import {
 } from '@apollo-annotation/mst'
 import { type AppRootModel, type Region } from '@jbrowse/core/util'
 
-import { changeRegistry } from './ChangeTypeRegistry'
+import { changeRegistry } from './ChangeTypeRegistry.js'
 import {
   type BackendDataStore,
   Operation,
   type OperationOptions,
   type SerializedOperation,
-} from './Operation'
+} from './Operation.js'
 
 export interface ClientDataStore {
   typeName: 'Client'
diff --git a/packages/apollo-common/src/ChangeTypeRegistry.ts b/packages/apollo-common/src/ChangeTypeRegistry.ts
index e6541a5c0..97d839a41 100644
--- a/packages/apollo-common/src/ChangeTypeRegistry.ts
+++ b/packages/apollo-common/src/ChangeTypeRegistry.ts
@@ -1,4 +1,4 @@
-import { type Change } from './Change'
+import { type Change } from './Change.js'
 
 // eslint-disable-next-line @typescript-eslint/no-explicit-any
 type ChangeType = new (...args: any[]) => Change
diff --git a/packages/apollo-common/src/CheckRegistry.ts b/packages/apollo-common/src/CheckRegistry.ts
index 629afc750..25400ac39 100644
--- a/packages/apollo-common/src/CheckRegistry.ts
+++ b/packages/apollo-common/src/CheckRegistry.ts
@@ -1,4 +1,4 @@
-import { type Check } from './Check'
+import { type Check } from './Check.js'
 
 class CheckRegistry {
   checks = new Map<string, Check>()
diff --git a/packages/apollo-common/src/FeatureChange.ts b/packages/apollo-common/src/FeatureChange.ts
index 78a710ef4..abc01387a 100644
--- a/packages/apollo-common/src/FeatureChange.ts
+++ b/packages/apollo-common/src/FeatureChange.ts
@@ -9,8 +9,8 @@ import {
   AssemblySpecificChange,
   type SerializedAssemblySpecificChange,
   isAssemblySpecificChange,
-} from './AssemblySpecificChange'
-import { type ChangeOptions } from './Change'
+} from './AssemblySpecificChange.js'
+import { type ChangeOptions } from './Change.js'
 
 export interface SerializedFeatureChange
   extends SerializedAssemblySpecificChange {
diff --git a/packages/apollo-common/src/OperationTypeRegistry.ts b/packages/apollo-common/src/OperationTypeRegistry.ts
index 50bb6bf0d..6db6ce675 100644
--- a/packages/apollo-common/src/OperationTypeRegistry.ts
+++ b/packages/apollo-common/src/OperationTypeRegistry.ts
@@ -1,4 +1,4 @@
-import { type Operation } from './Operation'
+import { type Operation } from './Operation.js'
 
 // eslint-disable-next-line @typescript-eslint/no-explicit-any
 type OperationType = new (...args: any[]) => Operation
diff --git a/packages/apollo-common/src/Validation.ts b/packages/apollo-common/src/Validation.ts
index d761f3122..805e06461 100644
--- a/packages/apollo-common/src/Validation.ts
+++ b/packages/apollo-common/src/Validation.ts
@@ -4,7 +4,7 @@ import { type ExecutionContext } from '@nestjs/common'
 import { type Reflector } from '@nestjs/core'
 import { type ClientSession, type Model } from 'mongoose'
 
-import { type Change, type ClientDataStore } from './Change'
+import { type Change, type ClientDataStore } from './Change.js'
 
 export interface Context {
   context: ExecutionContext
diff --git a/packages/apollo-common/src/declare.d.ts b/packages/apollo-common/src/declare.d.ts
new file mode 100644
index 000000000..10b14280c
--- /dev/null
+++ b/packages/apollo-common/src/declare.d.ts
@@ -0,0 +1,29 @@
+declare module 'bson-objectid' {
+  import { type Buffer } from 'node:buffer'
+
+  export default ObjectID
+
+  declare const ObjectID: ObjectIDCtor
+
+  declare interface ObjectID {
+    readonly id: string
+    readonly str: string
+
+    toHexString(): string
+    equals(other: ObjectID): boolean
+    getTimestamp(): Date
+  }
+
+  declare interface ObjectIDCtor {
+    (hexStringOrIdStringOrArrayOrBuffer?: string | number[] | Buffer): ObjectID
+
+    new (
+      hexStringOrIdStringOrArrayOrBuffer?: string | number[] | Buffer,
+    ): ObjectID
+
+    createFromTime(time: number): ObjectID
+    createFromHexString(hexString: string): ObjectID
+    isValid(hexStringOrObjectID: string | ObjectID): boolean
+    toString(): string
+  }
+}
diff --git a/packages/apollo-common/src/index.ts b/packages/apollo-common/src/index.ts
index ba38067a0..5723da9ff 100644
--- a/packages/apollo-common/src/index.ts
+++ b/packages/apollo-common/src/index.ts
@@ -1,10 +1,10 @@
-export * from './ApolloPlugin'
-export * from './AssemblySpecificChange'
-export * from './Change'
-export * from './ChangeTypeRegistry'
-export * from './Check'
-export * from './CheckRegistry'
-export * from './FeatureChange'
-export * from './Operation'
-export * from './OperationTypeRegistry'
-export * from './Validation'
+export * from './ApolloPlugin.js'
+export * from './AssemblySpecificChange.js'
+export * from './Change.js'
+export * from './ChangeTypeRegistry.js'
+export * from './Check.js'
+export * from './CheckRegistry.js'
+export * from './FeatureChange.js'
+export * from './Operation.js'
+export * from './OperationTypeRegistry.js'
+export * from './Validation.js'
diff --git a/packages/apollo-common/tsconfig.json b/packages/apollo-common/tsconfig.json
index 9ea29de08..6b4ef94f8 100644
--- a/packages/apollo-common/tsconfig.json
+++ b/packages/apollo-common/tsconfig.json
@@ -1,17 +1,14 @@
 {
-  "extends": "../../tsconfig-base.json",
+  "extends": "../../tsconfig",
   "compilerOptions": {
     "composite": true,
     "incremental": true,
     "outDir": "./dist",
     "rootDir": "./src",
-    "target": "ES2019",
-    "lib": ["ES2019", "DOM"],
-    "module": "CommonJS",
     "tsBuildInfoFile": "./dist/tsconfig.tsbuildinfo",
-    "experimentalDecorators": true,
-    "emitDecoratorMetadata": true,
-    "strictPropertyInitialization": false,
+    // For nodejs:
+    "lib": ["esnext"],
+    "types": ["node"],
   },
   "include": ["./src"],
   "references": [{ "path": "../apollo-schemas" }, { "path": "../apollo-mst" }],
diff --git a/packages/apollo-mst/package.json b/packages/apollo-mst/package.json
index 3e48cdb44..c1bdcefb8 100644
--- a/packages/apollo-mst/package.json
+++ b/packages/apollo-mst/package.json
@@ -1,14 +1,16 @@
 {
   "name": "@apollo-annotation/mst",
   "version": "0.3.11",
-  "main": "./dist/index.js",
+  "sideEffects": false,
+  "type": "module",
+  "exports": "./dist/index.js",
   "scripts": {
     "build": "tsc"
   },
   "dependencies": {
-    "@jbrowse/core": "^3.6.5",
+    "@jbrowse/core": "^4.1.1",
+    "@jbrowse/mobx-state-tree": "^5.5.0",
     "mobx": "^6.6.1",
-    "mobx-state-tree": "^5.4.0",
     "react-dom": "^18.2.0",
     "rxjs": "^7.4.0",
     "tslib": "^2.3.1"
diff --git a/packages/apollo-mst/src/AnnotationFeatureModel.ts b/packages/apollo-mst/src/AnnotationFeatureModel.ts
index cc7d38bf7..4e28fc3b1 100644
--- a/packages/apollo-mst/src/AnnotationFeatureModel.ts
+++ b/packages/apollo-mst/src/AnnotationFeatureModel.ts
@@ -12,9 +12,9 @@ import {
   getParentOfType,
   getSnapshot,
   types,
-} from 'mobx-state-tree'
+} from '@jbrowse/mobx-state-tree'
 
-import { ApolloAssembly } from '.'
+import { ApolloAssembly } from './index.js'
 
 const LateAnnotationFeature = types.late(
   (): IAnyModelType => AnnotationFeatureModel,
diff --git a/packages/apollo-mst/src/ApolloAssembly.ts b/packages/apollo-mst/src/ApolloAssembly.ts
index 980d4e17d..7c05d6efb 100644
--- a/packages/apollo-mst/src/ApolloAssembly.ts
+++ b/packages/apollo-mst/src/ApolloAssembly.ts
@@ -1,6 +1,6 @@
-import { type Instance, type SnapshotIn, types } from 'mobx-state-tree'
+import { type Instance, type SnapshotIn, types } from '@jbrowse/mobx-state-tree'
 
-import { ApolloRefSeq } from './ApolloRefSeq'
+import { ApolloRefSeq } from './ApolloRefSeq.js'
 
 export type BackendDriverType =
   | 'CollaborationServerDriver'
diff --git a/packages/apollo-mst/src/ApolloRefSeq.ts b/packages/apollo-mst/src/ApolloRefSeq.ts
index aea3e081a..1d7d7776f 100644
--- a/packages/apollo-mst/src/ApolloRefSeq.ts
+++ b/packages/apollo-mst/src/ApolloRefSeq.ts
@@ -4,13 +4,13 @@ import {
   type SnapshotIn,
   type SnapshotOrInstance,
   types,
-} from 'mobx-state-tree'
+} from '@jbrowse/mobx-state-tree'
 
 import {
   type AnnotationFeature,
   AnnotationFeatureModel,
   type AnnotationFeatureSnapshot,
-} from './AnnotationFeatureModel'
+} from './AnnotationFeatureModel.js'
 
 export const Sequence = types.model({
   start: types.number,
@@ -100,7 +100,7 @@ export const ApolloRefSeq = types
         self.sequence.length === consolidatedSequences.length &&
         self.sequence.every(
           (s, idx) =>
-            s.start === consolidatedSequences[idx].start &&
+            s.start === consolidatedSequences[idx]?.start &&
             s.stop === consolidatedSequences[idx].stop,
         )
       ) {
diff --git a/packages/apollo-mst/src/CheckResult.ts b/packages/apollo-mst/src/CheckResult.ts
index e2f541ca0..e311e9843 100644
--- a/packages/apollo-mst/src/CheckResult.ts
+++ b/packages/apollo-mst/src/CheckResult.ts
@@ -1,6 +1,6 @@
-import { type Instance, type SnapshotIn, types } from 'mobx-state-tree'
+import { type Instance, type SnapshotIn, types } from '@jbrowse/mobx-state-tree'
 
-import { AnnotationFeatureModel } from './AnnotationFeatureModel'
+import { AnnotationFeatureModel } from './AnnotationFeatureModel.js'
 
 export const CheckResult = types.model('CheckResult', {
   _id: types.identifier,
diff --git a/packages/apollo-mst/src/index.ts b/packages/apollo-mst/src/index.ts
index 1049dbd87..ca0a2678e 100644
--- a/packages/apollo-mst/src/index.ts
+++ b/packages/apollo-mst/src/index.ts
@@ -1,4 +1,4 @@
-export * from './AnnotationFeatureModel'
-export * from './ApolloAssembly'
-export * from './ApolloRefSeq'
-export * from './CheckResult'
+export * from './AnnotationFeatureModel.js'
+export * from './ApolloAssembly.js'
+export * from './ApolloRefSeq.js'
+export * from './CheckResult.js'
diff --git a/packages/apollo-mst/tsconfig.json b/packages/apollo-mst/tsconfig.json
index ae9e5b6c4..cb1a09eae 100644
--- a/packages/apollo-mst/tsconfig.json
+++ b/packages/apollo-mst/tsconfig.json
@@ -1,17 +1,11 @@
 {
-  "extends": "../../tsconfig-base.json",
+  "extends": "../../tsconfig",
   "compilerOptions": {
     "composite": true,
     "incremental": true,
     "outDir": "./dist",
     "rootDir": "./src",
-    "target": "ES2022",
-    "lib": ["ES2022", "DOM"],
-    "module": "CommonJS",
     "tsBuildInfoFile": "./dist/tsconfig.tsbuildinfo",
-    "experimentalDecorators": true,
-    "emitDecoratorMetadata": true,
-    "strictPropertyInitialization": false,
   },
   "include": ["./src"],
 }
diff --git a/packages/apollo-schemas/package.json b/packages/apollo-schemas/package.json
index 634026c4e..176148940 100644
--- a/packages/apollo-schemas/package.json
+++ b/packages/apollo-schemas/package.json
@@ -1,7 +1,9 @@
 {
   "name": "@apollo-annotation/schemas",
   "version": "0.3.11",
-  "main": "./dist/index.js",
+  "sideEffects": false,
+  "type": "module",
+  "exports": "./dist/index.js",
   "scripts": {
     "build": "tsc"
   },
@@ -16,7 +18,7 @@
   },
   "devDependencies": {
     "@apollo-annotation/mst": "workspace:^",
-    "@types/node": "^20.19.15",
+    "@types/node": "^24.10.9",
     "typescript": "^5.5.3"
   },
   "publishConfig": {
diff --git a/packages/apollo-schemas/src/assembly.schema.ts b/packages/apollo-schemas/src/assembly.schema.ts
index 728d8d8b9..c2ad5fb52 100644
--- a/packages/apollo-schemas/src/assembly.schema.ts
+++ b/packages/apollo-schemas/src/assembly.schema.ts
@@ -1,7 +1,7 @@
 import { Prop, Schema, SchemaFactory } from '@nestjs/mongoose'
 import { Schema as MongooseSchema, Types } from 'mongoose'
 
-import { File } from './file.schema'
+import { File } from './file.schema.js'
 
 export type AssemblyDocument = Assembly & Document
 
@@ -26,7 +26,7 @@ export class Assembly {
   user: string
 
   @Prop({ type: { fa: String, fai: String, gzi: String } })
-  externalLocation: { fa: string; fai: string; gzi?: string }
+  externalLocation?: { fa: string; fai: string; gzi?: string }
 
   @Prop({
     type: {
@@ -35,7 +35,7 @@ export class Assembly {
       gzi: { type: MongooseSchema.Types.ObjectId, ref: 'File' },
     },
   })
-  fileIds: { fa: string; fai: string; gzi: string } // Store fileId of fa/fai/gzi.
+  fileIds?: { fa: string; fai: string; gzi: string } // Store fileId of fa/fai/gzi.
 
   @Prop({ type: [{ type: MongooseSchema.Types.ObjectId, ref: 'Check' }] })
   checks: Types.ObjectId[]
diff --git a/packages/apollo-schemas/src/check.schema.ts b/packages/apollo-schemas/src/check.schema.ts
index 65ff29467..55da738b7 100644
--- a/packages/apollo-schemas/src/check.schema.ts
+++ b/packages/apollo-schemas/src/check.schema.ts
@@ -1,5 +1,5 @@
 import { Prop, Schema, SchemaFactory } from '@nestjs/mongoose'
-import { HydratedDocument, Types } from 'mongoose'
+import { type HydratedDocument, Types } from 'mongoose'
 
 export interface CheckDocument extends HydratedDocument<Check> {
   createdAt: Date
diff --git a/packages/apollo-schemas/src/checkResult.schema.ts b/packages/apollo-schemas/src/checkResult.schema.ts
index f96b31418..d8adbb483 100644
--- a/packages/apollo-schemas/src/checkResult.schema.ts
+++ b/packages/apollo-schemas/src/checkResult.schema.ts
@@ -1,6 +1,10 @@
 import { type CheckResultSnapshot } from '@apollo-annotation/mst'
 import { Prop, Schema, SchemaFactory } from '@nestjs/mongoose'
-import { HydratedDocument, Schema as MongooseSchema, Types } from 'mongoose'
+import {
+  type HydratedDocument,
+  Schema as MongooseSchema,
+  Types,
+} from 'mongoose'
 
 export type CheckResultDocument = HydratedDocument<CheckResult>
 
diff --git a/packages/apollo-schemas/src/feature.schema.ts b/packages/apollo-schemas/src/feature.schema.ts
index 2d3313410..ea75ab397 100644
--- a/packages/apollo-schemas/src/feature.schema.ts
+++ b/packages/apollo-schemas/src/feature.schema.ts
@@ -1,6 +1,10 @@
 import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
 import { Prop, Schema, SchemaFactory } from '@nestjs/mongoose'
-import { HydratedDocument, Schema as MongooseSchema, Types } from 'mongoose'
+import {
+  type HydratedDocument,
+  Schema as MongooseSchema,
+  Types,
+} from 'mongoose'
 
 export interface FeatureDocument extends HydratedDocument<Feature> {
   createdAt?: Date
diff --git a/packages/apollo-schemas/src/index.ts b/packages/apollo-schemas/src/index.ts
index 9df3c46cf..139d9606f 100644
--- a/packages/apollo-schemas/src/index.ts
+++ b/packages/apollo-schemas/src/index.ts
@@ -1,12 +1,12 @@
-export * from './assembly.schema'
-export * from './change.schema'
-export * from './check.schema'
-export * from './checkResult.schema'
-export * from './counter.schema'
-export * from './export.schema'
-export * from './feature.schema'
-export * from './file.schema'
-export * from './refSeq.schema'
-export * from './refSeqChunk.schema'
-export * from './user.schema'
-export * from './jbrowseConfig.schema'
+export * from './assembly.schema.js'
+export * from './change.schema.js'
+export * from './check.schema.js'
+export * from './checkResult.schema.js'
+export * from './counter.schema.js'
+export * from './export.schema.js'
+export * from './feature.schema.js'
+export * from './file.schema.js'
+export * from './refSeq.schema.js'
+export * from './refSeqChunk.schema.js'
+export * from './user.schema.js'
+export * from './jbrowseConfig.schema.js'
diff --git a/packages/apollo-schemas/src/refSeq.schema.ts b/packages/apollo-schemas/src/refSeq.schema.ts
index 0e8926e50..fb984ed14 100644
--- a/packages/apollo-schemas/src/refSeq.schema.ts
+++ b/packages/apollo-schemas/src/refSeq.schema.ts
@@ -1,7 +1,7 @@
 import { Prop, Schema, SchemaFactory } from '@nestjs/mongoose'
 import { Document, Schema as MongooseSchema, Types } from 'mongoose'
 
-import { Assembly } from './assembly.schema'
+import { Assembly } from './assembly.schema.js'
 
 export type RefSeqDocument = RefSeq & Document
 
diff --git a/packages/apollo-schemas/src/refSeqChunk.schema.ts b/packages/apollo-schemas/src/refSeqChunk.schema.ts
index ff7cada55..913590c98 100644
--- a/packages/apollo-schemas/src/refSeqChunk.schema.ts
+++ b/packages/apollo-schemas/src/refSeqChunk.schema.ts
@@ -1,7 +1,7 @@
 import { Prop, Schema, SchemaFactory } from '@nestjs/mongoose'
 import { Document, Schema as MongooseSchema } from 'mongoose'
 
-import { RefSeq } from './refSeq.schema'
+import { RefSeq } from './refSeq.schema.js'
 
 export type RefSeqChunkDocument = RefSeqChunk & Document
 
diff --git a/packages/apollo-schemas/tsconfig.json b/packages/apollo-schemas/tsconfig.json
index ae9e5b6c4..0810ebb98 100644
--- a/packages/apollo-schemas/tsconfig.json
+++ b/packages/apollo-schemas/tsconfig.json
@@ -1,17 +1,15 @@
 {
-  "extends": "../../tsconfig-base.json",
+  "extends": "../../tsconfig",
   "compilerOptions": {
     "composite": true,
     "incremental": true,
     "outDir": "./dist",
     "rootDir": "./src",
-    "target": "ES2022",
-    "lib": ["ES2022", "DOM"],
-    "module": "CommonJS",
     "tsBuildInfoFile": "./dist/tsconfig.tsbuildinfo",
     "experimentalDecorators": true,
     "emitDecoratorMetadata": true,
     "strictPropertyInitialization": false,
   },
   "include": ["./src"],
+  "references": [{ "path": "../apollo-mst" }],
 }
diff --git a/packages/apollo-shared/package.json b/packages/apollo-shared/package.json
index bab5643bc..de3ffec6f 100644
--- a/packages/apollo-shared/package.json
+++ b/packages/apollo-shared/package.json
@@ -1,7 +1,9 @@
 {
   "name": "@apollo-annotation/shared",
   "version": "0.3.11",
-  "main": "./dist/index.js",
+  "sideEffects": false,
+  "type": "module",
+  "exports": "./dist/index.js",
   "scripts": {
     "build": "yarn clean && tsc --build",
     "clean": "rimraf dist",
@@ -15,22 +17,22 @@
     "@apollo-annotation/schemas": "workspace:^",
     "@gmod/gff": "^2.0.0",
     "@gmod/indexedfasta": "^2.0.4",
-    "@jbrowse/core": "^3.6.5",
+    "@jbrowse/core": "^4.1.1",
     "bson-objectid": "^2.0.4",
     "generic-filehandle": "^3.0.0",
     "jwt-decode": "^3.1.2",
     "tslib": "^2.3.1"
   },
   "devDependencies": {
+    "@jbrowse/mobx-state-tree": "^5.5.0",
     "@nestjs/common": "^10.1.0",
     "@nestjs/core": "^10.1.0",
     "@types/chai": "^4.3.19",
-    "@types/node": "^20.19.15",
+    "@types/node": "^24.10.9",
     "chai": "^5.1.1",
     "chai-exclude": "^3.0.0",
     "glob": "^11.0.0",
     "mobx": "^6.6.1",
-    "mobx-state-tree": "^5.4.0",
     "mongoose": "^6.12.0",
     "react-dom": "^18.2.0",
     "rimraf": "^3.0.2",
@@ -39,14 +41,15 @@
     "typescript": "^5.5.3"
   },
   "peerDependencies": {
-    "@mui/material": "^7.0.0",
+    "@jbrowse/mobx-state-tree": "^5.5.0",
+    "@mui/material": "^7.3.7",
     "@mui/x-data-grid": "^8.0.0",
     "mobx": "^6.6.1",
     "mobx-react": "^7.2.1",
-    "mobx-state-tree": "^5.4.0",
     "prop-types": "^15.8.1",
     "react": "^18.2.0",
     "react-dom": "^18.2.0",
+    "reflect-metadata": "^0.1.13",
     "rxjs": "^7.4.0"
   },
   "publishConfig": {
diff --git a/packages/apollo-shared/src/Changes/AddAssemblyAliasesChange.ts b/packages/apollo-shared/src/Changes/AddAssemblyAliasesChange.ts
index 4a5a73d2e..9f59c8152 100644
--- a/packages/apollo-shared/src/Changes/AddAssemblyAliasesChange.ts
+++ b/packages/apollo-shared/src/Changes/AddAssemblyAliasesChange.ts
@@ -1,3 +1,6 @@
+/* eslint-disable @typescript-eslint/no-unsafe-member-access */
+/* eslint-disable @typescript-eslint/no-unsafe-call */
+/* eslint-disable @typescript-eslint/no-unsafe-assignment */
 import {
   AssemblySpecificChange,
   type Change,
@@ -30,7 +33,6 @@ export class AddAssemblyAliasesChange extends AssemblySpecificChange {
     if (!assembly) {
       throw new Error(`assembly ${this.assembly} not found`)
     }
-    // eslint-disable-next-line @typescript-eslint/no-unsafe-call, @typescript-eslint/no-unsafe-member-access
     assembly.configuration.aliases.set(this.aliases)
     return Promise.resolve()
   }
diff --git a/packages/apollo-shared/src/Changes/AddAssemblyAndFeaturesFromFileChange.ts b/packages/apollo-shared/src/Changes/AddAssemblyAndFeaturesFromFileChange.ts
index 8716ab917..a6e4da918 100644
--- a/packages/apollo-shared/src/Changes/AddAssemblyAndFeaturesFromFileChange.ts
+++ b/packages/apollo-shared/src/Changes/AddAssemblyAndFeaturesFromFileChange.ts
@@ -1,3 +1,7 @@
+/* eslint-disable @typescript-eslint/no-unsafe-member-access */
+/* eslint-disable @typescript-eslint/no-unsafe-argument */
+/* eslint-disable @typescript-eslint/no-unsafe-call */
+/* eslint-disable @typescript-eslint/no-unsafe-assignment */
 /* eslint-disable @typescript-eslint/require-await */
 
 import {
@@ -7,9 +11,8 @@ import {
   type SerializedAssemblySpecificChange,
   type ServerDataStore,
 } from '@apollo-annotation/common'
-import { type GFF3Feature } from '@gmod/gff'
 
-import { FromFileBaseChange } from './FromFileBaseChange'
+import { FromFileBaseChange } from './FromFileBaseChange.js'
 
 export interface SerializedAddAssemblyAndFeaturesFromFileChangeBase
   extends SerializedAssemblySpecificChange {
@@ -116,10 +119,7 @@ export class AddAssemblyAndFeaturesFromFileChange extends FromFileBaseChange {
         filesService.getFileStream(fileDoc),
         { bufferSize },
       )
-      // @ts-expect-error type is wrong here
-      // eslint-disable-next-line @typescript-eslint/await-thenable
-      for await (const f of featureStream) {
-        const gff3Feature = f as GFF3Feature
+      for await (const gff3Feature of featureStream) {
         logger.verbose?.(`ENTRY=${JSON.stringify(gff3Feature)}`)
         // Add new feature into database
         await this.addFeatureIntoDb(gff3Feature, backend)
diff --git a/packages/apollo-shared/src/Changes/AddAssemblyFromExternalChange.ts b/packages/apollo-shared/src/Changes/AddAssemblyFromExternalChange.ts
index d5e9f9601..d013babf2 100644
--- a/packages/apollo-shared/src/Changes/AddAssemblyFromExternalChange.ts
+++ b/packages/apollo-shared/src/Changes/AddAssemblyFromExternalChange.ts
@@ -1,4 +1,5 @@
-/* eslint-disable @typescript-eslint/restrict-template-expressions */
+/* eslint-disable @typescript-eslint/no-unsafe-member-access */
+/* eslint-disable @typescript-eslint/no-unsafe-assignment */
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 
 /* eslint-disable @typescript-eslint/require-await */
diff --git a/packages/apollo-shared/src/Changes/AddAssemblyFromFileChange.ts b/packages/apollo-shared/src/Changes/AddAssemblyFromFileChange.ts
index 40ac528d8..99f034c38 100644
--- a/packages/apollo-shared/src/Changes/AddAssemblyFromFileChange.ts
+++ b/packages/apollo-shared/src/Changes/AddAssemblyFromFileChange.ts
@@ -1,4 +1,7 @@
-/* eslint-disable @typescript-eslint/restrict-template-expressions */
+/* eslint-disable @typescript-eslint/no-unsafe-call */
+/* eslint-disable @typescript-eslint/no-unsafe-argument */
+/* eslint-disable @typescript-eslint/no-unsafe-member-access */
+/* eslint-disable @typescript-eslint/no-unsafe-assignment */
 /* eslint-disable @typescript-eslint/require-await */
 import {
   type ChangeOptions,
@@ -9,7 +12,7 @@ import {
 } from '@apollo-annotation/common'
 import { BgzipIndexedFasta } from '@gmod/indexedfasta'
 
-import { FromFileBaseChange } from './FromFileBaseChange'
+import { FromFileBaseChange } from './FromFileBaseChange.js'
 
 export interface SerializedAddAssemblyFromFileChangeBase
   extends SerializedAssemblySpecificChange {
diff --git a/packages/apollo-shared/src/Changes/AddFeatureChange.ts b/packages/apollo-shared/src/Changes/AddFeatureChange.ts
index 814073749..40ecb8b1a 100644
--- a/packages/apollo-shared/src/Changes/AddFeatureChange.ts
+++ b/packages/apollo-shared/src/Changes/AddFeatureChange.ts
@@ -1,3 +1,4 @@
+/* eslint-disable @typescript-eslint/no-unsafe-assignment */
 /* eslint-disable @typescript-eslint/restrict-template-expressions */
 /* eslint-disable @typescript-eslint/require-await */
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
@@ -11,7 +12,7 @@ import {
 } from '@apollo-annotation/common'
 import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
 
-import { DeleteFeatureChange } from './DeleteFeatureChange'
+import { DeleteFeatureChange } from './DeleteFeatureChange.js'
 
 interface SerializedAddFeatureChangeBase extends SerializedFeatureChange {
   typeName: 'AddFeatureChange'
diff --git a/packages/apollo-shared/src/Changes/AddFeaturesFromFileChange.ts b/packages/apollo-shared/src/Changes/AddFeaturesFromFileChange.ts
index 0c0ac8e21..41c70d3f2 100644
--- a/packages/apollo-shared/src/Changes/AddFeaturesFromFileChange.ts
+++ b/packages/apollo-shared/src/Changes/AddFeaturesFromFileChange.ts
@@ -6,9 +6,8 @@ import {
   type SerializedAssemblySpecificChange,
   type ServerDataStore,
 } from '@apollo-annotation/common'
-import { type GFF3Feature } from '@gmod/gff'
 
-import { FromFileBaseChange } from './FromFileBaseChange'
+import { FromFileBaseChange } from './FromFileBaseChange.js'
 
 export interface SerializedAddFeaturesFromFileChangeBase
   extends SerializedAssemblySpecificChange {
@@ -96,11 +95,7 @@ export class AddFeaturesFromFileChange extends FromFileBaseChange {
         { bufferSize },
       )
       let featureCount = 0
-      // @ts-expect-error type is wrong here
-      // eslint-disable-next-line @typescript-eslint/await-thenable
-      for await (const f of featureStream) {
-        const gff3Feature = f as GFF3Feature
-
+      for await (const gff3Feature of featureStream) {
         // Add new feature into database
         // We cannot use Mongo 'session' / transaction here because Mongo has 16 MB limit for transaction
         await this.addFeatureIntoDb(gff3Feature, backend)
diff --git a/packages/apollo-shared/src/Changes/AddRefSeqAliasesChange.ts b/packages/apollo-shared/src/Changes/AddRefSeqAliasesChange.ts
index 12dd935ee..be870c96c 100644
--- a/packages/apollo-shared/src/Changes/AddRefSeqAliasesChange.ts
+++ b/packages/apollo-shared/src/Changes/AddRefSeqAliasesChange.ts
@@ -1,3 +1,6 @@
+/* eslint-disable @typescript-eslint/no-unsafe-member-access */
+/* eslint-disable @typescript-eslint/no-unsafe-call */
+/* eslint-disable @typescript-eslint/no-unsafe-assignment */
 import {
   AssemblySpecificChange,
   type Change,
diff --git a/packages/apollo-shared/src/Changes/DeleteAssemblyChange.ts b/packages/apollo-shared/src/Changes/DeleteAssemblyChange.ts
index 0803acec0..0f5baa718 100644
--- a/packages/apollo-shared/src/Changes/DeleteAssemblyChange.ts
+++ b/packages/apollo-shared/src/Changes/DeleteAssemblyChange.ts
@@ -1,3 +1,4 @@
+/* eslint-disable @typescript-eslint/no-unsafe-assignment */
 /* eslint-disable @typescript-eslint/no-unsafe-return */
 /* eslint-disable @typescript-eslint/require-await */
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
diff --git a/packages/apollo-shared/src/Changes/DeleteFeatureChange.ts b/packages/apollo-shared/src/Changes/DeleteFeatureChange.ts
index 3beda2091..713b8b6f0 100644
--- a/packages/apollo-shared/src/Changes/DeleteFeatureChange.ts
+++ b/packages/apollo-shared/src/Changes/DeleteFeatureChange.ts
@@ -12,7 +12,7 @@ import {
 import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
 import { type Feature } from '@apollo-annotation/schemas'
 
-import { AddFeatureChange } from './AddFeatureChange'
+import { AddFeatureChange } from './AddFeatureChange.js'
 
 interface SerializedDeleteFeatureChangeBase extends SerializedFeatureChange {
   typeName: 'DeleteFeatureChange'
diff --git a/packages/apollo-shared/src/Changes/FromFileBaseChange.ts b/packages/apollo-shared/src/Changes/FromFileBaseChange.ts
index c74d52f89..d78adeb69 100644
--- a/packages/apollo-shared/src/Changes/FromFileBaseChange.ts
+++ b/packages/apollo-shared/src/Changes/FromFileBaseChange.ts
@@ -11,7 +11,7 @@ import {
 } from '@apollo-annotation/schemas'
 import { type GFF3Feature } from '@gmod/gff'
 
-import { gff3ToAnnotationFeature } from '../GFF3'
+import { gff3ToAnnotationFeature } from '../GFF3/index.js'
 
 export abstract class FromFileBaseChange extends AssemblySpecificChange {
   async addRefSeqIntoDb(
@@ -37,8 +37,6 @@ export abstract class FromFileBaseChange extends AssemblySpecificChange {
     logger.debug?.('starting sequence stream')
     let lineCount = 0
     const decoder = new TextDecoder()
-    // @ts-expect-error type is wrong here
-    // eslint-disable-next-line @typescript-eslint/await-thenable
     for await (const data of sequenceStream) {
       const chunk = decoder.decode(data)
       lastLineIsIncomplete = !chunk.endsWith('\n')
diff --git a/packages/apollo-shared/src/Changes/MergeExonsChange.ts b/packages/apollo-shared/src/Changes/MergeExonsChange.ts
index 639ee9a6f..742d2ea43 100644
--- a/packages/apollo-shared/src/Changes/MergeExonsChange.ts
+++ b/packages/apollo-shared/src/Changes/MergeExonsChange.ts
@@ -12,10 +12,10 @@ import {
 } from '@apollo-annotation/common'
 import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
 
-import { attributesToRecords, stringifyAttributes } from '../util'
+import { attributesToRecords, stringifyAttributes } from '../util.js'
 
-import { findAndDeleteChildFeature } from './DeleteFeatureChange'
-import { UndoMergeExonsChange } from './UndoMergeExonsChange'
+import { findAndDeleteChildFeature } from './DeleteFeatureChange.js'
+import { UndoMergeExonsChange } from './UndoMergeExonsChange.js'
 
 interface SerializedMergeExonsChangeBase extends SerializedFeatureChange {
   typeName: 'MergeExonsChange'
diff --git a/packages/apollo-shared/src/Changes/MergeTranscriptsChange.ts b/packages/apollo-shared/src/Changes/MergeTranscriptsChange.ts
index f74faba05..daa1af285 100644
--- a/packages/apollo-shared/src/Changes/MergeTranscriptsChange.ts
+++ b/packages/apollo-shared/src/Changes/MergeTranscriptsChange.ts
@@ -16,12 +16,12 @@ import {
 } from '@apollo-annotation/mst'
 import { type Feature } from '@apollo-annotation/schemas'
 import { doesIntersect2 } from '@jbrowse/core/util'
-import { getSnapshot } from 'mobx-state-tree'
+import { getSnapshot } from '@jbrowse/mobx-state-tree'
 
-import { attributesToRecords, stringifyAttributes } from '../util'
+import { attributesToRecords, stringifyAttributes } from '../util.js'
 
-import { findAndDeleteChildFeature } from './DeleteFeatureChange'
-import { UndoMergeTranscriptsChange } from './UndoMergeTranscriptsChange'
+import { findAndDeleteChildFeature } from './DeleteFeatureChange.js'
+import { UndoMergeTranscriptsChange } from './UndoMergeTranscriptsChange.js'
 
 interface SerializedMergeTranscriptsChangeBase extends SerializedFeatureChange {
   typeName: 'MergeTranscriptsChange'
diff --git a/packages/apollo-shared/src/Changes/SplitExonChange.ts b/packages/apollo-shared/src/Changes/SplitExonChange.ts
index c3a0772a4..bf14c49a3 100644
--- a/packages/apollo-shared/src/Changes/SplitExonChange.ts
+++ b/packages/apollo-shared/src/Changes/SplitExonChange.ts
@@ -11,8 +11,8 @@ import {
 } from '@apollo-annotation/common'
 import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
 
-import { findAndDeleteChildFeature } from './DeleteFeatureChange'
-import { UndoSplitExonChange } from './UndoSplitExonChange'
+import { findAndDeleteChildFeature } from './DeleteFeatureChange.js'
+import { UndoSplitExonChange } from './UndoSplitExonChange.js'
 
 interface SerializedSplitExonChangeBase extends SerializedFeatureChange {
   typeName: 'SplitExonChange'
diff --git a/packages/apollo-shared/src/Changes/UndoMergeExonsChange.ts b/packages/apollo-shared/src/Changes/UndoMergeExonsChange.ts
index 5e191cae6..389a36fde 100644
--- a/packages/apollo-shared/src/Changes/UndoMergeExonsChange.ts
+++ b/packages/apollo-shared/src/Changes/UndoMergeExonsChange.ts
@@ -10,7 +10,7 @@ import {
 } from '@apollo-annotation/common'
 import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
 
-import { MergeExonsChange } from './MergeExonsChange'
+import { MergeExonsChange } from './MergeExonsChange.js'
 
 interface SerializedUndoMergeExonsChangeBase extends SerializedFeatureChange {
   typeName: 'UndoMergeExonsChange'
diff --git a/packages/apollo-shared/src/Changes/UndoMergeTranscriptsChange.ts b/packages/apollo-shared/src/Changes/UndoMergeTranscriptsChange.ts
index 2332b8887..6a753393d 100644
--- a/packages/apollo-shared/src/Changes/UndoMergeTranscriptsChange.ts
+++ b/packages/apollo-shared/src/Changes/UndoMergeTranscriptsChange.ts
@@ -10,7 +10,7 @@ import {
 } from '@apollo-annotation/common'
 import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
 
-import { MergeTranscriptsChange } from './MergeTranscriptsChange'
+import { MergeTranscriptsChange } from './MergeTranscriptsChange.js'
 
 interface SerializedUndoMergeTranscriptsChangeBase
   extends SerializedFeatureChange {
diff --git a/packages/apollo-shared/src/Changes/UndoSplitExonChange.ts b/packages/apollo-shared/src/Changes/UndoSplitExonChange.ts
index a54b42907..30484d6b3 100644
--- a/packages/apollo-shared/src/Changes/UndoSplitExonChange.ts
+++ b/packages/apollo-shared/src/Changes/UndoSplitExonChange.ts
@@ -10,8 +10,8 @@ import {
 } from '@apollo-annotation/common'
 import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
 
-import { findAndDeleteChildFeature } from './DeleteFeatureChange'
-import { SplitExonChange } from './SplitExonChange'
+import { findAndDeleteChildFeature } from './DeleteFeatureChange.js'
+import { SplitExonChange } from './SplitExonChange.js'
 
 interface SerializedUndoSplitExonChangeBase extends SerializedFeatureChange {
   typeName: 'UndoSplitExonChange'
diff --git a/packages/apollo-shared/src/Changes/index.ts b/packages/apollo-shared/src/Changes/index.ts
index d04d0e82a..ac5ecf25d 100644
--- a/packages/apollo-shared/src/Changes/index.ts
+++ b/packages/apollo-shared/src/Changes/index.ts
@@ -1,26 +1,26 @@
-import { AddAssemblyAliasesChange } from './AddAssemblyAliasesChange'
-import { AddAssemblyAndFeaturesFromFileChange } from './AddAssemblyAndFeaturesFromFileChange'
-import { AddAssemblyFromExternalChange } from './AddAssemblyFromExternalChange'
-import { AddAssemblyFromFileChange } from './AddAssemblyFromFileChange'
-import { AddFeatureChange } from './AddFeatureChange'
-import { AddFeaturesFromFileChange } from './AddFeaturesFromFileChange'
-import { AddRefSeqAliasesChange } from './AddRefSeqAliasesChange'
-import { DeleteAssemblyChange } from './DeleteAssemblyChange'
-import { DeleteFeatureChange } from './DeleteFeatureChange'
-import { DeleteUserChange } from './DeleteUserChange'
-import { FeatureAttributeChange } from './FeatureAttributeChange'
-import { ImportJBrowseConfigChange } from './ImportJBrowseConfigChange'
-import { LocationEndChange } from './LocationEndChange'
-import { LocationStartChange } from './LocationStartChange'
-import { MergeExonsChange } from './MergeExonsChange'
-import { MergeTranscriptsChange } from './MergeTranscriptsChange'
-import { SplitExonChange } from './SplitExonChange'
-import { StrandChange } from './StrandChange'
-import { TypeChange } from './TypeChange'
-import { UndoMergeExonsChange } from './UndoMergeExonsChange'
-import { UndoMergeTranscriptsChange } from './UndoMergeTranscriptsChange'
-import { UndoSplitExonChange } from './UndoSplitExonChange'
-import { UserChange } from './UserChange'
+import { AddAssemblyAliasesChange } from './AddAssemblyAliasesChange.js'
+import { AddAssemblyAndFeaturesFromFileChange } from './AddAssemblyAndFeaturesFromFileChange.js'
+import { AddAssemblyFromExternalChange } from './AddAssemblyFromExternalChange.js'
+import { AddAssemblyFromFileChange } from './AddAssemblyFromFileChange.js'
+import { AddFeatureChange } from './AddFeatureChange.js'
+import { AddFeaturesFromFileChange } from './AddFeaturesFromFileChange.js'
+import { AddRefSeqAliasesChange } from './AddRefSeqAliasesChange.js'
+import { DeleteAssemblyChange } from './DeleteAssemblyChange.js'
+import { DeleteFeatureChange } from './DeleteFeatureChange.js'
+import { DeleteUserChange } from './DeleteUserChange.js'
+import { FeatureAttributeChange } from './FeatureAttributeChange.js'
+import { ImportJBrowseConfigChange } from './ImportJBrowseConfigChange.js'
+import { LocationEndChange } from './LocationEndChange.js'
+import { LocationStartChange } from './LocationStartChange.js'
+import { MergeExonsChange } from './MergeExonsChange.js'
+import { MergeTranscriptsChange } from './MergeTranscriptsChange.js'
+import { SplitExonChange } from './SplitExonChange.js'
+import { StrandChange } from './StrandChange.js'
+import { TypeChange } from './TypeChange.js'
+import { UndoMergeExonsChange } from './UndoMergeExonsChange.js'
+import { UndoMergeTranscriptsChange } from './UndoMergeTranscriptsChange.js'
+import { UndoSplitExonChange } from './UndoSplitExonChange.js'
+import { UserChange } from './UserChange.js'
 
 export const changes = {
   AddAssemblyAndFeaturesFromFileChange,
@@ -48,26 +48,26 @@ export const changes = {
   AddAssemblyAliasesChange,
 }
 
-export * from './AddAssemblyAndFeaturesFromFileChange'
-export * from './AddAssemblyFromFileChange'
-export * from './AddAssemblyFromExternalChange'
-export * from './AddFeatureChange'
-export * from './AddFeaturesFromFileChange'
-export * from './DeleteAssemblyChange'
-export * from './DeleteFeatureChange'
-export * from './DeleteUserChange'
-export * from './FeatureAttributeChange'
-export * from './ImportJBrowseConfigChange'
-export * from './LocationEndChange'
-export * from './LocationStartChange'
-export * from './MergeExonsChange'
-export * from './SplitExonChange'
-export * from './MergeTranscriptsChange'
-export * from './UndoMergeExonsChange'
-export * from './UndoSplitExonChange'
-export * from './UndoMergeTranscriptsChange'
-export * from './StrandChange'
-export * from './TypeChange'
-export * from './UserChange'
-export * from './AddRefSeqAliasesChange'
-export * from './AddAssemblyAliasesChange'
+export * from './AddAssemblyAndFeaturesFromFileChange.js'
+export * from './AddAssemblyFromFileChange.js'
+export * from './AddAssemblyFromExternalChange.js'
+export * from './AddFeatureChange.js'
+export * from './AddFeaturesFromFileChange.js'
+export * from './DeleteAssemblyChange.js'
+export * from './DeleteFeatureChange.js'
+export * from './DeleteUserChange.js'
+export * from './FeatureAttributeChange.js'
+export * from './ImportJBrowseConfigChange.js'
+export * from './LocationEndChange.js'
+export * from './LocationStartChange.js'
+export * from './MergeExonsChange.js'
+export * from './SplitExonChange.js'
+export * from './MergeTranscriptsChange.js'
+export * from './UndoMergeExonsChange.js'
+export * from './UndoSplitExonChange.js'
+export * from './UndoMergeTranscriptsChange.js'
+export * from './StrandChange.js'
+export * from './TypeChange.js'
+export * from './UserChange.js'
+export * from './AddRefSeqAliasesChange.js'
+export * from './AddAssemblyAliasesChange.js'
diff --git a/packages/apollo-shared/src/Checks/CDSCheck.ts b/packages/apollo-shared/src/Checks/CDSCheck.ts
index 1a929ddc2..3cbac2bfe 100644
--- a/packages/apollo-shared/src/Checks/CDSCheck.ts
+++ b/packages/apollo-shared/src/Checks/CDSCheck.ts
@@ -6,7 +6,7 @@ import {
 import { intersection2 } from '@jbrowse/core/util'
 import ObjectID from 'bson-objectid'
 
-import { getPrintableId } from './util'
+import { getPrintableId } from './util.js'
 
 enum STOP_CODONS {
   'TAG',
diff --git a/packages/apollo-shared/src/Checks/TranscriptCheck.ts b/packages/apollo-shared/src/Checks/TranscriptCheck.ts
index dc569fa85..b3b1745c9 100644
--- a/packages/apollo-shared/src/Checks/TranscriptCheck.ts
+++ b/packages/apollo-shared/src/Checks/TranscriptCheck.ts
@@ -6,7 +6,7 @@ import {
 import { revcom } from '@jbrowse/core/util'
 import ObjectID from 'bson-objectid'
 
-import { getPrintableId } from './util'
+import { getPrintableId } from './util.js'
 
 interface SpliceSequence {
   fivePrimeSeq: string
diff --git a/packages/apollo-shared/src/Checks/index.ts b/packages/apollo-shared/src/Checks/index.ts
index 35fab0527..bd5aad505 100644
--- a/packages/apollo-shared/src/Checks/index.ts
+++ b/packages/apollo-shared/src/Checks/index.ts
@@ -1,2 +1,2 @@
-export * from './CDSCheck'
-export * from './TranscriptCheck'
+export * from './CDSCheck.js'
+export * from './TranscriptCheck.js'
diff --git a/packages/apollo-shared/src/Common/index.ts b/packages/apollo-shared/src/Common/index.ts
index d6f93705a..3cfa14e55 100644
--- a/packages/apollo-shared/src/Common/index.ts
+++ b/packages/apollo-shared/src/Common/index.ts
@@ -1 +1 @@
-export * from './jwtPayload'
+export * from './jwtPayload.js'
diff --git a/packages/apollo-shared/src/GFF3/annotationFeatureToGFF3.test.ts b/packages/apollo-shared/src/GFF3/annotationFeatureToGFF3.test.ts
index 630238c3c..e138bc2a1 100644
--- a/packages/apollo-shared/src/GFF3/annotationFeatureToGFF3.test.ts
+++ b/packages/apollo-shared/src/GFF3/annotationFeatureToGFF3.test.ts
@@ -7,8 +7,8 @@ import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
 import { formatSync } from '@gmod/gff'
 import { assert, expect } from 'chai'
 
-import { annotationFeatureToGFF3 } from './annotationFeatureToGFF3'
-import { readAnnotationFeatureSnapshot, testCases } from './testUtil'
+import { annotationFeatureToGFF3 } from './annotationFeatureToGFF3.js'
+import { readAnnotationFeatureSnapshot, testCases } from './testUtil.js'
 
 describe('Converts AnnotationFeatureSnapshot JSON to GFF3 when', () => {
   for (const testCase of testCases) {
diff --git a/packages/apollo-shared/src/GFF3/gff3ToAnnotationFeature.test.ts b/packages/apollo-shared/src/GFF3/gff3ToAnnotationFeature.test.ts
index ff4de8ab5..2b64c92fa 100644
--- a/packages/apollo-shared/src/GFF3/gff3ToAnnotationFeature.test.ts
+++ b/packages/apollo-shared/src/GFF3/gff3ToAnnotationFeature.test.ts
@@ -7,8 +7,8 @@ import { type GFF3Feature, parseStringSync } from '@gmod/gff'
 import { assert, use } from 'chai'
 import chaiExclude from 'chai-exclude'
 
-import { gff3ToAnnotationFeature } from './gff3ToAnnotationFeature'
-import { readAnnotationFeatureSnapshot, testCases } from './testUtil'
+import { gff3ToAnnotationFeature } from './gff3ToAnnotationFeature.js'
+import { readAnnotationFeatureSnapshot, testCases } from './testUtil.js'
 
 use(chaiExclude)
 
diff --git a/packages/apollo-shared/src/GFF3/gff3ToAnnotationFeature.ts b/packages/apollo-shared/src/GFF3/gff3ToAnnotationFeature.ts
index 1804dc669..fc4961391 100644
--- a/packages/apollo-shared/src/GFF3/gff3ToAnnotationFeature.ts
+++ b/packages/apollo-shared/src/GFF3/gff3ToAnnotationFeature.ts
@@ -3,7 +3,7 @@ import { type GFF3Feature, type GFF3FeatureLineWithRefs } from '@gmod/gff'
 import { doesIntersect2 } from '@jbrowse/core/util'
 import ObjectID from 'bson-objectid'
 
-import { gffToInternal, isGFFReservedAttribute } from './gffReservedKeys'
+import { gffToInternal, isGFFReservedAttribute } from './gffReservedKeys.js'
 
 export function gff3ToAnnotationFeature(
   gff3Feature: GFF3Feature,
diff --git a/packages/apollo-shared/src/GFF3/index.ts b/packages/apollo-shared/src/GFF3/index.ts
index 45cec9a92..9e8e08ec7 100644
--- a/packages/apollo-shared/src/GFF3/index.ts
+++ b/packages/apollo-shared/src/GFF3/index.ts
@@ -1,3 +1,3 @@
-export * from './annotationFeatureToGFF3'
-export * from './gffReservedKeys'
-export * from './gff3ToAnnotationFeature'
+export * from './annotationFeatureToGFF3.js'
+export * from './gffReservedKeys.js'
+export * from './gff3ToAnnotationFeature.js'
diff --git a/packages/apollo-shared/src/Operations/index.ts b/packages/apollo-shared/src/Operations/index.ts
index 859d4346c..96e42e163 100644
--- a/packages/apollo-shared/src/Operations/index.ts
+++ b/packages/apollo-shared/src/Operations/index.ts
@@ -1,6 +1,6 @@
-import { GetAssembliesOperation } from './GetAssembliesOperation'
-import { GetFeaturesOperation } from './GetFeaturesOperation'
+import { GetAssembliesOperation } from './GetAssembliesOperation.js'
+import { GetFeaturesOperation } from './GetFeaturesOperation.js'
 
 export const operations = { GetAssembliesOperation, GetFeaturesOperation }
-export * from './GetAssembliesOperation'
-export * from './GetFeaturesOperation'
+export * from './GetAssembliesOperation.js'
+export * from './GetFeaturesOperation.js'
diff --git a/packages/apollo-shared/src/Validations/CoreValidation.ts b/packages/apollo-shared/src/Validations/CoreValidation.ts
index e92e93767..1d5467852 100644
--- a/packages/apollo-shared/src/Validations/CoreValidation.ts
+++ b/packages/apollo-shared/src/Validations/CoreValidation.ts
@@ -1,10 +1,10 @@
 /* eslint-disable @typescript-eslint/require-await */
 import { type Change } from '@apollo-annotation/common'
 
-import { type TypeChange } from '../Changes'
+import { type TypeChange } from '../Changes/index.js'
 
-import { Validation } from './Validation'
-import soSequenceTypes from './soSequenceTypes'
+import { Validation } from './Validation.js'
+import soSequenceTypes from './soSequenceTypes.js'
 
 export function isTypeChange(thing: Change): thing is TypeChange {
   return 'oldType' in thing && 'newType' in thing
diff --git a/packages/apollo-shared/src/Validations/ParentChildValidation.ts b/packages/apollo-shared/src/Validations/ParentChildValidation.ts
index 670adb26f..afc7aabf8 100644
--- a/packages/apollo-shared/src/Validations/ParentChildValidation.ts
+++ b/packages/apollo-shared/src/Validations/ParentChildValidation.ts
@@ -9,10 +9,10 @@ import {
   type LocationStartChange,
   isLocationEndChange,
   isLocationStartChange,
-} from '../Changes'
-import { getPrintableId } from '../util'
+} from '../Changes/index.js'
+import { getPrintableId } from '../util.js'
 
-import { Validation, type ValidationResult } from './Validation'
+import { Validation, type ValidationResult } from './Validation.js'
 
 export class ParentChildValidation extends Validation {
   name = 'ParentChildValidation' as const
diff --git a/packages/apollo-shared/src/Validations/ValidationSet.ts b/packages/apollo-shared/src/Validations/ValidationSet.ts
index 5a0d62510..aaff41017 100644
--- a/packages/apollo-shared/src/Validations/ValidationSet.ts
+++ b/packages/apollo-shared/src/Validations/ValidationSet.ts
@@ -6,7 +6,7 @@ import {
   type Context,
   type Validation,
   type ValidationResult,
-} from './Validation'
+} from './Validation.js'
 
 export class ValidationResultSet {
   results: ValidationResult[] = []
diff --git a/packages/apollo-shared/src/Validations/index.ts b/packages/apollo-shared/src/Validations/index.ts
index af1362d56..44916b7f9 100644
--- a/packages/apollo-shared/src/Validations/index.ts
+++ b/packages/apollo-shared/src/Validations/index.ts
@@ -1,4 +1,4 @@
-export * from './Validation'
-export * from './ValidationSet'
-export * from './CoreValidation'
-export * from './ParentChildValidation'
+export * from './Validation.js'
+export * from './ValidationSet.js'
+export * from './CoreValidation.js'
+export * from './ParentChildValidation.js'
diff --git a/packages/apollo-shared/src/declare.d.ts b/packages/apollo-shared/src/declare.d.ts
new file mode 100644
index 000000000..efa84fc14
--- /dev/null
+++ b/packages/apollo-shared/src/declare.d.ts
@@ -0,0 +1,58 @@
+declare module 'bson-objectid' {
+  import { type Buffer } from 'node:buffer'
+
+  export default ObjectID
+
+  declare const ObjectID: ObjectIDCtor
+
+  declare interface ObjectID {
+    readonly id: string
+    readonly str: string
+
+    toHexString(): string
+    equals(other: ObjectID): boolean
+    getTimestamp(): Date
+  }
+
+  declare interface ObjectIDCtor {
+    (hexStringOrIdStringOrArrayOrBuffer?: string | number[] | Buffer): ObjectID
+
+    new (
+      hexStringOrIdStringOrArrayOrBuffer?: string | number[] | Buffer,
+    ): ObjectID
+
+    createFromTime(time: number): ObjectID
+    createFromHexString(hexString: string): ObjectID
+    isValid(hexStringOrObjectID: string | ObjectID): boolean
+    toString(): string
+  }
+}
+
+declare module 'jwt-decode' {
+  export class InvalidTokenError extends Error {}
+
+  export interface JwtDecodeOptions {
+    header?: boolean
+  }
+
+  export interface JwtHeader {
+    type?: string
+    alg?: string
+  }
+
+  export interface JwtPayload {
+    iss?: string
+    sub?: string
+    aud?: string[] | string
+    exp?: number
+    nbf?: number
+    iat?: number
+    jti?: string
+  }
+
+  // eslint-disable-next-line @typescript-eslint/no-unnecessary-type-parameters, @typescript-eslint/no-unnecessary-type-constraint
+  export default function jwtDecode<T extends unknown>(
+    token: string,
+    options?: JwtDecodeOptions,
+  ): T
+}
diff --git a/packages/apollo-shared/src/index.ts b/packages/apollo-shared/src/index.ts
index 52381ad7a..aa18bbf15 100644
--- a/packages/apollo-shared/src/index.ts
+++ b/packages/apollo-shared/src/index.ts
@@ -1,8 +1,8 @@
-export * from './Changes'
-export * from './Operations'
-export * from './Validations'
-export * from './Common'
-export * from './Checks'
-export * from './util'
-export * from './Messages'
-export * from './GFF3'
+export * from './Changes/index.js'
+export * from './Operations/index.js'
+export * from './Validations/index.js'
+export * from './Common/index.js'
+export * from './Checks/index.js'
+export * from './util.js'
+export * from './Messages.js'
+export * from './GFF3/index.js'
diff --git a/packages/apollo-shared/tsconfig.json b/packages/apollo-shared/tsconfig.json
index d786167aa..21a09645c 100644
--- a/packages/apollo-shared/tsconfig.json
+++ b/packages/apollo-shared/tsconfig.json
@@ -1,14 +1,16 @@
 {
-  "extends": "../../tsconfig-base.json",
+  "extends": "../../tsconfig",
   "compilerOptions": {
     "composite": true,
     "incremental": true,
     "outDir": "./dist",
     "rootDir": "./src",
-    "target": "ES2022",
-    "lib": ["ES2022", "DOM"],
-    "module": "CommonJS",
     "tsBuildInfoFile": "./dist/tsconfig.tsbuildinfo",
+    // TODO: enable this and fix the problems it reveals
+    "noUncheckedIndexedAccess": false,
+    // For nodejs:
+    "lib": ["esnext"],
+    "types": ["node"],
   },
   "include": ["./src"],
   "references": [
diff --git a/packages/jbrowse-plugin-apollo/.gitignore b/packages/jbrowse-plugin-apollo/.gitignore
index 09057ef93..78efc3ca6 100644
--- a/packages/jbrowse-plugin-apollo/.gitignore
+++ b/packages/jbrowse-plugin-apollo/.gitignore
@@ -7,3 +7,5 @@ cypress/downloads
 cypress/cypress-image-diff-html-report
 cypress/cypress-image-diff-screenshots/comparison
 cypress/cypress-image-diff-screenshots/diff
+
+data/
diff --git a/packages/jbrowse-plugin-apollo/cypress.config.js b/packages/jbrowse-plugin-apollo/cypress.config.ts
similarity index 59%
rename from packages/jbrowse-plugin-apollo/cypress.config.js
rename to packages/jbrowse-plugin-apollo/cypress.config.ts
index 149ceb4c1..9596e1edb 100644
--- a/packages/jbrowse-plugin-apollo/cypress.config.js
+++ b/packages/jbrowse-plugin-apollo/cypress.config.ts
@@ -1,15 +1,12 @@
-/* eslint-disable @typescript-eslint/no-require-imports */
-/* eslint-disable @typescript-eslint/unbound-method */
 /* eslint-disable @typescript-eslint/no-unsafe-argument */
 
-const fs = require('node:fs')
+import fs from 'node:fs'
 
-const { defineConfig } = require('cypress')
-// eslint-disable-next-line @typescript-eslint/no-unsafe-assignment
-const getCompareSnapshotsPlugin = require('cypress-image-diff-js/plugin')
-const { configurePlugin } = require('cypress-mongodb')
+import { defineConfig } from 'cypress'
+import getCompareSnapshotsPlugin from 'cypress-image-diff-js/plugin'
+import { configurePlugin } from 'cypress-mongodb'
 
-module.exports = defineConfig({
+export default defineConfig({
   // Make viewport long and thin to avoid the scrollbar on the right interfere
   // with the coordinates
   viewportHeight: 2000,
@@ -28,7 +25,7 @@ module.exports = defineConfig({
   e2e: {
     baseUrl: 'http://localhost:8999',
     setupNodeEvents(on, config) {
-      // eslint-disable-next-line @typescript-eslint/no-unsafe-call
+      // @ts-expect-error types are wrong
       getCompareSnapshotsPlugin(on, config)
       configurePlugin(on)
       on('task', {
diff --git a/packages/jbrowse-plugin-apollo/cypress/tsconfig.json b/packages/jbrowse-plugin-apollo/cypress/tsconfig.json
index d7ad9fdaa..3c48941b1 100644
--- a/packages/jbrowse-plugin-apollo/cypress/tsconfig.json
+++ b/packages/jbrowse-plugin-apollo/cypress/tsconfig.json
@@ -1,7 +1,7 @@
 {
   "compilerOptions": {
     "target": "es5",
-    "lib": ["es5", "dom"],
+    "lib": ["es2022", "dom"],
     "types": ["cypress", "node"],
     "strict": true,
     "esModuleInterop": true,
diff --git a/packages/jbrowse-plugin-apollo/jest.config.js b/packages/jbrowse-plugin-apollo/jest.config.cjs
similarity index 63%
rename from packages/jbrowse-plugin-apollo/jest.config.js
rename to packages/jbrowse-plugin-apollo/jest.config.cjs
index 3bb440424..1ce6fad02 100644
--- a/packages/jbrowse-plugin-apollo/jest.config.js
+++ b/packages/jbrowse-plugin-apollo/jest.config.cjs
@@ -1,9 +1,13 @@
+/* eslint-disable @typescript-eslint/no-require-imports */
+
 /** @type {import('ts-jest').JestConfigWithTsJest} */
 
+const { createDefaultEsmPreset } = require('ts-jest')
+
 module.exports = {
-  preset: 'ts-jest',
   testPathIgnorePatterns: ['<rootDir>/cypress/'],
   automock: false,
   setupFiles: ['./jestSetup.js', 'fake-indexeddb/auto'],
   collectCoverageFrom: ['src/**/*.{js,jsx,ts,tsx}'],
+  ...createDefaultEsmPreset(),
 }
diff --git a/packages/jbrowse-plugin-apollo/jestSetup.js b/packages/jbrowse-plugin-apollo/jestSetup.js
index 0a36090e2..4665e0bd5 100644
--- a/packages/jbrowse-plugin-apollo/jestSetup.js
+++ b/packages/jbrowse-plugin-apollo/jestSetup.js
@@ -1,4 +1,4 @@
-/* eslint-disable @typescript-eslint/no-require-imports */
 /* eslint-disable @typescript-eslint/no-unsafe-call */
 
-require('jest-fetch-mock').enableMocks()
+import jestFetchMock from 'jest-fetch-mock'
+jestFetchMock.enableMocks()
diff --git a/packages/jbrowse-plugin-apollo/package.json b/packages/jbrowse-plugin-apollo/package.json
index 223c58163..d113d2b47 100644
--- a/packages/jbrowse-plugin-apollo/package.json
+++ b/packages/jbrowse-plugin-apollo/package.json
@@ -13,9 +13,7 @@
   },
   "license": "Apache-2.0",
   "author": "JBrowse Team",
-  "main": "dist/index.js",
-  "module": "dist/index.esm.js",
-  "typings": "dist/index.d.ts",
+  "type": "module",
   "files": [
     "dist",
     "src"
@@ -24,12 +22,12 @@
     "setup": "rimraf .jbrowse && jbrowse create .jbrowse",
     "clean": "rimraf dist",
     "start": "yarn clean && npm-run-all --parallel start:watch start:server",
-    "start:watch": "JB_NPM=false NODE_ENV=development rollup --config --watch",
+    "start:watch": "JB_NPM=false NODE_ENV=development rollup --config rollup/rollup.config.mjs --watch",
     "start:server": "serve --no-request-logging --cors --listen 9000 --no-port-switching .",
-    "build": "yarn build:shared && yarn clean && rollup --config",
+    "build": "yarn build:shared && yarn clean && rollup --config rollup/rollup.config.mjs",
     "browse": "serve --no-request-logging --listen 8999 --no-port-switching --symlinks .jbrowse",
-    "test": "jest",
-    "test:ci": "jest --coverage",
+    "test": "yarn node --experimental-vm-modules $(yarn bin jest)",
+    "test:ci": "yarn node --experimental-vm-modules $(yarn bin jest) --coverage",
     "start:collab-cypress": "yarn workspace @apollo-annotation/collaboration-server run cypress:start",
     "test:e2e": "yarn build && start-test \"npm-run-all --parallel start:server browse start:collab-cypress\" \"9000|8999|http://localhost:3999/health\" \"npm-run-all cypress:run\"",
     "test:e2e:debug": "yarn build && start-test \"npm-run-all --parallel start:server browse start:collab-cypress\" \"9000|8999|http://localhost:3999/health\" \"npm-run-all cypress:debug\"",
@@ -54,9 +52,9 @@
     "@emotion/react": "^11.10.6",
     "@emotion/styled": "^11.10.6",
     "@gmod/gff": "^2.0.0",
-    "@jbrowse/plugin-authentication": "^3.6.5",
-    "@jbrowse/plugin-linear-genome-view": "^3.6.5",
-    "@mui/icons-material": "^6.5.0",
+    "@jbrowse/plugin-authentication": "^4.1.1",
+    "@jbrowse/plugin-linear-genome-view": "^4.1.1",
+    "@mui/icons-material": "^7.3.7",
     "@types/jsonpath": "^0.2.0",
     "autosuggest-highlight": "^3.3.4",
     "bson-objectid": "^2.0.4",
@@ -71,18 +69,38 @@
     "tslib": "^2.3.1"
   },
   "devDependencies": {
-    "@jbrowse/cli": "^3.6.5",
-    "@jbrowse/core": "^3.6.5",
+    "@babel/core": "^7.28.6",
+    "@babel/plugin-proposal-class-properties": "^7.18.6",
+    "@babel/preset-env": "^7.28.6",
+    "@jbrowse/cli": "^4.1.1",
+    "@jbrowse/core": "^4.1.1",
     "@jbrowse/development-tools": "^2.2.1",
+    "@jbrowse/mobx-state-tree": "^5.5.0",
     "@jest/globals": "^29.0.3",
-    "@mui/material": "^7.0.0",
+    "@mui/material": "^7.3.7",
     "@mui/x-data-grid": "^8.0.0",
+    "@rollup/plugin-babel": "^6.1.0",
+    "@rollup/plugin-commonjs": "^29.0.0",
+    "@rollup/plugin-json": "^6.1.0",
+    "@rollup/plugin-node-resolve": "^16.0.3",
+    "@rollup/plugin-typescript": "^12.3.0",
     "@types/autosuggest-highlight": "^3",
+    "@types/babel-plugin-macros": "^3",
+    "@types/babel__core": "^7",
+    "@types/babel__preset-env": "^7",
     "@types/file-saver": "^2",
-    "@types/node": "^20.19.15",
+    "@types/lodash.merge": "^4",
+    "@types/node": "^24.10.9",
     "@types/prop-types": "^15",
     "@types/react": "^18.3.4",
     "@types/react-dom": "^18",
+    "babel-plugin-annotate-pure-calls": "^0.5.0",
+    "babel-plugin-dev-expression": "^0.2.3",
+    "babel-plugin-macros": "^3.1.0",
+    "babel-plugin-polyfill-regenerator": "^0.6.6",
+    "babel-plugin-transform-rename-import": "^2.3.0",
+    "builtin-modules": "^5.0.0",
+    "chalk": "^5.6.2",
     "cypress": "12.17.3",
     "cypress-image-diff-html-report": "^2.2.0",
     "cypress-image-diff-js": "^2.3.0",
@@ -90,31 +108,36 @@
     "fake-indexeddb": "^4.0.2",
     "jest": "^29.6.2",
     "jest-fetch-mock": "^3.0.3",
+    "jest-util": "^30.2.0",
     "librpc-web-mod": "^1.1.9",
+    "lodash.merge": "^4.6.2",
     "mobx": "^6.6.1",
     "mobx-react": "^7.2.1",
-    "mobx-state-tree": "^5.4.0",
     "npm-run-all": "^4.1.5",
     "prop-types": "^15.8.1",
     "react": "^18.2.0",
     "react-dom": "^18.2.0",
     "rimraf": "^3.0.2",
-    "rollup": "^2.79.2",
+    "rollup": "^4.57.0",
+    "rollup-plugin-external-globals": "^0.13.0",
+    "rollup-plugin-polyfill-node": "^0.13.0",
+    "rollup-plugin-sourcemaps": "^0.6.3",
+    "rollup-plugin-terser": "^7.0.2",
     "rxjs": "^7.4.0",
     "serve": "^14.0.1",
     "shx": "^0.3.3",
     "start-server-and-test": "^1.11.7",
-    "ts-jest": "^29.1.1",
+    "ts-jest": "^29.4.6",
     "ts-node": "^10.3.0",
     "tss-react": "^4.6.1",
     "typescript": "^5.5.3"
   },
   "peerDependencies": {
-    "@jbrowse/core": "^3.0.1",
-    "@mui/material": "^7.0.0",
+    "@jbrowse/core": "^4.1.1",
+    "@jbrowse/mobx-state-tree": "^5.5.0",
+    "@mui/material": "^7.3.7",
     "mobx": "^6.6.1",
     "mobx-react": "^9.0.0",
-    "mobx-state-tree": "^5.4.0",
     "prop-types": "^15.8.1",
     "react": "^18.2.0",
     "react-dom": "^18.2.0",
diff --git a/packages/jbrowse-plugin-apollo/rollup/babelPluginJBrowse.mjs b/packages/jbrowse-plugin-apollo/rollup/babelPluginJBrowse.mjs
new file mode 100644
index 000000000..aef0651ea
--- /dev/null
+++ b/packages/jbrowse-plugin-apollo/rollup/babelPluginJBrowse.mjs
@@ -0,0 +1,134 @@
+/* eslint-disable @typescript-eslint/no-unnecessary-condition */
+/* eslint-disable @typescript-eslint/no-unsafe-argument */
+/* eslint-disable @typescript-eslint/no-unsafe-return */
+/* eslint-disable @typescript-eslint/no-unsafe-call */
+/* eslint-disable @typescript-eslint/no-unsafe-assignment */
+/* eslint-disable @typescript-eslint/no-unsafe-member-access */
+// Based on https://github.com/jaredpalmer/tsdx/blob/8b91c747c2235ed4fbf853a39fb6800cbf70b2b3/src/babelPluginTsdx.ts
+
+import { createRequire } from 'node:module'
+
+import { createConfigItem } from '@babel/core'
+import { createBabelInputPluginFactory } from '@rollup/plugin-babel'
+import merge from 'lodash.merge'
+
+const require = createRequire(import.meta.url)
+
+// replace lodash with lodash-es, but not lodash/fp
+const replacements = [{ original: 'lodash(?!/fp)', replacement: 'lodash-es' }]
+
+function mergeConfigItems(type, ...configItemsToMerge) {
+  const mergedItems = []
+
+  for (const configItemToMerge of configItemsToMerge) {
+    for (const item of configItemToMerge) {
+      const itemToMergeWithIndex = mergedItems.findIndex(
+        (mergedItem) => mergedItem.file.resolved === item.file.resolved,
+      )
+
+      if (itemToMergeWithIndex === -1) {
+        mergedItems.push(item)
+        continue
+      }
+
+      mergedItems[itemToMergeWithIndex] = createConfigItem(
+        [
+          mergedItems[itemToMergeWithIndex].file.resolved,
+          merge(mergedItems[itemToMergeWithIndex].options, item.options),
+        ],
+        { type },
+      )
+    }
+  }
+
+  return mergedItems
+}
+
+function createConfigItems(type, items) {
+  return items.map(({ name, ...options }) => {
+    return createConfigItem([require.resolve(name), options], { type })
+  })
+}
+
+export const babelPluginJBrowse = createBabelInputPluginFactory(() => ({
+  // Passed the plugin options.
+  options({ custom: customOptions, ...pluginOptions }) {
+    return {
+      // Pull out any custom options that the plugin might have.
+      customOptions,
+
+      // Pass the options back with the two custom options removed.
+      pluginOptions,
+    }
+  },
+  config(config, { customOptions }) {
+    const defaultPlugins = createConfigItems(
+      'plugin',
+      [
+        // {
+        //   name: '@babel/plugin-transform-react-jsx',
+        //   pragma: customOptions.jsx || 'h',
+        //   pragmaFrag: customOptions.jsxFragment || 'Fragment',
+        // },
+        { name: 'babel-plugin-macros' },
+        { name: 'babel-plugin-annotate-pure-calls' },
+        { name: 'babel-plugin-dev-expression' },
+        customOptions.format !== 'cjs' && {
+          name: 'babel-plugin-transform-rename-import',
+          replacements,
+        },
+        {
+          name: 'babel-plugin-polyfill-regenerator',
+          // don't pollute global env as this is being used in a library
+          method: 'usage-pure',
+        },
+        { name: '@babel/plugin-proposal-class-properties' },
+      ].filter(Boolean),
+    )
+
+    const babelOptions = config.options || {}
+    babelOptions.presets = babelOptions.presets ?? []
+
+    const presetEnvIdx = babelOptions.presets.findIndex((preset) =>
+      preset.file.request.includes('@babel/preset-env'),
+    )
+
+    // if they use preset-env, merge their options with ours
+    if (presetEnvIdx === -1) {
+      // if no preset-env, add it & merge with their presets
+      const defaultPresets = createConfigItems('preset', [
+        {
+          name: '@babel/preset-env',
+          targets: customOptions.targets,
+          modules: false,
+        },
+      ])
+
+      babelOptions.presets = mergeConfigItems(
+        'preset',
+        defaultPresets,
+        babelOptions.presets,
+      )
+    } else {
+      const presetEnv = babelOptions.presets[presetEnvIdx]
+      babelOptions.presets[presetEnvIdx] = createConfigItem(
+        [
+          presetEnv.file.resolved,
+          merge({ targets: customOptions.targets }, presetEnv.options, {
+            modules: false,
+          }),
+        ],
+        { type: `preset` },
+      )
+    }
+
+    // Merge babelrc & our plugins together
+    babelOptions.plugins = mergeConfigItems(
+      'plugin',
+      defaultPlugins,
+      babelOptions.plugins ?? [],
+    )
+
+    return babelOptions
+  },
+}))
diff --git a/packages/jbrowse-plugin-apollo/rollup/createRollupConfig.mjs b/packages/jbrowse-plugin-apollo/rollup/createRollupConfig.mjs
new file mode 100644
index 000000000..2ac818eef
--- /dev/null
+++ b/packages/jbrowse-plugin-apollo/rollup/createRollupConfig.mjs
@@ -0,0 +1,262 @@
+/* eslint-disable @typescript-eslint/no-unsafe-return */
+/* eslint-disable @typescript-eslint/no-unsafe-member-access */
+/* eslint-disable @typescript-eslint/no-unsafe-call */
+/* eslint-disable @typescript-eslint/no-unsafe-assignment */
+import fs from 'node:fs'
+import path from 'node:path'
+
+import commonjs from '@rollup/plugin-commonjs'
+import json from '@rollup/plugin-json'
+import resolve, {
+  DEFAULTS as RESOLVE_DEFAULTS,
+} from '@rollup/plugin-node-resolve'
+import typescript from '@rollup/plugin-typescript'
+import nodeBuiltins from 'builtin-modules'
+import { defineConfig } from 'rollup'
+import externalGlobals from 'rollup-plugin-external-globals'
+import nodePolyfills from 'rollup-plugin-polyfill-node'
+import sourceMaps from 'rollup-plugin-sourcemaps'
+import { terser } from 'rollup-plugin-terser'
+
+import { babelPluginJBrowse } from './babelPluginJBrowse.mjs'
+import {
+  external,
+  omitUnresolved,
+  safePackageName,
+  writeIndex,
+} from './util.mjs'
+
+const appPath = fs.realpathSync(process.cwd())
+const packageJsonPath = path.join(appPath, 'package.json')
+const packageJsonText = fs.readFileSync(packageJsonPath, 'utf8')
+const packageJson = JSON.parse(packageJsonText)
+const packageName = safePackageName(packageJson.name || '')
+const umdName = `JBrowsePlugin${packageJson.config?.jbrowse?.plugin?.name}`
+
+const distPath = path.join(appPath, 'dist')
+const srcPath = path.join(appPath, 'src')
+
+const nodeEnv = process.env.NODE_ENV ?? 'production'
+
+function createGlobalMap(jbrowseGlobals, dotSyntax = false) {
+  const globalMap = {}
+  for (const global of jbrowseGlobals) {
+    globalMap[global] = dotSyntax
+      ? `JBrowseExports.${global}`
+      : `JBrowseExports["${global}"]`
+  }
+  return globalMap
+}
+
+let tsDeclarationGenerated = false
+
+function getPlugins(mode, jbrowseGlobals) {
+  const plugins = [
+    resolve({
+      mainFields: ['module', 'main', 'browser'],
+      extensions: [...RESOLVE_DEFAULTS.extensions, '.jsx'],
+      preferBuiltins: false,
+    }),
+    // all bundled external modules need to be converted from CJS to ESM
+    commonjs(),
+    json(),
+    typescript({
+      exclude: [
+        // all TS test files, regardless whether co-located or in test/ etc
+        '**/*.{spec,test}.ts{x,}',
+      ],
+      // moduleResolution: 'node',
+      // tsconfig: './tsconfig.json',
+      outDir: distPath,
+      // target: 'esnext',
+      ...(tsDeclarationGenerated
+        ? { declarationDir: distPath }
+        : { declaration: false, declarationMap: false }),
+    }),
+    (mode === 'cjs' || mode === 'esmBundle') &&
+      externalGlobals(createGlobalMap(jbrowseGlobals)),
+    babelPluginJBrowse({
+      exclude: ['node_modules/**', '__virtual__/**'],
+      custom: {
+        extractErrors: false,
+        format: mode === 'esmBundle' || mode === 'npm' ? 'esm' : mode,
+      },
+      babelHelpers: 'bundled',
+    }),
+    mode === 'npm' && sourceMaps(),
+    mode === 'npm' && writeIndex(packageName, distPath),
+    (mode === 'esmBundle' || mode === 'umd') &&
+      // By default, nodePolyfills only polyfills code in node_modules/. We set
+      // to null here to include the plugin source code itself (and for Yarn 2/3
+      // compatibility, since it doesn't use node_modules/).
+      nodePolyfills({ include: null }),
+    (mode === 'cjs' || mode === 'esmBundle') && omitUnresolved(),
+  ].filter(Boolean)
+
+  if (!tsDeclarationGenerated) {
+    tsDeclarationGenerated = true
+  }
+  return plugins
+}
+
+export function createRollupConfig(jbrowseGlobals, options) {
+  const includeUMD = Boolean(
+    options?.includeUMD === true || options?.includeUMD === undefined,
+  )
+  const includeCJS = Boolean(options?.includeCJS === true)
+  const includeESMBundle = Boolean(options?.includeESMBundle === true)
+  const includeNPM = Boolean(
+    options?.includeNPM === true || options?.includeNPM === undefined,
+  )
+  const npmConfig =
+    includeNPM &&
+    defineConfig({
+      input: path.join(srcPath, 'index.ts'),
+      external,
+      treeshake: { propertyReadSideEffects: false },
+      plugins: getPlugins('npm', jbrowseGlobals),
+      output: [
+        {
+          file: path.join(distPath, 'index.esm.js'),
+          format: 'esm',
+          freeze: false,
+          esModule: true,
+          sourcemap: true,
+          exports: 'named',
+        },
+        {
+          file: path.join(distPath, `${packageName}.cjs.development.js`),
+          format: 'cjs',
+          freeze: false,
+          esModule: true,
+          sourcemap: true,
+          exports: 'named',
+        },
+        nodeEnv === 'production' && {
+          file: path.join(distPath, `${packageName}.cjs.production.min.js`),
+          format: 'cjs',
+          freeze: false,
+          esModule: true,
+          sourcemap: true,
+          exports: 'named',
+          plugins: [
+            terser({
+              output: { comments: false },
+              compress: { keep_infinity: true, pure_getters: true, passes: 10 },
+              ecma: 5,
+              toplevel: true,
+            }),
+          ],
+        },
+      ].filter(Boolean),
+    })
+  const umdConfig =
+    includeUMD &&
+    defineConfig({
+      input: path.join(srcPath, 'index.ts'),
+      external: (id) => {
+        const isExternal = external(id)
+        if (isExternal && !jbrowseGlobals.includes(id)) {
+          return false
+        }
+        return isExternal
+      },
+      treeshake: { propertyReadSideEffects: false },
+      plugins: getPlugins('umd', jbrowseGlobals),
+      output: [
+        {
+          file: path.join(distPath, `${packageName}.umd.development.js`),
+          format: 'umd',
+          name: umdName,
+          freeze: false,
+          esModule: true,
+          sourcemap: true,
+          exports: 'named',
+          inlineDynamicImports: true,
+          globals: createGlobalMap(jbrowseGlobals, true),
+        },
+        nodeEnv === 'production' && {
+          file: path.join(distPath, `${packageName}.umd.production.min.js`),
+          format: 'umd',
+          name: umdName,
+          freeze: false,
+          esModule: true,
+          sourcemap: true,
+          exports: 'named',
+          inlineDynamicImports: true,
+          globals: createGlobalMap(jbrowseGlobals, true),
+          plugins: [
+            terser({
+              output: { comments: false },
+              compress: { keep_infinity: true, pure_getters: true, passes: 10 },
+              ecma: 5,
+              toplevel: true,
+            }),
+          ],
+        },
+      ].filter(Boolean),
+      watch: { clearScreen: false },
+    })
+  const esmBundleConfig =
+    includeESMBundle &&
+    defineConfig({
+      input: path.join(srcPath, 'index.ts'),
+      external: (id) => {
+        const isExternal = external(id)
+        if (isExternal && !jbrowseGlobals.includes(id)) {
+          return false
+        }
+        return isExternal
+      },
+      treeshake: { propertyReadSideEffects: false, moduleSideEffects: false },
+      plugins: getPlugins('esmBundle', jbrowseGlobals),
+      output: [
+        {
+          file: path.join(distPath, `${packageName}.esm.js`),
+          format: 'esm',
+          freeze: false,
+          esModule: true,
+          sourcemap: true,
+          exports: 'named',
+          inlineDynamicImports: true,
+        },
+      ],
+      watch: { clearScreen: false },
+    })
+  const cjsConfig =
+    includeCJS &&
+    defineConfig({
+      input: path.join(srcPath, 'index.ts'),
+      external: (id) => {
+        if (nodeBuiltins.includes(id)) {
+          return true
+        }
+        const isExternal = external(id)
+        if (isExternal && !jbrowseGlobals.includes(id)) {
+          return false
+        }
+        return isExternal
+      },
+      treeshake: { propertyReadSideEffects: false, moduleSideEffects: false },
+      plugins: getPlugins('cjs', jbrowseGlobals),
+      output: [
+        {
+          file: path.join(distPath, `${packageName}.cjs.js`),
+          format: 'cjs',
+          freeze: false,
+          esModule: true,
+          sourcemap: true,
+          exports: 'named',
+          inlineDynamicImports: true,
+        },
+      ],
+      watch: { clearScreen: false },
+    })
+  const configs = []
+  for (const conf of [umdConfig, esmBundleConfig, npmConfig, cjsConfig]) {
+    if (conf) {
+      configs.push(conf)
+    }
+  }
+  return defineConfig(configs)
+}
diff --git a/packages/jbrowse-plugin-apollo/rollup.config.js b/packages/jbrowse-plugin-apollo/rollup/rollup.config.mjs
similarity index 88%
rename from packages/jbrowse-plugin-apollo/rollup.config.js
rename to packages/jbrowse-plugin-apollo/rollup/rollup.config.mjs
index 3c07910a1..9b140945a 100644
--- a/packages/jbrowse-plugin-apollo/rollup.config.js
+++ b/packages/jbrowse-plugin-apollo/rollup/rollup.config.mjs
@@ -1,7 +1,8 @@
 /** @type {import('rollup').RollupOptions} */
 
 import globals from '@jbrowse/core/ReExports/list'
-import { createRollupConfig } from '@jbrowse/development-tools'
+
+import { createRollupConfig } from './createRollupConfig.mjs'
 
 function stringToBoolean(string) {
   if (string === undefined) {
@@ -32,7 +33,7 @@ for (const config of rollupConfig) {
   config.onwarn = (warning, warn) => {
     if (
       warning.code === 'MODULE_LEVEL_DIRECTIVE' &&
-      warning.message.includes(`'use client'`)
+      warning.message.includes(`use client`)
     ) {
       return
     }
diff --git a/packages/jbrowse-plugin-apollo/rollup/util.mjs b/packages/jbrowse-plugin-apollo/rollup/util.mjs
new file mode 100644
index 000000000..ac896476e
--- /dev/null
+++ b/packages/jbrowse-plugin-apollo/rollup/util.mjs
@@ -0,0 +1,72 @@
+/* eslint-disable @typescript-eslint/no-unsafe-assignment */
+/* eslint-disable @typescript-eslint/no-unsafe-argument */
+/* eslint-disable @typescript-eslint/no-unsafe-return */
+/* eslint-disable @typescript-eslint/no-unsafe-call */
+/* eslint-disable @typescript-eslint/no-unsafe-member-access */
+import fs from 'node:fs'
+import path from 'node:path'
+
+import chalk from 'chalk'
+
+export function safePackageName(name) {
+  return name
+    .toLowerCase()
+    .replaceAll(/(^@.*\/)|((^[^a-zA-Z]+)|[^\w.-])|([^a-zA-Z0-9]+$)/g, '')
+}
+
+export function external(id) {
+  if (id.startsWith('regenerator-runtime')) {
+    return false
+  }
+  return !id.startsWith('.') && !path.isAbsolute(id)
+}
+
+export function writeIndex(packageName, distPath) {
+  return {
+    name: 'write-index-file',
+    generateBundle() {
+      const baseLine = `module.exports = require('./${packageName}`
+      const contents = `'use strict'
+
+if (process.env.NODE_ENV === 'production') {
+${baseLine}.cjs.production.min.js')
+} else {
+${baseLine}.cjs.development.js')
+}
+`
+      if (!fs.existsSync(distPath)) {
+        fs.mkdirSync(distPath, { recursive: true })
+      }
+      fs.writeFileSync(path.join(distPath, 'index.js'), contents)
+    },
+  }
+}
+
+export function omitUnresolved() {
+  const suffix = '?unresolved'
+  return {
+    name: 'logger',
+    async resolveId(source, importer, options) {
+      const resolution = await this.resolve(source, importer, {
+        skipSelf: true,
+        ...options,
+      })
+      if (!resolution) {
+        return `${source}${suffix}`
+      }
+      return null
+    },
+    load(id) {
+      if (id.endsWith(suffix)) {
+        const importee = id.slice(0, -suffix.length)
+        console.warn(
+          chalk.bold.yellow(
+            `Omitting ${importee} from the build because it could not be resolved`,
+          ),
+        )
+        return `export default {};`
+      }
+      return null
+    },
+  }
+}
diff --git a/packages/jbrowse-plugin-apollo/src/ApolloInternetAccount/components/AuthTypeSelector.tsx b/packages/jbrowse-plugin-apollo/src/ApolloInternetAccount/components/AuthTypeSelector.tsx
index b6387f9e8..5e80ee088 100644
--- a/packages/jbrowse-plugin-apollo/src/ApolloInternetAccount/components/AuthTypeSelector.tsx
+++ b/packages/jbrowse-plugin-apollo/src/ApolloInternetAccount/components/AuthTypeSelector.tsx
@@ -1,5 +1,6 @@
 /* eslint-disable @typescript-eslint/use-unknown-in-catch-callback-variable */
 import { isAbortException } from '@jbrowse/core/util/aborting'
+import { makeStyles } from '@jbrowse/core/util/tss-react'
 import {
   Button,
   DialogActions,
@@ -8,7 +9,6 @@ import {
   Divider,
 } from '@mui/material'
 import React, { useEffect, useState } from 'react'
-import { makeStyles } from 'tss-react/mui'
 
 import { Dialog } from '../../components/Dialog'
 import { createFetchErrorMessage } from '../../util'
diff --git a/packages/jbrowse-plugin-apollo/src/ApolloInternetAccount/components/LoginButtons.tsx b/packages/jbrowse-plugin-apollo/src/ApolloInternetAccount/components/LoginButtons.tsx
index f7f60b63b..752f64b4d 100644
--- a/packages/jbrowse-plugin-apollo/src/ApolloInternetAccount/components/LoginButtons.tsx
+++ b/packages/jbrowse-plugin-apollo/src/ApolloInternetAccount/components/LoginButtons.tsx
@@ -1,7 +1,7 @@
+import { makeStyles } from '@jbrowse/core/util/tss-react'
 import AccountCircleIcon from '@mui/icons-material/AccountCircle'
 import { Button, type ButtonProps } from '@mui/material'
 import React from 'react'
-import { makeStyles } from 'tss-react/mui'
 
 import { Google, Microsoft } from './LoginIcons'
 
diff --git a/packages/jbrowse-plugin-apollo/src/ApolloInternetAccount/configSchema.ts b/packages/jbrowse-plugin-apollo/src/ApolloInternetAccount/configSchema.ts
index 09e670135..f6092cbe8 100644
--- a/packages/jbrowse-plugin-apollo/src/ApolloInternetAccount/configSchema.ts
+++ b/packages/jbrowse-plugin-apollo/src/ApolloInternetAccount/configSchema.ts
@@ -1,6 +1,6 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration'
 import { BaseInternetAccountConfig } from '@jbrowse/core/pluggableElementTypes'
-import { type Instance } from 'mobx-state-tree'
+import { type Instance } from '@jbrowse/mobx-state-tree'
 
 const ApolloConfigSchema = ConfigurationSchema(
   'ApolloInternetAccount',
diff --git a/packages/jbrowse-plugin-apollo/src/ApolloInternetAccount/model.ts b/packages/jbrowse-plugin-apollo/src/ApolloInternetAccount/model.ts
index f474cc506..7cd37ee37 100644
--- a/packages/jbrowse-plugin-apollo/src/ApolloInternetAccount/model.ts
+++ b/packages/jbrowse-plugin-apollo/src/ApolloInternetAccount/model.ts
@@ -22,8 +22,14 @@ import {
   isAbstractMenuManager,
   isElectron,
 } from '@jbrowse/core/util'
+import {
+  type Instance,
+  flow,
+  getRoot,
+  isAlive,
+  types,
+} from '@jbrowse/mobx-state-tree'
 import { autorun } from 'mobx'
-import { type Instance, flow, getRoot, isAlive, types } from 'mobx-state-tree'
 import { io } from 'socket.io-client'
 
 import { addTopLevelAdminMenus } from '../menus/topLevelMenuAdmin'
diff --git a/packages/jbrowse-plugin-apollo/src/ApolloJobModel.ts b/packages/jbrowse-plugin-apollo/src/ApolloJobModel.ts
index f59e0350f..0b928d2c8 100644
--- a/packages/jbrowse-plugin-apollo/src/ApolloJobModel.ts
+++ b/packages/jbrowse-plugin-apollo/src/ApolloJobModel.ts
@@ -5,15 +5,15 @@ import {
   getSession,
   isSessionModelWithWidgets,
 } from '@jbrowse/core/util'
-import { types } from 'mobx-state-tree'
+import { types } from '@jbrowse/mobx-state-tree'
 
-interface JobsEntry {
+export interface JobsEntry {
   name: string
   cancelCallback?: () => void
   progressPct?: number
   statusMessage?: string
 }
-interface JobsListModel {
+export interface JobsListModel {
   id: number
   type: 'JobsListWidget'
   jobs: JobsEntry[]
diff --git a/packages/jbrowse-plugin-apollo/src/BackendDrivers/DesktopFileDriver.ts b/packages/jbrowse-plugin-apollo/src/BackendDrivers/DesktopFileDriver.ts
index 2eb28c304..47d7afde3 100644
--- a/packages/jbrowse-plugin-apollo/src/BackendDrivers/DesktopFileDriver.ts
+++ b/packages/jbrowse-plugin-apollo/src/BackendDrivers/DesktopFileDriver.ts
@@ -16,7 +16,7 @@ import {
 import { type GFF3Item, formatSync } from '@gmod/gff'
 import { getConf } from '@jbrowse/core/configuration'
 import { type Region, getSession } from '@jbrowse/core/util'
-import { getSnapshot } from 'mobx-state-tree'
+import { getSnapshot } from '@jbrowse/mobx-state-tree'
 
 import { checkFeatures, loadAssemblyIntoClient } from '../util'
 
diff --git a/packages/jbrowse-plugin-apollo/src/ChangeManager.ts b/packages/jbrowse-plugin-apollo/src/ChangeManager.ts
index 2d11bcb0f..b5a474e02 100644
--- a/packages/jbrowse-plugin-apollo/src/ChangeManager.ts
+++ b/packages/jbrowse-plugin-apollo/src/ChangeManager.ts
@@ -11,7 +11,7 @@ import {
   validationRegistry,
 } from '@apollo-annotation/shared'
 import { getSession } from '@jbrowse/core/util'
-import { type IAnyStateTreeNode } from 'mobx-state-tree'
+import { type IAnyStateTreeNode } from '@jbrowse/mobx-state-tree'
 
 import { type ApolloSessionModel } from './session'
 
diff --git a/packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/ApolloFeatureDetailsWidget.tsx b/packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/ApolloFeatureDetailsWidget.tsx
index a4865a0c2..0c0478067 100644
--- a/packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/ApolloFeatureDetailsWidget.tsx
+++ b/packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/ApolloFeatureDetailsWidget.tsx
@@ -1,4 +1,5 @@
 import { getSession } from '@jbrowse/core/util'
+import { makeStyles } from '@jbrowse/core/util/tss-react'
 import ExpandMoreIcon from '@mui/icons-material/ExpandMore'
 import {
   Accordion,
@@ -8,7 +9,6 @@ import {
 } from '@mui/material'
 import { observer } from 'mobx-react'
 import React, { useEffect, useState } from 'react'
-import { makeStyles } from 'tss-react/mui'
 
 import { type ApolloSessionModel } from '../session'
 
diff --git a/packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/ApolloTranscriptDetailsWidget.tsx b/packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/ApolloTranscriptDetailsWidget.tsx
index b00cc311a..d2271604a 100644
--- a/packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/ApolloTranscriptDetailsWidget.tsx
+++ b/packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/ApolloTranscriptDetailsWidget.tsx
@@ -5,6 +5,8 @@ import {
   getEnv,
   getSession,
 } from '@jbrowse/core/util'
+import { makeStyles } from '@jbrowse/core/util/tss-react'
+import { getRoot } from '@jbrowse/mobx-state-tree'
 import ExpandMoreIcon from '@mui/icons-material/ExpandMore'
 import InfoIcon from '@mui/icons-material/Info'
 import {
@@ -15,9 +17,7 @@ import {
   Typography,
 } from '@mui/material'
 import { observer } from 'mobx-react'
-import { getRoot } from 'mobx-state-tree'
 import React, { useEffect, useState } from 'react'
-import { makeStyles } from 'tss-react/mui'
 
 import { type ApolloInternetAccountModel } from '../ApolloInternetAccount/model'
 import { type ApolloSessionModel } from '../session'
diff --git a/packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/AttributeKey.tsx b/packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/AttributeKey.tsx
index 50133509a..c1b3d44df 100644
--- a/packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/AttributeKey.tsx
+++ b/packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/AttributeKey.tsx
@@ -4,10 +4,10 @@ import {
   isGFFColumnInternal,
   isGFFInternalAttribute,
 } from '@apollo-annotation/shared'
+import { makeStyles } from '@jbrowse/core/util/tss-react'
 import InfoIcon from '@mui/icons-material/Info'
 import { Chip, Tooltip, Typography } from '@mui/material'
 import React from 'react'
-import { makeStyles } from 'tss-react/mui'
 
 const useStyles = makeStyles()((theme) => ({
   attributeKey: {
diff --git a/packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/Attributes.tsx b/packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/Attributes.tsx
index 2ff3c122e..2951224ec 100644
--- a/packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/Attributes.tsx
+++ b/packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/Attributes.tsx
@@ -1,6 +1,8 @@
 import { type AnnotationFeature } from '@apollo-annotation/mst'
 import { FeatureAttributeChange } from '@apollo-annotation/shared'
 import { type AbstractSessionModel, getEnv } from '@jbrowse/core/util'
+import { makeStyles } from '@jbrowse/core/util/tss-react'
+import { getSnapshot } from '@jbrowse/mobx-state-tree'
 import DeleteIcon from '@mui/icons-material/Delete'
 import EditIcon from '@mui/icons-material/Edit'
 import MoreHorizIcon from '@mui/icons-material/MoreHoriz'
@@ -18,9 +20,7 @@ import {
 } from '@mui/material'
 import { entries } from 'mobx'
 import { observer } from 'mobx-react'
-import { getSnapshot } from 'mobx-state-tree'
 import React, { useState } from 'react'
-import { makeStyles } from 'tss-react/mui'
 
 import { type ApolloSessionModel } from '../session'
 
diff --git a/packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/Sequence.tsx b/packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/Sequence.tsx
index 7662d423c..eb2b8abc6 100644
--- a/packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/Sequence.tsx
+++ b/packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/Sequence.tsx
@@ -1,9 +1,9 @@
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 import { type AnnotationFeature } from '@apollo-annotation/mst'
 import { splitStringIntoChunks } from '@apollo-annotation/shared'
+import { makeStyles } from '@jbrowse/core/util/tss-react'
 import { observer } from 'mobx-react'
 import React from 'react'
-import { makeStyles } from 'tss-react/mui'
 
 import { type ApolloSessionModel } from '../session'
 
diff --git a/packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/model.ts b/packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/model.ts
index 7eb966e48..b79b57242 100644
--- a/packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/model.ts
+++ b/packages/jbrowse-plugin-apollo/src/FeatureDetailsWidget/model.ts
@@ -6,13 +6,13 @@ import {
 } from '@apollo-annotation/mst'
 import { getSession } from '@jbrowse/core/util'
 import { ElementId } from '@jbrowse/core/util/types/mst'
-import { autorun } from 'mobx'
 import {
   type Instance,
   type SnapshotIn,
   addDisposer,
   types,
-} from 'mobx-state-tree'
+} from '@jbrowse/mobx-state-tree'
+import { autorun } from 'mobx'
 
 import { type ApolloSessionModel } from '../session'
 
diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/components/LinearApolloDisplay.tsx b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/components/LinearApolloDisplay.tsx
index 3f7976ef0..ea356ae56 100644
--- a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/components/LinearApolloDisplay.tsx
+++ b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/components/LinearApolloDisplay.tsx
@@ -1,6 +1,7 @@
 /* eslint-disable @typescript-eslint/unbound-method */
+
 /* eslint-disable @typescript-eslint/no-misused-promises */
-/* eslint-disable @typescript-eslint/no-unnecessary-condition */
+
 import { Menu, type MenuItem } from '@jbrowse/core/ui'
 import { getContainingView } from '@jbrowse/core/util'
 import { type LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
@@ -84,6 +85,8 @@ export const LinearApolloDisplay = observer(function LinearApolloDisplay(
             <CircularProgress size="18px" />
           </div>
         ) : null}
+        {/* This type is wrong in @jbrowse/core */}
+        {/* eslint-disable-next-line @typescript-eslint/no-unnecessary-condition */}
         {message ? (
           <Alert
             severity="warning"
@@ -156,7 +159,6 @@ export const LinearApolloDisplay = observer(function LinearApolloDisplay(
                   ? { top: contextCoord[1], left: contextCoord[0] }
                   : undefined
               }
-              style={{ zIndex: theme.zIndex.tooltip }}
               menuItems={contextMenuItems}
             />
           </>
diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/base.ts b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/base.ts
index b506f2d48..450014c86 100644
--- a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/base.ts
+++ b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/base.ts
@@ -5,8 +5,11 @@
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 import { type AnnotationFeature } from '@apollo-annotation/mst'
 import type PluginManager from '@jbrowse/core/PluginManager'
-import { ConfigurationReference, getConf } from '@jbrowse/core/configuration'
-import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration/configurationSchema'
+import {
+  type AnyConfigurationSchemaType,
+  ConfigurationReference,
+  getConf,
+} from '@jbrowse/core/configuration'
 import { BaseDisplay } from '@jbrowse/core/pluggableElementTypes'
 import {
   type AbstractSessionModel,
@@ -16,9 +19,15 @@ import {
 } from '@jbrowse/core/util'
 import { getParentRenderProps } from '@jbrowse/core/util/tracks'
 // import type LinearGenomeViewPlugin from '@jbrowse/plugin-linear-genome-view'
+import {
+  addDisposer,
+  cast,
+  getRoot,
+  getSnapshot,
+  types,
+} from '@jbrowse/mobx-state-tree'
 import { type LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 import { autorun } from 'mobx'
-import { addDisposer, cast, getRoot, getSnapshot, types } from 'mobx-state-tree'
 
 import { type ApolloInternetAccountModel } from '../../ApolloInternetAccount/model'
 import { FilterFeatures } from '../../components/FilterFeatures'
diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/index.ts b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/index.ts
index f1131b62f..f745581f9 100644
--- a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/index.ts
+++ b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/index.ts
@@ -1,6 +1,6 @@
 import type PluginManager from '@jbrowse/core/PluginManager'
-import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration/configurationSchema'
-import { type Instance, types } from 'mobx-state-tree'
+import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration'
+import { type Instance, types } from '@jbrowse/mobx-state-tree'
 
 import { TabularEditorStateModelType } from '../../TabularEditor'
 
diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/layouts.ts b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/layouts.ts
index 12c467570..e4e93949d 100644
--- a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/layouts.ts
+++ b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/layouts.ts
@@ -2,10 +2,10 @@
 
 import { type AnnotationFeature } from '@apollo-annotation/mst'
 import type PluginManager from '@jbrowse/core/PluginManager'
-import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration/configurationSchema'
+import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration'
 import { type AbstractSessionModel, doesIntersect2 } from '@jbrowse/core/util'
+import { addDisposer, isAlive } from '@jbrowse/mobx-state-tree'
 import { autorun, observable } from 'mobx'
-import { addDisposer, isAlive } from 'mobx-state-tree'
 
 import { type ApolloSessionModel } from '../../session'
 import { boxGlyph, geneGlyph, genericChildGlyph } from '../glyphs'
diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/mouseEvents.ts b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/mouseEvents.ts
index d575e280f..b34cbdbe0 100644
--- a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/mouseEvents.ts
+++ b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/mouseEvents.ts
@@ -4,10 +4,10 @@ import {
   LocationStartChange,
 } from '@apollo-annotation/shared'
 import type PluginManager from '@jbrowse/core/PluginManager'
-import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration/configurationSchema'
+import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration'
 import { type MenuItem } from '@jbrowse/core/ui'
+import { type Instance, addDisposer } from '@jbrowse/mobx-state-tree'
 import { autorun } from 'mobx'
-import { type Instance, addDisposer } from 'mobx-state-tree'
 import { type CSSProperties } from 'react'
 
 import {
diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/rendering.ts b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/rendering.ts
index dddc3dec5..bf8acdccb 100644
--- a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/rendering.ts
+++ b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/rendering.ts
@@ -1,10 +1,10 @@
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 import type PluginManager from '@jbrowse/core/PluginManager'
-import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration/configurationSchema'
+import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration'
 import { doesIntersect2 } from '@jbrowse/core/util'
+import { type Instance, addDisposer, types } from '@jbrowse/mobx-state-tree'
 import { type Theme, createTheme } from '@mui/material'
 import { autorun } from 'mobx'
-import { type Instance, addDisposer, types } from 'mobx-state-tree'
 
 import { type ApolloSessionModel } from '../../session'
 
diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloReferenceSequenceDisplay/components/LinearApolloReferenceSequenceDisplay.tsx b/packages/jbrowse-plugin-apollo/src/LinearApolloReferenceSequenceDisplay/components/LinearApolloReferenceSequenceDisplay.tsx
index 70be3328b..ab91cfd6d 100644
--- a/packages/jbrowse-plugin-apollo/src/LinearApolloReferenceSequenceDisplay/components/LinearApolloReferenceSequenceDisplay.tsx
+++ b/packages/jbrowse-plugin-apollo/src/LinearApolloReferenceSequenceDisplay/components/LinearApolloReferenceSequenceDisplay.tsx
@@ -1,4 +1,5 @@
 /* eslint-disable @typescript-eslint/unbound-method */
+
 /* eslint-disable @typescript-eslint/no-misused-promises */
 import { getContainingView } from '@jbrowse/core/util'
 import { type LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
@@ -34,6 +35,7 @@ export const LinearApolloReferenceSequenceDisplay = observer(
     const lgv = getContainingView(model) as unknown as LinearGenomeViewModel
     const message = regionCannotBeRendered()
 
+    // This type is wrong in @jbrowse/core
     // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
     if (message) {
       return (
diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloReferenceSequenceDisplay/stateModel/base.ts b/packages/jbrowse-plugin-apollo/src/LinearApolloReferenceSequenceDisplay/stateModel/base.ts
index 7af793c60..add1343f4 100644
--- a/packages/jbrowse-plugin-apollo/src/LinearApolloReferenceSequenceDisplay/stateModel/base.ts
+++ b/packages/jbrowse-plugin-apollo/src/LinearApolloReferenceSequenceDisplay/stateModel/base.ts
@@ -5,8 +5,11 @@
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 import { type AnnotationFeature } from '@apollo-annotation/mst'
 import type PluginManager from '@jbrowse/core/PluginManager'
-import { ConfigurationReference, getConf } from '@jbrowse/core/configuration'
-import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration/configurationSchema'
+import {
+  type AnyConfigurationSchemaType,
+  ConfigurationReference,
+  getConf,
+} from '@jbrowse/core/configuration'
 import { BaseDisplay } from '@jbrowse/core/pluggableElementTypes'
 import {
   type AbstractSessionModel,
@@ -15,9 +18,9 @@ import {
 } from '@jbrowse/core/util'
 import { getParentRenderProps } from '@jbrowse/core/util/tracks'
 // import type LinearGenomeViewPlugin from '@jbrowse/plugin-linear-genome-view'
+import { addDisposer, getRoot, types } from '@jbrowse/mobx-state-tree'
 import { type LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 import { autorun } from 'mobx'
-import { addDisposer, getRoot, types } from 'mobx-state-tree'
 
 import { type ApolloInternetAccountModel } from '../../ApolloInternetAccount/model'
 import { type ApolloSessionModel, type HoveredFeature } from '../../session'
diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloReferenceSequenceDisplay/stateModel/index.ts b/packages/jbrowse-plugin-apollo/src/LinearApolloReferenceSequenceDisplay/stateModel/index.ts
index d61c257b3..49954d5bb 100644
--- a/packages/jbrowse-plugin-apollo/src/LinearApolloReferenceSequenceDisplay/stateModel/index.ts
+++ b/packages/jbrowse-plugin-apollo/src/LinearApolloReferenceSequenceDisplay/stateModel/index.ts
@@ -1,6 +1,6 @@
 import type PluginManager from '@jbrowse/core/PluginManager'
-import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration/configurationSchema'
-import { type Instance } from 'mobx-state-tree'
+import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration'
+import { type Instance } from '@jbrowse/mobx-state-tree'
 
 import { renderingModelFactory } from './rendering'
 
diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloReferenceSequenceDisplay/stateModel/rendering.ts b/packages/jbrowse-plugin-apollo/src/LinearApolloReferenceSequenceDisplay/stateModel/rendering.ts
index 3a3a04da3..02e10b1ef 100644
--- a/packages/jbrowse-plugin-apollo/src/LinearApolloReferenceSequenceDisplay/stateModel/rendering.ts
+++ b/packages/jbrowse-plugin-apollo/src/LinearApolloReferenceSequenceDisplay/stateModel/rendering.ts
@@ -1,9 +1,9 @@
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 import type PluginManager from '@jbrowse/core/PluginManager'
-import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration/configurationSchema'
+import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration'
+import { type Instance, addDisposer } from '@jbrowse/mobx-state-tree'
 import { type Theme, createTheme } from '@mui/material'
 import { autorun } from 'mobx'
-import { type Instance, addDisposer } from 'mobx-state-tree'
 
 import { drawSequenceOverlay } from '../drawSequenceOverlay'
 import { drawSequenceTrack } from '../drawSequenceTrack'
diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/components/LinearApolloSixFrameDisplay.tsx b/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/components/LinearApolloSixFrameDisplay.tsx
index dbcd03bf3..30ea241f7 100644
--- a/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/components/LinearApolloSixFrameDisplay.tsx
+++ b/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/components/LinearApolloSixFrameDisplay.tsx
@@ -1,6 +1,7 @@
 /* eslint-disable @typescript-eslint/unbound-method */
+
 /* eslint-disable @typescript-eslint/no-misused-promises */
-/* eslint-disable @typescript-eslint/no-unnecessary-condition */
+
 import { type CheckResultI } from '@apollo-annotation/mst'
 import { Menu, type MenuItem } from '@jbrowse/core/ui'
 import {
@@ -64,6 +65,7 @@ export const LinearApolloSixFrameDisplay = observer(
     }, [theme, setTheme])
     const [contextCoord, setContextCoord] = useState<Coord>()
     const [contextMenuItems, setContextMenuItems] = useState<MenuItem[]>([])
+
     const message = regionCannotBeRendered()
     if (!isShown) {
       return null
@@ -94,6 +96,8 @@ export const LinearApolloSixFrameDisplay = observer(
               <LockIcon />
             </div>
           ) : null}
+          {/* This type is wrong in @jbrowse/core */}
+          {/* eslint-disable-next-line @typescript-eslint/no-unnecessary-condition */}
           {message ? (
             <Alert
               severity="warning"
diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/glyphs/GeneGlyph.ts b/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/glyphs/GeneGlyph.ts
index 373c131de..0cd64f97e 100644
--- a/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/glyphs/GeneGlyph.ts
+++ b/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/glyphs/GeneGlyph.ts
@@ -11,10 +11,10 @@ import {
   intersection2,
   measureText,
 } from '@jbrowse/core/util'
+import { getSnapshot } from '@jbrowse/mobx-state-tree'
 import { type LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 import { alpha } from '@mui/material'
 import equal from 'fast-deep-equal/es6'
-import { getSnapshot } from 'mobx-state-tree'
 
 import { MergeExons, SplitExon } from '../../components'
 import { FilterTranscripts } from '../../components/FilterTranscripts'
diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/base.ts b/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/base.ts
index 8f50b5196..86fb6f19b 100644
--- a/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/base.ts
+++ b/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/base.ts
@@ -5,8 +5,11 @@
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 import { type AnnotationFeature } from '@apollo-annotation/mst'
 import type PluginManager from '@jbrowse/core/PluginManager'
-import { ConfigurationReference, getConf } from '@jbrowse/core/configuration'
-import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration/configurationSchema'
+import {
+  type AnyConfigurationSchemaType,
+  ConfigurationReference,
+  getConf,
+} from '@jbrowse/core/configuration'
 import { BaseDisplay } from '@jbrowse/core/pluggableElementTypes'
 import {
   type AbstractSessionModel,
@@ -16,9 +19,15 @@ import {
 } from '@jbrowse/core/util'
 import { getParentRenderProps } from '@jbrowse/core/util/tracks'
 // import type LinearGenomeViewPlugin from '@jbrowse/plugin-linear-genome-view'
+import {
+  addDisposer,
+  cast,
+  getRoot,
+  getSnapshot,
+  types,
+} from '@jbrowse/mobx-state-tree'
 import { type LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 import { autorun } from 'mobx'
-import { addDisposer, cast, getRoot, getSnapshot, types } from 'mobx-state-tree'
 
 import { type ApolloInternetAccountModel } from '../../ApolloInternetAccount/model'
 import { FilterFeatures } from '../../components/FilterFeatures'
diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/index.ts b/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/index.ts
index 980ffc9bc..301dcd311 100644
--- a/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/index.ts
+++ b/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/index.ts
@@ -1,6 +1,6 @@
 import type PluginManager from '@jbrowse/core/PluginManager'
-import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration/configurationSchema'
-import { type Instance, types } from 'mobx-state-tree'
+import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration'
+import { type Instance, types } from '@jbrowse/mobx-state-tree'
 
 import { TabularEditorStateModelType } from '../../TabularEditor'
 
diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/layouts.ts b/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/layouts.ts
index 3c2a0e461..961cafe96 100644
--- a/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/layouts.ts
+++ b/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/layouts.ts
@@ -2,14 +2,14 @@
 
 import { type AnnotationFeature } from '@apollo-annotation/mst'
 import type PluginManager from '@jbrowse/core/PluginManager'
-import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration/configurationSchema'
+import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration'
 import {
   type AbstractSessionModel,
   doesIntersect2,
   getFrame,
 } from '@jbrowse/core/util'
+import { addDisposer, isAlive } from '@jbrowse/mobx-state-tree'
 import { autorun, observable } from 'mobx'
-import { addDisposer, isAlive } from 'mobx-state-tree'
 
 import { type ApolloSessionModel } from '../../session'
 import { geneGlyph } from '../glyphs'
diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/mouseEvents.ts b/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/mouseEvents.ts
index e764ec683..192bedb37 100644
--- a/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/mouseEvents.ts
+++ b/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/mouseEvents.ts
@@ -4,11 +4,11 @@ import {
   LocationStartChange,
 } from '@apollo-annotation/shared'
 import type PluginManager from '@jbrowse/core/PluginManager'
-import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration/configurationSchema'
+import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration'
 import { type MenuItem } from '@jbrowse/core/ui'
 import { getFrame } from '@jbrowse/core/util'
+import { type Instance, addDisposer, cast } from '@jbrowse/mobx-state-tree'
 import { autorun } from 'mobx'
-import { type Instance, addDisposer, cast } from 'mobx-state-tree'
 import { type CSSProperties } from 'react'
 
 import {
diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/rendering.ts b/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/rendering.ts
index 5d5622709..6a932bc24 100644
--- a/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/rendering.ts
+++ b/packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/rendering.ts
@@ -1,15 +1,15 @@
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 import type PluginManager from '@jbrowse/core/PluginManager'
-import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration/configurationSchema'
+import { type AnyConfigurationSchemaType } from '@jbrowse/core/configuration'
 import {
   defaultCodonTable,
   doesIntersect2,
   getFrame,
   revcom,
 } from '@jbrowse/core/util'
+import { type Instance, addDisposer, types } from '@jbrowse/mobx-state-tree'
 import { type Theme, createTheme } from '@mui/material'
 import { autorun } from 'mobx'
-import { type Instance, addDisposer, types } from 'mobx-state-tree'
 
 import { type ApolloSessionModel } from '../../session'
 import { codonColorCode } from '../../util/displayUtils'
diff --git a/packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/fulltext.ts b/packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/fulltext.ts
index 3f0ab451c..576d1f617 100644
--- a/packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/fulltext.ts
+++ b/packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/fulltext.ts
@@ -28,7 +28,14 @@ function jsonPathQuery(
   if (path === PREFIXED_ID_PATH) {
     return [applyPrefixes(node.id, prefixes)]
   }
-  return jsonpath.query(node, path)
+  let response
+  try {
+    response = jsonpath.query(node, path)
+  } catch {
+    // eslint-disable-next-line unicorn/prefer-structured-clone
+    response = jsonpath.query(JSON.parse(JSON.stringify(node)), path)
+  }
+  return response
 }
 
 function wordsInString(str: string) {
diff --git a/packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/index.test.ts b/packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/index.test.ts
index 8c9d05440..a57f2dcfa 100644
--- a/packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/index.test.ts
+++ b/packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/index.test.ts
@@ -1,6 +1,7 @@
 /* eslint-disable @typescript-eslint/no-unsafe-return */
 /* eslint-disable @typescript-eslint/no-unsafe-assignment */
 import path from 'node:path'
+import { fileURLToPath } from 'node:url'
 
 import { beforeAll, describe, expect, it, jest } from '@jest/globals'
 
@@ -8,6 +9,8 @@ import { type OntologyClass, isOntologyClass } from '..'
 
 import OntologyStore from '.'
 
+const __dirname = path.dirname(fileURLToPath(import.meta.url))
+
 jest.setTimeout(1_000_000_000)
 
 const prefixes = new Map([
diff --git a/packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/indexeddb-storage.ts b/packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/indexeddb-storage.ts
index 2c22040e7..f0fde12a9 100644
--- a/packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/indexeddb-storage.ts
+++ b/packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/indexeddb-storage.ts
@@ -1,4 +1,5 @@
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
+
 import { openLocation } from '@jbrowse/core/util/io'
 import equal from 'fast-deep-equal/es6'
 import {
diff --git a/packages/jbrowse-plugin-apollo/src/OntologyManager/index.ts b/packages/jbrowse-plugin-apollo/src/OntologyManager/index.ts
index 223ae8f8c..1b463d188 100644
--- a/packages/jbrowse-plugin-apollo/src/OntologyManager/index.ts
+++ b/packages/jbrowse-plugin-apollo/src/OntologyManager/index.ts
@@ -8,7 +8,6 @@ import {
   LocalPathLocation,
   UriLocation,
 } from '@jbrowse/core/util/types/mst'
-import { autorun } from 'mobx'
 import {
   type Instance,
   addDisposer,
@@ -17,7 +16,8 @@ import {
   getSnapshot,
   isAlive,
   types,
-} from 'mobx-state-tree'
+} from '@jbrowse/mobx-state-tree'
+import { autorun } from 'mobx'
 
 import type ApolloPluginConfigurationSchema from '../config'
 import { type ApolloRootModel } from '../types'
diff --git a/packages/jbrowse-plugin-apollo/src/TabularEditor/HybridGrid/Feature.tsx b/packages/jbrowse-plugin-apollo/src/TabularEditor/HybridGrid/Feature.tsx
index c1980c940..3c135d301 100644
--- a/packages/jbrowse-plugin-apollo/src/TabularEditor/HybridGrid/Feature.tsx
+++ b/packages/jbrowse-plugin-apollo/src/TabularEditor/HybridGrid/Feature.tsx
@@ -1,11 +1,11 @@
-/* eslint-disable unicorn/no-nested-ternary */
 /* eslint-disable @typescript-eslint/unbound-method */
+/* eslint-disable unicorn/no-nested-ternary */
 
 import { type AnnotationFeature } from '@apollo-annotation/mst'
 import { type AbstractSessionModel } from '@jbrowse/core/util'
+import { makeStyles } from '@jbrowse/core/util/tss-react'
 import { observer } from 'mobx-react'
 import React from 'react'
-import { makeStyles } from 'tss-react/mui'
 
 import { isOntologyClass } from '../../OntologyManager'
 import type OntologyStore from '../../OntologyManager/OntologyStore'
diff --git a/packages/jbrowse-plugin-apollo/src/TabularEditor/HybridGrid/FeatureAttributes.tsx b/packages/jbrowse-plugin-apollo/src/TabularEditor/HybridGrid/FeatureAttributes.tsx
index 47872d503..6faa7b525 100644
--- a/packages/jbrowse-plugin-apollo/src/TabularEditor/HybridGrid/FeatureAttributes.tsx
+++ b/packages/jbrowse-plugin-apollo/src/TabularEditor/HybridGrid/FeatureAttributes.tsx
@@ -1,7 +1,7 @@
 /* eslint-disable @typescript-eslint/restrict-template-expressions */
 import { type AnnotationFeature } from '@apollo-annotation/mst'
+import { getSnapshot } from '@jbrowse/mobx-state-tree'
 import { observer } from 'mobx-react'
-import { getSnapshot } from 'mobx-state-tree'
 import React from 'react'
 
 import Highlight from './Highlight'
diff --git a/packages/jbrowse-plugin-apollo/src/TabularEditor/HybridGrid/Highlight.tsx b/packages/jbrowse-plugin-apollo/src/TabularEditor/HybridGrid/Highlight.tsx
index 03e973289..617d596c1 100644
--- a/packages/jbrowse-plugin-apollo/src/TabularEditor/HybridGrid/Highlight.tsx
+++ b/packages/jbrowse-plugin-apollo/src/TabularEditor/HybridGrid/Highlight.tsx
@@ -1,5 +1,5 @@
+import { makeStyles } from '@jbrowse/core/util/tss-react'
 import React from 'react'
-import { makeStyles } from 'tss-react/mui'
 
 const useStyles = makeStyles()({
   highlighted: {
diff --git a/packages/jbrowse-plugin-apollo/src/TabularEditor/HybridGrid/HybridGrid.tsx b/packages/jbrowse-plugin-apollo/src/TabularEditor/HybridGrid/HybridGrid.tsx
index b9658f306..903995be5 100644
--- a/packages/jbrowse-plugin-apollo/src/TabularEditor/HybridGrid/HybridGrid.tsx
+++ b/packages/jbrowse-plugin-apollo/src/TabularEditor/HybridGrid/HybridGrid.tsx
@@ -1,8 +1,8 @@
 import { Menu, type MenuItem } from '@jbrowse/core/ui'
+import { makeStyles } from '@jbrowse/core/util/tss-react'
 import { useTheme } from '@mui/material'
 import { observer } from 'mobx-react'
 import React, { useEffect, useRef, useState } from 'react'
-import { makeStyles } from 'tss-react/mui'
 
 import { type DisplayStateModel } from '../types'
 
diff --git a/packages/jbrowse-plugin-apollo/src/TabularEditor/HybridGrid/NumberCell.tsx b/packages/jbrowse-plugin-apollo/src/TabularEditor/HybridGrid/NumberCell.tsx
index b9c9ead33..2ed925f63 100644
--- a/packages/jbrowse-plugin-apollo/src/TabularEditor/HybridGrid/NumberCell.tsx
+++ b/packages/jbrowse-plugin-apollo/src/TabularEditor/HybridGrid/NumberCell.tsx
@@ -1,7 +1,7 @@
 /* eslint-disable @typescript-eslint/unbound-method */
+import { makeStyles } from '@jbrowse/core/util/tss-react'
 import { observer } from 'mobx-react'
 import React, { useEffect, useState } from 'react'
-import { makeStyles } from 'tss-react/mui'
 
 const useStyles = makeStyles()((theme) => ({
   inputWrapper: {
diff --git a/packages/jbrowse-plugin-apollo/src/TabularEditor/HybridGrid/ToolBar.tsx b/packages/jbrowse-plugin-apollo/src/TabularEditor/HybridGrid/ToolBar.tsx
index f67db21c4..a2c29aee2 100644
--- a/packages/jbrowse-plugin-apollo/src/TabularEditor/HybridGrid/ToolBar.tsx
+++ b/packages/jbrowse-plugin-apollo/src/TabularEditor/HybridGrid/ToolBar.tsx
@@ -1,10 +1,11 @@
 /* eslint-disable @typescript-eslint/unbound-method */
+
+import { makeStyles } from '@jbrowse/core/util/tss-react'
 import ClearIcon from '@mui/icons-material/Clear'
 import UnfoldLessIcon from '@mui/icons-material/UnfoldLess'
 import { IconButton, InputAdornment, TextField, Tooltip } from '@mui/material'
 import { observer } from 'mobx-react'
 import React from 'react'
-import { makeStyles } from 'tss-react/mui'
 
 import { type DisplayStateModel } from '../types'
 
diff --git a/packages/jbrowse-plugin-apollo/src/TabularEditor/model.ts b/packages/jbrowse-plugin-apollo/src/TabularEditor/model.ts
index 43ec657fc..5afe4385c 100644
--- a/packages/jbrowse-plugin-apollo/src/TabularEditor/model.ts
+++ b/packages/jbrowse-plugin-apollo/src/TabularEditor/model.ts
@@ -1,4 +1,4 @@
-import { type Instance, getParent, types } from 'mobx-state-tree'
+import { type Instance, getParent, types } from '@jbrowse/mobx-state-tree'
 
 import { type DisplayStateModel } from './types'
 
diff --git a/packages/jbrowse-plugin-apollo/src/components/AddAssembly.tsx b/packages/jbrowse-plugin-apollo/src/components/AddAssembly.tsx
index 8f458a0fc..d9e0f6e3b 100644
--- a/packages/jbrowse-plugin-apollo/src/components/AddAssembly.tsx
+++ b/packages/jbrowse-plugin-apollo/src/components/AddAssembly.tsx
@@ -1,5 +1,5 @@
 /* eslint-disable @typescript-eslint/unbound-method */
-/* eslint-disable @typescript-eslint/no-unnecessary-condition */
+
 /* eslint-disable @typescript-eslint/no-unsafe-assignment */
 /* eslint-disable @typescript-eslint/no-unsafe-member-access */
 /* eslint-disable @typescript-eslint/no-misused-promises */
@@ -10,6 +10,8 @@ import {
 } from '@apollo-annotation/shared'
 import { readConfObject } from '@jbrowse/core/configuration'
 import { type AbstractSessionModel } from '@jbrowse/core/util'
+import { makeStyles } from '@jbrowse/core/util/tss-react'
+import { getRoot } from '@jbrowse/mobx-state-tree'
 import InfoIcon from '@mui/icons-material/Info'
 import LinkIcon from '@mui/icons-material/Link'
 import RadioButtonCheckedIcon from '@mui/icons-material/RadioButtonChecked'
@@ -38,9 +40,7 @@ import {
   Typography,
 } from '@mui/material'
 import ObjectID from 'bson-objectid'
-import { getRoot } from 'mobx-state-tree'
 import React, { useState } from 'react'
-import { makeStyles } from 'tss-react/mui'
 
 import { type ApolloInternetAccountModel } from '../ApolloInternetAccount/model'
 import { type ChangeManager } from '../ChangeManager'
@@ -194,42 +194,37 @@ export function AddAssembly({
       locationType: 'UriLocation',
       uri,
     })
-    if (apolloFetchFile) {
-      const job = {
-        name: `UploadAssemblyFile for ${assemblyName}`,
-        statusMessage: 'Pre-validating',
-        progressPct: 0,
-        cancelCallback: () => {
-          controller.abort('AddAssembly')
-          jobsManager.abortJob(job.name)
-        },
-      }
-      jobsManager.runJob(job)
-      jobsManager.update(
-        job.name,
-        `Uploading ${file.name}, this may take awhile`,
+    const job = {
+      name: `UploadAssemblyFile for ${assemblyName}`,
+      statusMessage: 'Pre-validating',
+      progressPct: 0,
+      cancelCallback: () => {
+        controller.abort('AddAssembly')
+        jobsManager.abortJob(job.name)
+      },
+    }
+    jobsManager.runJob(job)
+    jobsManager.update(job.name, `Uploading ${file.name}, this may take awhile`)
+    const { signal } = controller
+
+    const response = await apolloFetchFile(uri, {
+      method: 'POST',
+      body: formData,
+      signal,
+    })
+    if (!response.ok) {
+      const newErrorMessage = await createFetchErrorMessage(
+        response,
+        'Error when inserting new assembly (while uploading file)',
       )
-      const { signal } = controller
-
-      const response = await apolloFetchFile(uri, {
-        method: 'POST',
-        body: formData,
-        signal,
-      })
-      if (!response.ok) {
-        const newErrorMessage = await createFetchErrorMessage(
-          response,
-          'Error when inserting new assembly (while uploading file)',
-        )
-        jobsManager.abortJob(job.name, newErrorMessage)
-        setErrorMessage(newErrorMessage)
-        return ''
-      }
-      const result = await response.json()
-      const fileId = result._id as string
-      jobsManager.done(job)
-      return fileId
+      jobsManager.abortJob(job.name, newErrorMessage)
+      setErrorMessage(newErrorMessage)
+      return ''
     }
+    const result = await response.json()
+    const fileId = result._id as string
+    jobsManager.done(job)
+    return fileId
     throw new Error('Failed to fetch')
   }
 
diff --git a/packages/jbrowse-plugin-apollo/src/components/CopyFeature.tsx b/packages/jbrowse-plugin-apollo/src/components/CopyFeature.tsx
index 064445957..f226dab4f 100644
--- a/packages/jbrowse-plugin-apollo/src/components/CopyFeature.tsx
+++ b/packages/jbrowse-plugin-apollo/src/components/CopyFeature.tsx
@@ -10,6 +10,7 @@ import {
 import { AddFeatureChange } from '@apollo-annotation/shared'
 import { readConfObject } from '@jbrowse/core/configuration'
 import { type AbstractSessionModel } from '@jbrowse/core/util'
+import { getSnapshot } from '@jbrowse/mobx-state-tree'
 import {
   Button,
   DialogActions,
@@ -22,7 +23,6 @@ import {
 } from '@mui/material'
 import ObjectID from 'bson-objectid'
 import { type IKeyValueMap } from 'mobx'
-import { getSnapshot } from 'mobx-state-tree'
 import React, { useEffect, useState } from 'react'
 
 import { type ChangeManager } from '../ChangeManager'
diff --git a/packages/jbrowse-plugin-apollo/src/components/CreateApolloAnnotation.tsx b/packages/jbrowse-plugin-apollo/src/components/CreateApolloAnnotation.tsx
index 577de75a8..bd3861dd0 100644
--- a/packages/jbrowse-plugin-apollo/src/components/CreateApolloAnnotation.tsx
+++ b/packages/jbrowse-plugin-apollo/src/components/CreateApolloAnnotation.tsx
@@ -10,6 +10,7 @@ import {
 } from '@apollo-annotation/shared'
 import { type Assembly } from '@jbrowse/core/assemblyManager/assembly'
 import { type AbstractSessionModel } from '@jbrowse/core/util'
+import { getSnapshot } from '@jbrowse/mobx-state-tree'
 import {
   Box,
   Button,
@@ -26,7 +27,6 @@ import {
   Typography,
 } from '@mui/material'
 import ObjectID from 'bson-objectid'
-import { getSnapshot } from 'mobx-state-tree'
 import React, { useEffect, useMemo, useState } from 'react'
 
 import { type ApolloSessionModel } from '../session'
diff --git a/packages/jbrowse-plugin-apollo/src/components/DeleteAssembly.tsx b/packages/jbrowse-plugin-apollo/src/components/DeleteAssembly.tsx
index 52d22e695..da16dc691 100644
--- a/packages/jbrowse-plugin-apollo/src/components/DeleteAssembly.tsx
+++ b/packages/jbrowse-plugin-apollo/src/components/DeleteAssembly.tsx
@@ -1,6 +1,7 @@
 /* eslint-disable @typescript-eslint/unbound-method */
 /* eslint-disable @typescript-eslint/no-misused-promises */
 import { DeleteAssemblyChange } from '@apollo-annotation/shared'
+import { getRoot } from '@jbrowse/mobx-state-tree'
 import {
   Button,
   Checkbox,
@@ -13,7 +14,6 @@ import {
   Select,
   type SelectChangeEvent,
 } from '@mui/material'
-import { getRoot } from 'mobx-state-tree'
 import React, { useState } from 'react'
 
 import { type ApolloInternetAccountModel } from '../ApolloInternetAccount/model'
diff --git a/packages/jbrowse-plugin-apollo/src/components/DeleteFeature.tsx b/packages/jbrowse-plugin-apollo/src/components/DeleteFeature.tsx
index aa2ff90f6..30538b363 100644
--- a/packages/jbrowse-plugin-apollo/src/components/DeleteFeature.tsx
+++ b/packages/jbrowse-plugin-apollo/src/components/DeleteFeature.tsx
@@ -6,13 +6,13 @@ import {
   LocationEndChange,
   LocationStartChange,
 } from '@apollo-annotation/shared'
+import { getSnapshot } from '@jbrowse/mobx-state-tree'
 import {
   Button,
   DialogActions,
   DialogContent,
   DialogContentText,
 } from '@mui/material'
-import { getSnapshot } from 'mobx-state-tree'
 import React, { useState } from 'react'
 
 import { type ChangeManager } from '../ChangeManager'
diff --git a/packages/jbrowse-plugin-apollo/src/components/Dialog.tsx b/packages/jbrowse-plugin-apollo/src/components/Dialog.tsx
index c0b0da54c..e31d9d1e2 100644
--- a/packages/jbrowse-plugin-apollo/src/components/Dialog.tsx
+++ b/packages/jbrowse-plugin-apollo/src/components/Dialog.tsx
@@ -1,10 +1,10 @@
 /* eslint-disable @typescript-eslint/unbound-method */
 import { Dialog as JBDialog } from '@jbrowse/core/ui'
+import { makeStyles } from '@jbrowse/core/util/tss-react'
 import CloseIcon from '@mui/icons-material/Close'
 import { type DialogProps, DialogTitle, IconButton } from '@mui/material'
 import { observer } from 'mobx-react'
 import React from 'react'
-import { makeStyles } from 'tss-react/mui'
 
 const useStyles = makeStyles()((theme) => ({
   dialogTitle: {
diff --git a/packages/jbrowse-plugin-apollo/src/components/DownloadGFF3.tsx b/packages/jbrowse-plugin-apollo/src/components/DownloadGFF3.tsx
index 0c2d05b96..c9eab6506 100644
--- a/packages/jbrowse-plugin-apollo/src/components/DownloadGFF3.tsx
+++ b/packages/jbrowse-plugin-apollo/src/components/DownloadGFF3.tsx
@@ -8,6 +8,7 @@ import { annotationFeatureToGFF3 } from '@apollo-annotation/shared'
 import { type GFF3Item, formatSync } from '@gmod/gff'
 import { type Assembly } from '@jbrowse/core/assemblyManager/assembly'
 import { getConf } from '@jbrowse/core/configuration'
+import { type IMSTMap, getSnapshot } from '@jbrowse/mobx-state-tree'
 import {
   Button,
   Checkbox,
@@ -21,7 +22,6 @@ import {
   type SelectChangeEvent,
 } from '@mui/material'
 import { saveAs } from 'file-saver'
-import { type IMSTMap, getSnapshot } from 'mobx-state-tree'
 import React, { useState } from 'react'
 
 import {
diff --git a/packages/jbrowse-plugin-apollo/src/components/LogOut.tsx b/packages/jbrowse-plugin-apollo/src/components/LogOut.tsx
index a6a5657ae..3f9a97282 100644
--- a/packages/jbrowse-plugin-apollo/src/components/LogOut.tsx
+++ b/packages/jbrowse-plugin-apollo/src/components/LogOut.tsx
@@ -1,4 +1,5 @@
 /* eslint-disable @typescript-eslint/unbound-method */
+import { getRoot } from '@jbrowse/mobx-state-tree'
 import {
   Button,
   DialogActions,
@@ -8,7 +9,6 @@ import {
   Select,
   type SelectChangeEvent,
 } from '@mui/material'
-import { getRoot } from 'mobx-state-tree'
 import React, { useState } from 'react'
 
 import { type ApolloInternetAccountModel } from '../ApolloInternetAccount/model'
diff --git a/packages/jbrowse-plugin-apollo/src/components/ManageChecks.tsx b/packages/jbrowse-plugin-apollo/src/components/ManageChecks.tsx
index 88c591e71..27970c0d3 100644
--- a/packages/jbrowse-plugin-apollo/src/components/ManageChecks.tsx
+++ b/packages/jbrowse-plugin-apollo/src/components/ManageChecks.tsx
@@ -2,6 +2,7 @@
 /* eslint-disable @typescript-eslint/unbound-method */
 /* eslint-disable @typescript-eslint/no-misused-promises */
 import { type AbstractSessionModel } from '@jbrowse/core/util'
+import { getRoot } from '@jbrowse/mobx-state-tree'
 import {
   Button,
   Checkbox,
@@ -19,7 +20,6 @@ import {
   TableHead,
   TableRow,
 } from '@mui/material'
-import { getRoot } from 'mobx-state-tree'
 import React, { useEffect, useState } from 'react'
 
 import { type ApolloInternetAccountModel } from '../ApolloInternetAccount/model'
diff --git a/packages/jbrowse-plugin-apollo/src/components/ManageUsers.tsx b/packages/jbrowse-plugin-apollo/src/components/ManageUsers.tsx
index 3dfe8374c..823b0e191 100644
--- a/packages/jbrowse-plugin-apollo/src/components/ManageUsers.tsx
+++ b/packages/jbrowse-plugin-apollo/src/components/ManageUsers.tsx
@@ -1,12 +1,12 @@
 /* eslint-disable @typescript-eslint/unbound-method */
 /* eslint-disable @typescript-eslint/use-unknown-in-catch-callback-variable */
-/* eslint-disable @typescript-eslint/no-unnecessary-condition */
+
 /* eslint-disable @typescript-eslint/no-misused-promises */
 /* eslint-disable @typescript-eslint/no-unsafe-assignment */
 /* eslint-disable @typescript-eslint/no-unsafe-member-access */
 /* eslint-disable @typescript-eslint/no-unsafe-return */
 import { DeleteUserChange, UserChange } from '@apollo-annotation/shared'
-import { type AbstractRootModel } from '@jbrowse/core/util'
+import { getRoot } from '@jbrowse/mobx-state-tree'
 import DeleteIcon from '@mui/icons-material/Delete'
 import {
   Button,
@@ -27,12 +27,12 @@ import {
   type GridRowParams,
   GridToolbar,
 } from '@mui/x-data-grid'
-import { getRoot } from 'mobx-state-tree'
 import React, { useEffect, useState } from 'react'
 
 import { type ApolloInternetAccountModel } from '../ApolloInternetAccount/model'
 import { type ChangeManager } from '../ChangeManager'
 import { type ApolloSessionModel } from '../session'
+import { type ApolloRootModel, isApolloInternetAccount } from '../types'
 import { createFetchErrorMessage } from '../util'
 
 import { Dialog } from './Dialog'
@@ -50,19 +50,15 @@ interface ManageUsersProps {
   changeManager: ChangeManager
 }
 
-interface ApolloRootModel extends AbstractRootModel {
-  internetAccounts: ApolloInternetAccountModel[]
-}
-
 export function ManageUsers({
   changeManager,
   handleClose,
   session,
 }: ManageUsersProps) {
   const { internetAccounts } = getRoot<ApolloRootModel>(session)
-  const apolloInternetAccounts = internetAccounts.filter(
-    (ia) => ia.type === 'ApolloInternetAccount' && ia.role?.includes('admin'),
-  )
+  const apolloInternetAccounts: ApolloInternetAccountModel[] = internetAccounts
+    .filter((ia) => isApolloInternetAccount(ia))
+    .filter((ia) => ia.role?.includes('admin'))
   if (apolloInternetAccounts.length === 0) {
     throw new Error('No Apollo internet account found')
   }
@@ -80,21 +76,17 @@ export function ManageUsers({
         locationType: 'UriLocation',
         uri,
       })
-      if (apolloFetch) {
-        const response = await apolloFetch(uri, { method: 'GET' })
-        if (!response.ok) {
-          const newErrorMessage = await createFetchErrorMessage(
-            response,
-            'Error when getting user data from db',
-          )
-          setErrorMessage(newErrorMessage)
-          return
-        }
-        const data = (await response.json()) as UserResponse[]
-        setUsers(
-          data.map((u) => (u.role === undefined ? { ...u, role: '' } : u)),
+      const response = await apolloFetch(uri, { method: 'GET' })
+      if (!response.ok) {
+        const newErrorMessage = await createFetchErrorMessage(
+          response,
+          'Error when getting user data from db',
         )
+        setErrorMessage(newErrorMessage)
+        return
       }
+      const data = (await response.json()) as UserResponse[]
+      setUsers(data.map((u) => (u.role === undefined ? { ...u, role: '' } : u)))
     }
     getUsers().catch((error) => {
       setErrorMessage(String(error))
diff --git a/packages/jbrowse-plugin-apollo/src/components/MergeExons.tsx b/packages/jbrowse-plugin-apollo/src/components/MergeExons.tsx
index 675b40609..8f9b6f92b 100644
--- a/packages/jbrowse-plugin-apollo/src/components/MergeExons.tsx
+++ b/packages/jbrowse-plugin-apollo/src/components/MergeExons.tsx
@@ -2,6 +2,7 @@
 
 import { type AnnotationFeature } from '@apollo-annotation/mst'
 import { MergeExonsChange } from '@apollo-annotation/shared'
+import { getSnapshot } from '@jbrowse/mobx-state-tree'
 import {
   Box,
   Button,
@@ -14,7 +15,6 @@ import {
   RadioGroup,
   type SelectChangeEvent,
 } from '@mui/material'
-import { getSnapshot } from 'mobx-state-tree'
 import React, { useState } from 'react'
 
 import { type ChangeManager } from '../ChangeManager'
diff --git a/packages/jbrowse-plugin-apollo/src/components/MergeTranscripts.tsx b/packages/jbrowse-plugin-apollo/src/components/MergeTranscripts.tsx
index 2de2b47b9..963916870 100644
--- a/packages/jbrowse-plugin-apollo/src/components/MergeTranscripts.tsx
+++ b/packages/jbrowse-plugin-apollo/src/components/MergeTranscripts.tsx
@@ -1,6 +1,7 @@
 /* eslint-disable @typescript-eslint/unbound-method */
 import { type AnnotationFeature } from '@apollo-annotation/mst'
 import { MergeTranscriptsChange } from '@apollo-annotation/shared'
+import { getSnapshot } from '@jbrowse/mobx-state-tree'
 import {
   Box,
   Button,
@@ -13,7 +14,6 @@ import {
   RadioGroup,
   type SelectChangeEvent,
 } from '@mui/material'
-import { getSnapshot } from 'mobx-state-tree'
 import React, { useState } from 'react'
 
 import { type ChangeManager } from '../ChangeManager'
diff --git a/packages/jbrowse-plugin-apollo/src/components/OntologyTermMultiSelect.tsx b/packages/jbrowse-plugin-apollo/src/components/OntologyTermMultiSelect.tsx
index 184b721bf..43cabd0ce 100644
--- a/packages/jbrowse-plugin-apollo/src/components/OntologyTermMultiSelect.tsx
+++ b/packages/jbrowse-plugin-apollo/src/components/OntologyTermMultiSelect.tsx
@@ -2,6 +2,7 @@
 /* eslint-disable @typescript-eslint/use-unknown-in-catch-callback-variable */
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 import { isAbortException } from '@jbrowse/core/util/aborting'
+import { getParent } from '@jbrowse/mobx-state-tree'
 import {
   Autocomplete,
   type AutocompleteRenderValueGetItemProps,
@@ -14,7 +15,6 @@ import {
 import { debounce } from '@mui/material/utils'
 import highlightMatch from 'autosuggest-highlight/match'
 import highlightParse from 'autosuggest-highlight/parse'
-import { getParent } from 'mobx-state-tree'
 import * as React from 'react'
 
 import {
diff --git a/packages/jbrowse-plugin-apollo/src/components/SplitExon.tsx b/packages/jbrowse-plugin-apollo/src/components/SplitExon.tsx
index 9d4586f12..e3874cf2c 100644
--- a/packages/jbrowse-plugin-apollo/src/components/SplitExon.tsx
+++ b/packages/jbrowse-plugin-apollo/src/components/SplitExon.tsx
@@ -5,6 +5,7 @@ import {
   type AnnotationFeatureSnapshot,
 } from '@apollo-annotation/mst'
 import { SplitExonChange } from '@apollo-annotation/shared'
+import { getSnapshot } from '@jbrowse/mobx-state-tree'
 import {
   Button,
   DialogActions,
@@ -12,7 +13,6 @@ import {
   DialogContentText,
 } from '@mui/material'
 import ObjectID from 'bson-objectid'
-import { getSnapshot } from 'mobx-state-tree'
 import React, { useState } from 'react'
 
 import { type ChangeManager } from '../ChangeManager'
diff --git a/packages/jbrowse-plugin-apollo/src/components/ViewChangeLog.tsx b/packages/jbrowse-plugin-apollo/src/components/ViewChangeLog.tsx
index 320bcc9f0..8bed28af3 100644
--- a/packages/jbrowse-plugin-apollo/src/components/ViewChangeLog.tsx
+++ b/packages/jbrowse-plugin-apollo/src/components/ViewChangeLog.tsx
@@ -6,6 +6,8 @@
 /* eslint-disable @typescript-eslint/no-unsafe-member-access */
 /* eslint-disable @typescript-eslint/no-unsafe-return */
 import { changeRegistry } from '@apollo-annotation/common'
+import { makeStyles } from '@jbrowse/core/util/tss-react'
+import { getRoot } from '@jbrowse/mobx-state-tree'
 import {
   Button,
   DialogActions,
@@ -21,9 +23,7 @@ import {
   type GridRowsProp,
   GridToolbar,
 } from '@mui/x-data-grid'
-import { getRoot } from 'mobx-state-tree'
 import React, { useEffect, useState } from 'react'
-import { makeStyles } from 'tss-react/mui'
 
 import { type ApolloInternetAccountModel } from '../ApolloInternetAccount/model'
 import {
diff --git a/packages/jbrowse-plugin-apollo/src/components/ViewCheckResults.tsx b/packages/jbrowse-plugin-apollo/src/components/ViewCheckResults.tsx
index 2c9479a7d..0e8303dec 100644
--- a/packages/jbrowse-plugin-apollo/src/components/ViewCheckResults.tsx
+++ b/packages/jbrowse-plugin-apollo/src/components/ViewCheckResults.tsx
@@ -4,6 +4,7 @@
 /* eslint-disable @typescript-eslint/no-unsafe-argument */
 /* eslint-disable @typescript-eslint/no-unsafe-member-access */
 /* eslint-disable @typescript-eslint/no-unsafe-return */
+import { getRoot } from '@jbrowse/mobx-state-tree'
 import {
   Button,
   DialogActions,
@@ -19,7 +20,6 @@ import {
   type GridRowsProp,
   GridToolbar,
 } from '@mui/x-data-grid'
-import { getRoot } from 'mobx-state-tree'
 import React, { useEffect, useState } from 'react'
 
 import { type ApolloInternetAccountModel } from '../ApolloInternetAccount/model'
diff --git a/packages/jbrowse-plugin-apollo/src/config.ts b/packages/jbrowse-plugin-apollo/src/config.ts
index 411223d52..0960d4bc5 100644
--- a/packages/jbrowse-plugin-apollo/src/config.ts
+++ b/packages/jbrowse-plugin-apollo/src/config.ts
@@ -1,5 +1,5 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration'
-import { types } from 'mobx-state-tree'
+import { types } from '@jbrowse/mobx-state-tree'
 
 import { OntologyRecordConfiguration } from './OntologyManager'
 
diff --git a/packages/jbrowse-plugin-apollo/src/extensions/annotationFromJBrowseFeature.ts b/packages/jbrowse-plugin-apollo/src/extensions/annotationFromJBrowseFeature.ts
index b52584719..899fed311 100644
--- a/packages/jbrowse-plugin-apollo/src/extensions/annotationFromJBrowseFeature.ts
+++ b/packages/jbrowse-plugin-apollo/src/extensions/annotationFromJBrowseFeature.ts
@@ -7,8 +7,8 @@ import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
 import { gff3ToAnnotationFeature } from '@apollo-annotation/shared'
 import { type GFF3Feature } from '@gmod/gff'
 import { type Assembly } from '@jbrowse/core/assemblyManager/assembly'
+import { type PluggableElementType } from '@jbrowse/core/pluggableElementTypes'
 import type DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType'
-import type PluggableElementBase from '@jbrowse/core/pluggableElementTypes/PluggableElementBase'
 import {
   type AbstractSessionModel,
   getContainingView,
@@ -24,23 +24,26 @@ function simpleFeatureToGFF3Feature(
   feature: Feature,
   refSeqId: string,
 ): GFF3Feature {
-  // eslint-disable-next-line unicorn/prefer-structured-clone
-  const xfeature = JSON.parse(JSON.stringify(feature))
-  const children = xfeature.subfeatures
+  const children = feature.get('subfeatures')
   const gff3Feature = [
     {
-      start: (xfeature.start as number) + 1,
-      end: xfeature.end as number,
+      start: feature.get('start') + 1,
+      end: feature.get('end'),
       seq_id: refSeqId,
-      source: xfeature.source ?? null,
-      type: xfeature.type ?? null,
-      score: xfeature.score ?? null,
-      strand: xfeature.strand ? (xfeature.strand === 1 ? '+' : '-') : null,
+      source: feature.get('source') ?? null,
+      type: feature.get('type') ?? null,
+      score: feature.get('score') ?? null,
+      strand: feature.get('strand')
+        ? // eslint-disable-next-line unicorn/no-nested-ternary
+          feature.get('strand') === 1
+          ? '+'
+          : '-'
+        : null,
       phase:
-        xfeature.phase !== null || xfeature.phase !== undefined
-          ? (xfeature.phase as string)
+        feature.get('phase') !== null || feature.get('phase') !== undefined
+          ? (feature.get('phase') as string)
           : null,
-      attributes: convertFeatureAttributes(xfeature),
+      attributes: convertFeatureAttributes(feature),
       derived_features: [],
       child_features: children
         ? children.map((x: Feature) => simpleFeatureToGFF3Feature(x, refSeqId))
@@ -71,7 +74,7 @@ function convertFeatureAttributes(feature: Feature): Record<string, string[]> {
     'source',
     'score',
   ])
-  for (const [key, value] of Object.entries(feature)) {
+  for (const [key, value] of Object.entries(feature.toJSON())) {
     if (defaultFields.has(key)) {
       continue
     }
@@ -81,7 +84,7 @@ function convertFeatureAttributes(feature: Feature): Record<string, string[]> {
 }
 
 export function annotationFromJBrowseFeature(
-  pluggableElement: PluggableElementBase,
+  pluggableElement: PluggableElementType,
 ) {
   if (pluggableElement.name !== 'LinearBasicDisplay') {
     return pluggableElement
@@ -124,10 +127,9 @@ export function annotationFromJBrowseFeature(
         }
         return refSeqId
       },
-      getAnnotationFeature(assembly: Assembly) {
+      getAnnotationFeature(assembly: Assembly, feature: Feature) {
         const refSeqId = self.getRefSeqId(assembly)
-        const sfeature: Feature = self.contextMenuFeature.data
-        return jbrowseFeatureToAnnotationFeature(sfeature, refSeqId)
+        return jbrowseFeatureToAnnotationFeature(feature, refSeqId)
       },
     }))
     .views((self) => {
@@ -156,7 +158,10 @@ export function annotationFromJBrowseFeature(
                       handleClose: () => {
                         doneCallback()
                       },
-                      annotationFeature: self.getAnnotationFeature(assembly),
+                      annotationFeature: self.getAnnotationFeature(
+                        assembly,
+                        feature,
+                      ),
                       assembly,
                       refSeqId: self.getRefSeqId(assembly),
                       region,
diff --git a/packages/jbrowse-plugin-apollo/src/extensions/annotationFromPileup.ts b/packages/jbrowse-plugin-apollo/src/extensions/annotationFromPileup.ts
index c064996a8..090d41369 100644
--- a/packages/jbrowse-plugin-apollo/src/extensions/annotationFromPileup.ts
+++ b/packages/jbrowse-plugin-apollo/src/extensions/annotationFromPileup.ts
@@ -5,8 +5,10 @@
 /* eslint-disable @typescript-eslint/no-unsafe-return */
 import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
 import { type Assembly } from '@jbrowse/core/assemblyManager/assembly'
-import { type DisplayType } from '@jbrowse/core/pluggableElementTypes'
-import type PluggableElementBase from '@jbrowse/core/pluggableElementTypes/PluggableElementBase'
+import {
+  type DisplayType,
+  type PluggableElementType,
+} from '@jbrowse/core/pluggableElementTypes'
 import {
   type AbstractSessionModel,
   getContainingView,
@@ -30,7 +32,7 @@ function parseCigar(cigar: string): [string, number][] {
   return result
 }
 
-export function annotationFromPileup(pluggableElement: PluggableElementBase) {
+export function annotationFromPileup(pluggableElement: PluggableElementType) {
   if (pluggableElement.name !== 'LinearPileupDisplay') {
     return pluggableElement
   }
diff --git a/packages/jbrowse-plugin-apollo/src/makeDisplayComponent.tsx b/packages/jbrowse-plugin-apollo/src/makeDisplayComponent.tsx
index 3d82b9778..adcc48868 100644
--- a/packages/jbrowse-plugin-apollo/src/makeDisplayComponent.tsx
+++ b/packages/jbrowse-plugin-apollo/src/makeDisplayComponent.tsx
@@ -1,11 +1,12 @@
 /* eslint-disable @typescript-eslint/unbound-method */
+
 import { getSession } from '@jbrowse/core/util'
+import { makeStyles } from '@jbrowse/core/util/tss-react'
 import ExpandLessIcon from '@mui/icons-material/ExpandLess'
 import ExpandMoreIcon from '@mui/icons-material/ExpandMore'
 import { Alert, Typography, alpha } from '@mui/material'
 import { observer } from 'mobx-react'
 import React, { useCallback, useEffect, useRef } from 'react'
-import { makeStyles } from 'tss-react/mui'
 
 import { LinearApolloDisplay } from './LinearApolloDisplay/components'
 import { type LinearApolloDisplay as LinearApolloDisplayI } from './LinearApolloDisplay/stateModel'
diff --git a/packages/jbrowse-plugin-apollo/src/session/ClientDataStore.ts b/packages/jbrowse-plugin-apollo/src/session/ClientDataStore.ts
index e22349fdc..33a8587c3 100644
--- a/packages/jbrowse-plugin-apollo/src/session/ClientDataStore.ts
+++ b/packages/jbrowse-plugin-apollo/src/session/ClientDataStore.ts
@@ -13,14 +13,16 @@ import {
   CheckResult,
   type CheckResultSnapshot,
 } from '@apollo-annotation/mst'
-import { getConf, readConfObject } from '@jbrowse/core/configuration'
-import { type ConfigurationModel } from '@jbrowse/core/configuration/types'
+import {
+  type AnyConfigurationModel,
+  getConf,
+  readConfObject,
+} from '@jbrowse/core/configuration'
 import { type Region, getSession, isElectron } from '@jbrowse/core/util'
 import {
   type LocalPathLocation,
   type UriLocation,
 } from '@jbrowse/core/util/types/mst'
-import { autorun } from 'mobx'
 import {
   type Instance,
   addDisposer,
@@ -29,7 +31,8 @@ import {
   getRoot,
   resolveIdentifier,
   types,
-} from 'mobx-state-tree'
+} from '@jbrowse/mobx-state-tree'
+import { autorun } from 'mobx'
 
 import {
   type ApolloInternetAccount,
@@ -41,7 +44,6 @@ import {
 import { ChangeManager } from '../ChangeManager'
 import {
   OntologyManagerType,
-  type OntologyRecordConfiguration,
   type TextIndexFieldDefinition,
 } from '../OntologyManager'
 import type ApolloPluginConfigurationSchema from '../config'
@@ -177,9 +179,7 @@ export function clientDataStoreFactory(
             // take precedence over the ontologies in the configuration.
             const { ontologyManager, pluginConfiguration } = self
             const configuredOntologies =
-              pluginConfiguration.ontologies as ConfigurationModel<
-                typeof OntologyRecordConfiguration
-              >[]
+              pluginConfiguration.ontologies as AnyConfigurationModel[]
             for (const ont of configuredOntologies || []) {
               const [name, version, source, indexFields] = [
                 readConfObject(ont, 'name') as string,
diff --git a/packages/jbrowse-plugin-apollo/src/session/session.ts b/packages/jbrowse-plugin-apollo/src/session/session.ts
index bf983dcd6..d013cf3a1 100644
--- a/packages/jbrowse-plugin-apollo/src/session/session.ts
+++ b/packages/jbrowse-plugin-apollo/src/session/session.ts
@@ -1,4 +1,3 @@
-/* eslint-disable @typescript-eslint/no-unsafe-return */
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 /* eslint-disable @typescript-eslint/no-unsafe-assignment */
 import { type ClientDataStore as ClientDataStoreType } from '@apollo-annotation/common'
@@ -20,9 +19,6 @@ import {
   type AbstractSessionModel,
   type SessionWithAddTracks,
 } from '@jbrowse/core/util'
-import { type LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
-import SaveIcon from '@mui/icons-material/Save'
-import { autorun, observable } from 'mobx'
 import {
   type Instance,
   type SnapshotOut,
@@ -31,7 +27,10 @@ import {
   getRoot,
   getSnapshot,
   types,
-} from 'mobx-state-tree'
+} from '@jbrowse/mobx-state-tree'
+import { type LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
+import SaveIcon from '@mui/icons-material/Save'
+import { autorun, observable } from 'mobx'
 
 import { type ApolloInternetAccountModel } from '../ApolloInternetAccount/model'
 import { ApolloJobModel } from '../ApolloJobModel'
@@ -384,10 +383,7 @@ export function extendSession(
                     if (Object.keys(filteredConfig).length === 0) {
                       filteredConfig = undefined
                     }
-                    const trackConfigSnapshot = getSnapshot(conf) as {
-                      trackId: string
-                      type: string
-                    }
+                    const trackConfigSnapshot = getSnapshot(conf)
                     const newTrackId = trackId.slice(
                       0,
                       trackId.length - sessionTrackIdentifier.length,
@@ -405,6 +401,7 @@ export function extendSession(
                         oldJBrowseConfig: filteredConfig,
                         newJBrowseConfig: {
                           ...filteredConfig,
+                          // @ts-expect-error The track types are in the snapshot
                           tracks: filteredConfig?.tracks && [
                             ...filteredConfig.tracks,
                             newTrackConfigSnapshot,
diff --git a/packages/jbrowse-plugin-apollo/src/types.ts b/packages/jbrowse-plugin-apollo/src/types.ts
index d44209754..151e165b4 100644
--- a/packages/jbrowse-plugin-apollo/src/types.ts
+++ b/packages/jbrowse-plugin-apollo/src/types.ts
@@ -8,3 +8,9 @@ export interface ApolloRootModel extends Omit<AppRootModel, 'session'> {
   session: ApolloSessionModel
   internetAccounts: (BaseInternetAccountModel | ApolloInternetAccountModel)[]
 }
+
+export function isApolloInternetAccount(
+  internetAccount: BaseInternetAccountModel | ApolloInternetAccountModel,
+): internetAccount is ApolloInternetAccountModel {
+  return internetAccount.type === 'ApolloInternetAccount'
+}
diff --git a/packages/jbrowse-plugin-apollo/src/util/displayUtils.ts b/packages/jbrowse-plugin-apollo/src/util/displayUtils.ts
index 4883febb0..2f148ba24 100644
--- a/packages/jbrowse-plugin-apollo/src/util/displayUtils.ts
+++ b/packages/jbrowse-plugin-apollo/src/util/displayUtils.ts
@@ -1,6 +1,6 @@
 import { type CheckResultIdsType } from '@apollo-annotation/mst'
+import { makeStyles } from '@jbrowse/core/util/tss-react'
 import { type Theme } from '@mui/material'
-import { makeStyles } from 'tss-react/mui'
 
 export { default as EditZoomThresholdDialog } from '../components/EditZoomThresholdDialog'
 
diff --git a/packages/jbrowse-plugin-apollo/src/util/index.ts b/packages/jbrowse-plugin-apollo/src/util/index.ts
index 972f55b06..4f734d87b 100644
--- a/packages/jbrowse-plugin-apollo/src/util/index.ts
+++ b/packages/jbrowse-plugin-apollo/src/util/index.ts
@@ -1,4 +1,4 @@
-import { getParent } from 'mobx-state-tree'
+import { getParent } from '@jbrowse/mobx-state-tree'
 
 import { type ApolloInternetAccountModel } from '../ApolloInternetAccount/model'
 import { type ApolloSessionModel } from '../session'
diff --git a/packages/jbrowse-plugin-apollo/src/util/loadAssemblyIntoClient.ts b/packages/jbrowse-plugin-apollo/src/util/loadAssemblyIntoClient.ts
index e6c0ec2b2..d211d57e5 100644
--- a/packages/jbrowse-plugin-apollo/src/util/loadAssemblyIntoClient.ts
+++ b/packages/jbrowse-plugin-apollo/src/util/loadAssemblyIntoClient.ts
@@ -10,7 +10,7 @@ import {
   type GFF3Sequence,
   parseStringSync,
 } from '@gmod/gff'
-import { getSnapshot } from 'mobx-state-tree'
+import { getSnapshot } from '@jbrowse/mobx-state-tree'
 
 export async function loadAssemblyIntoClient(
   assemblyId: string,
diff --git a/packages/jbrowse-plugin-apollo/tsconfig.eslint.json b/packages/jbrowse-plugin-apollo/tsconfig.eslint.json
deleted file mode 100644
index 49e941452..000000000
--- a/packages/jbrowse-plugin-apollo/tsconfig.eslint.json
+++ /dev/null
@@ -1,4 +0,0 @@
-{
-  "extends": "../../tsconfig.json",
-  "include": ["jest.config.js", "jestSetup.js", "rollup.config.js"],
-}
diff --git a/packages/jbrowse-plugin-apollo/tsconfig.json b/packages/jbrowse-plugin-apollo/tsconfig.json
index 8d0ad7652..a03e307f3 100644
--- a/packages/jbrowse-plugin-apollo/tsconfig.json
+++ b/packages/jbrowse-plugin-apollo/tsconfig.json
@@ -1,12 +1,13 @@
 {
-  "extends": "../../tsconfig-base.json",
+  "extends": "../../tsconfig",
   "compilerOptions": {
-    "declaration": false,
-    "target": "ES6",
     "rootDir": "./src",
     "noEmit": true,
-    "noEmitOnError": false,
     "resolveJsonModule": true,
+    "module": "esnext",
+    "moduleResolution": "bundler",
+    // TODO: enable this and fix the problems it reveals
+    "noUncheckedIndexedAccess": false,
   },
   "include": ["src"],
   "exclude": ["**/dist/"],
@@ -14,5 +15,6 @@
     { "path": "../apollo-common" },
     { "path": "../apollo-mst" },
     { "path": "../apollo-shared" },
+    { "path": "./tsconfig.node.json" },
   ],
 }
diff --git a/packages/jbrowse-plugin-apollo/tsconfig.node.json b/packages/jbrowse-plugin-apollo/tsconfig.node.json
new file mode 100644
index 000000000..5f4aa6dc8
--- /dev/null
+++ b/packages/jbrowse-plugin-apollo/tsconfig.node.json
@@ -0,0 +1,14 @@
+{
+  "extends": "../../tsconfig.node",
+  "compilerOptions": { "noEmit": false, "outDir": "./conf" },
+  "include": [
+    "./*.js",
+    "./.*.js",
+    "./*.mjs",
+    "./.*.mjs",
+    "./*.cjs",
+    "./.*.cjs",
+    "./rollup/*.mjs",
+    "cypress.config.ts",
+  ],
+}
diff --git a/packages/website/package.json b/packages/website/package.json
index 7e4a2c9d3..1e6df1ffb 100755
--- a/packages/website/package.json
+++ b/packages/website/package.json
@@ -27,7 +27,7 @@
     "@docusaurus/theme-classic": "^3.5.2",
     "@docusaurus/tsconfig": "^3.5.2",
     "@docusaurus/types": "^3.5.2",
-    "@types/node": "^20.19.15",
+    "@types/node": "^24.10.9",
     "@types/react": "^18.3.4",
     "typescript": "^5.5.3"
   }
diff --git a/tsconfig-base.json b/tsconfig-base.json
deleted file mode 100644
index fff121c6f..000000000
--- a/tsconfig-base.json
+++ /dev/null
@@ -1,73 +0,0 @@
-{
-  "compilerOptions": {
-    /* Visit https://aka.ms/tsconfig.json to read more about this file */
-
-    /* Basic Options */
-    // "incremental": true,                   /* Enable incremental compilation */
-    "target": "es5" /* Specify ECMAScript target version: 'ES3' (default), 'ES5', 'ES2015', 'ES2016', 'ES2017', 'ES2018', 'ES2019', 'ES2020', or 'ESNEXT'. */,
-    "module": "esnext" /* Specify module code generation: 'none', 'commonjs', 'amd', 'system', 'umd', 'es2015', 'es2020', or 'ESNext'. */,
-    "lib": [
-      "dom",
-      "esnext",
-    ] /* Specify library files to be included in the compilation. */,
-    // "allowJs": true,                       /* Allow javascript files to be compiled. */
-    // "checkJs": true,                       /* Report errors in .js files. */
-    "jsx": "react" /* Specify JSX code generation: 'preserve', 'react-native', or 'react'. */,
-    "declaration": true /* Generates corresponding '.d.ts' file. */,
-    // "declarationMap": true,                /* Generates a sourcemap for each corresponding '.d.ts' file. */
-    "sourceMap": true /* Generates corresponding '.map' file. */,
-    // "outFile": "./",                       /* Concatenate and emit output to single file. */
-    // "outDir": "./",                        /* Redirect output structure to the directory. */
-    // "rootDir": "./",                       /* Specify the root directory of input files. Use to control the output directory structure with --outDir. */
-    // "composite": true,                     /* Enable project compilation */
-    // "tsBuildInfoFile": "./",               /* Specify file to store incremental compilation information */
-    // "removeComments": true,                /* Do not emit comments to output. */
-    // "noEmit": true,                        /* Do not emit outputs. */
-    "importHelpers": true /* Import emit helpers from 'tslib'. */,
-    "downlevelIteration": true /* Provide full support for iterables in 'for-of', spread, and destructuring when targeting 'ES5' or 'ES3'. */,
-    // "isolatedModules": true,               /* Transpile each file as a separate module (similar to 'ts.transpileModule'). */
-
-    /* Strict Type-Checking Options */
-    "strict": true /* Enable all strict type-checking options. */,
-    // "noImplicitAny": true,                 /* Raise error on expressions and declarations with an implied 'any' type. */
-    // "strictNullChecks": true,              /* Enable strict null checks. */
-    // "strictFunctionTypes": true,           /* Enable strict checking of function types. */
-    // "strictBindCallApply": true,           /* Enable strict 'bind', 'call', and 'apply' methods on functions. */
-    // "strictPropertyInitialization": true,  /* Enable strict checking of property initialization in classes. */
-    // "noImplicitThis": true,                /* Raise error on 'this' expressions with an implied 'any' type. */
-    // "alwaysStrict": true,                  /* Parse in strict mode and emit "use strict" for each source file. */
-
-    /* Additional Checks */
-    // "noUnusedLocals": true,                /* Report errors on unused locals. */
-    // "noUnusedParameters": true,            /* Report errors on unused parameters. */
-    "noImplicitReturns": true /* Report error when not all code paths in function return a value. */,
-    "noFallthroughCasesInSwitch": true /* Report errors for fallthrough cases in switch statement. */,
-    // "noUncheckedIndexedAccess": true,      /* Include 'undefined' in index signature results */
-
-    /* Module Resolution Options */
-    "moduleResolution": "node" /* Specify module resolution strategy: 'node' (Node.js) or 'classic' (TypeScript pre-1.6). */,
-    // "baseUrl": "./",                       /* Base directory to resolve non-absolute module names. */
-    // "paths": {},                           /* A series of entries which re-map imports to lookup locations relative to the 'baseUrl'. */
-    // "rootDirs": [],                        /* List of root folders whose combined content represents the structure of the project at runtime. */
-    // "typeRoots": [],                       /* List of folders to include type definitions from. */
-    // "types": [],                           /* Type declaration files to be included in compilation. */
-    // "allowSyntheticDefaultImports": true,  /* Allow default imports from modules with no default export. This does not affect code emit, just typechecking. */
-    "esModuleInterop": true /* Enables emit interoperability between CommonJS and ES Modules via creation of namespace objects for all imports. Implies 'allowSyntheticDefaultImports'. */,
-    // "preserveSymlinks": true,              /* Do not resolve the real path of symlinks. */
-    // "allowUmdGlobalAccess": true,          /* Allow accessing UMD globals from modules. */
-
-    /* Source Map Options */
-    // "sourceRoot": "",                      /* Specify the location where debugger should locate TypeScript files instead of source locations. */
-    // "mapRoot": "",                         /* Specify the location where debugger should locate map files instead of generated locations. */
-    // "inlineSourceMap": true,               /* Emit a single file with source maps instead of having a separate file. */
-    // "inlineSources": true,                 /* Emit the source alongside the sourcemaps within a single file; requires '--inlineSourceMap' or '--sourceMap' to be set. */
-
-    /* Experimental Options */
-    // "experimentalDecorators": true,        /* Enables experimental support for ES7 decorators. */
-    // "emitDecoratorMetadata": true,         /* Enables experimental support for emitting type metadata for decorators. */
-
-    /* Advanced Options */
-    "skipLibCheck": true /* Skip type checking of declaration files. */,
-    "forceConsistentCasingInFileNames": true /* Disallow inconsistently-cased references to the same file. */,
-  },
-}
diff --git a/tsconfig.json b/tsconfig.json
index d6a0d0570..f6df364c2 100644
--- a/tsconfig.json
+++ b/tsconfig.json
@@ -1,18 +1,40 @@
 {
-  "extends": "./tsconfig-base.json",
   "compilerOptions": {
-    "types": ["@types/node"],
-    "noEmit": true,
-    "allowJs": true,
+    /* Visit https://aka.ms/tsconfig.json to read more about this file */
+    // Environment Settings
+    // See also https://aka.ms/tsconfig/module
+    "module": "nodenext",
+    "target": "esnext",
+    "types": [],
+
+    // Other Outputs
+    "sourceMap": true,
+    "declaration": true,
+    "declarationMap": true,
+
+    // Stricter Typechecking Options
+    "noUncheckedIndexedAccess": true,
+    // TODO: enable this and fix the problems it reveals
+    // "exactOptionalPropertyTypes": true,
+
+    // Style Options
+    // "noImplicitReturns": true,
+    // "noImplicitOverride": true,
+    // "noUnusedLocals": true,
+    // "noUnusedParameters": true,
+    // "noFallthroughCasesInSwitch": true,
+    // "noPropertyAccessFromIndexSignature": true,
+
+    // Recommended Options
+    "strict": true,
+    "jsx": "react-jsx",
+    "verbatimModuleSyntax": false,
+    "isolatedModules": true,
+    // TODO: enable this one TypeScript version is updated
+    // "noUncheckedSideEffectImports": true,
+    "moduleDetection": "force",
+    "skipLibCheck": true,
   },
-  "include": [
-    "./*.js",
-    "./.*.js",
-    "./*.mjs",
-    "./.*.mjs",
-    "./*.cjs",
-    "./.*.cjs",
-    "scripts/*.ts",
-    ".husky/*.js",
-  ],
+  "files": [],
+  "references": [{ "path": "./tsconfig.node.json" }],
 }
diff --git a/tsconfig.node.json b/tsconfig.node.json
new file mode 100644
index 000000000..554dd4c30
--- /dev/null
+++ b/tsconfig.node.json
@@ -0,0 +1,51 @@
+{
+  // Visit https://aka.ms/tsconfig to read more about this file
+  "compilerOptions": {
+    // Environment Settings
+    // See also https://aka.ms/tsconfig/module
+    "module": "nodenext",
+    "target": "esnext",
+    // For nodejs:
+    "lib": ["esnext"],
+    "types": ["node"],
+
+    // Other Outputs
+    "sourceMap": true,
+    "declaration": true,
+    "declarationMap": true,
+
+    // Stricter Typechecking Options
+    "noUncheckedIndexedAccess": true,
+    "exactOptionalPropertyTypes": true,
+
+    // Style Options
+    // "noImplicitReturns": true,
+    // "noImplicitOverride": true,
+    // "noUnusedLocals": true,
+    // "noUnusedParameters": true,
+    // "noFallthroughCasesInSwitch": true,
+    // "noPropertyAccessFromIndexSignature": true,
+
+    // Recommended Options
+    "strict": true,
+    "jsx": "react-jsx",
+    "verbatimModuleSyntax": false,
+    "isolatedModules": true,
+    "moduleDetection": "force",
+    "skipLibCheck": true,
+
+    "composite": true,
+    "allowJs": true,
+    "noEmit": true,
+  },
+  "include": [
+    "./*.js",
+    "./.*.js",
+    "./*.mjs",
+    "./.*.mjs",
+    "./*.cjs",
+    "./.*.cjs",
+    "./scripts/*.ts",
+    "./.husky/*.cjs",
+  ],
+}
diff --git a/yarn.lock b/yarn.lock
index f7a98680f..165a3fe9a 100644
--- a/yarn.lock
+++ b/yarn.lock
@@ -334,15 +334,13 @@ __metadata:
     "@types/cli-progress": "npm:^3"
     "@types/cross-spawn": "npm:^6.0.6"
     "@types/inquirer": "npm:^9.0.7"
-    "@types/mocha": "npm:^10"
-    "@types/node": "npm:^20.19.15"
+    "@types/node": "npm:^24.10.9"
     babel-plugin-istanbul: "npm:^6.1.1"
     bson: "npm:^6.3.0"
     cli-progress: "npm:^3.12.0"
     conf: "npm:^12.0.0"
     cross-spawn: "npm:^7.0.3"
     joi: "npm:^17.7.0"
-    mocha: "npm:^10.2.0"
     mongodb: "npm:^4.7.0"
     nanoid: "npm:^4.0.2"
     nyc: "npm:^15.1.0"
@@ -376,8 +374,9 @@ __metadata:
     "@emotion/styled": "npm:^11.10.6"
     "@gmod/gff": "npm:^2.0.0"
     "@gmod/indexedfasta": "npm:^2.0.4"
-    "@jbrowse/core": "npm:^3.6.5"
-    "@mui/material": "npm:^7.0.0"
+    "@jbrowse/core": "npm:^4.1.1"
+    "@jbrowse/mobx-state-tree": "npm:^5.5.0"
+    "@mui/material": "npm:^7.3.7"
     "@nestjs/cli": "npm:^10.1.10"
     "@nestjs/common": "npm:^10.1.0"
     "@nestjs/config": "npm:^3.0.0"
@@ -394,10 +393,9 @@ __metadata:
     "@nestjs/websockets": "npm:^10.1.0"
     "@types/express": "npm:^4.17.13"
     "@types/express-session": "npm:^1"
-    "@types/jest": "npm:^27.0.1"
-    "@types/multer": "npm:^1.4.7"
-    "@types/node": "npm:^20.19.15"
-    "@types/node-fetch": "npm:^2.6.2"
+    "@types/jest": "npm:^30.0.0"
+    "@types/multer": "npm:^2.0.0"
+    "@types/node": "npm:^24.10.9"
     "@types/passport-google-oauth20": "npm:^2.0.11"
     "@types/passport-jwt": "npm:^3.0.6"
     "@types/passport-local": "npm:^1.0.34"
@@ -416,12 +414,10 @@ __metadata:
     material-ui-popup-state: "npm:^5.0.4"
     mobx: "npm:^6.6.1"
     mobx-react: "npm:^7.2.1"
-    mobx-state-tree: "npm:^5.4.0"
     mongodb: "npm:^4.7.0"
     mongoose: "npm:^6.12.0"
     mongoose-id-validator: "npm:^0.6.0"
-    multer: "npm:^1.4.5-lts.1"
-    node-fetch: "npm:^2.6.7"
+    multer: "npm:^2.0.2"
     passport: "npm:^0.5.0"
     passport-google-oauth20: "npm:^2.0.0"
     passport-jwt: "npm:^4.0.0"
@@ -439,7 +435,7 @@ __metadata:
     source-map-support: "npm:^0.5.20"
     stream-concat: "npm:^1.0.0"
     supertest: "npm:^6.1.3"
-    ts-jest: "npm:^29.1.1"
+    ts-jest: "npm:^29.4.6"
     ts-loader: "npm:^9.2.3"
     ts-node: "npm:^10.3.0"
     ts-node-dev: "npm:^1.1.8"
@@ -457,24 +453,25 @@ __metadata:
     "@apollo-annotation/mst": "workspace:^"
     "@apollo-annotation/schemas": "workspace:^"
     "@gmod/gff": "npm:^2.0.0"
-    "@jbrowse/core": "npm:^3.6.5"
+    "@jbrowse/core": "npm:^4.1.1"
     "@nestjs/common": "npm:^10.1.0"
     "@nestjs/core": "npm:^10.1.0"
-    "@types/node": "npm:^20.19.15"
+    "@types/node": "npm:^24.10.9"
     bson-objectid: "npm:^2.0.4"
     generic-filehandle: "npm:^3.0.0"
     mongoose: "npm:^6.12.0"
     tslib: "npm:^2.3.1"
     typescript: "npm:^5.5.3"
   peerDependencies:
-    "@mui/material": ^7.0.0
+    "@jbrowse/mobx-state-tree": ^5.5.0
+    "@mui/material": ^7.3.7
     "@mui/x-data-grid": ^8.0.0
     mobx: ^6.6.1
     mobx-react: ^7.2.1
-    mobx-state-tree: ^5.4.0
     prop-types: ^15.8.1
     react: ^18.2.0
     react-dom: ^18.2.0
+    reflect-metadata: ^0.1.13
     rxjs: ^7.4.0
     tss-react: ^4.6.1
   languageName: unknown
@@ -487,27 +484,47 @@ __metadata:
     "@apollo-annotation/common": "workspace:^"
     "@apollo-annotation/mst": "workspace:^"
     "@apollo-annotation/shared": "workspace:^"
+    "@babel/core": "npm:^7.28.6"
+    "@babel/plugin-proposal-class-properties": "npm:^7.18.6"
+    "@babel/preset-env": "npm:^7.28.6"
     "@emotion/react": "npm:^11.10.6"
     "@emotion/styled": "npm:^11.10.6"
     "@gmod/gff": "npm:^2.0.0"
-    "@jbrowse/cli": "npm:^3.6.5"
-    "@jbrowse/core": "npm:^3.6.5"
+    "@jbrowse/cli": "npm:^4.1.1"
+    "@jbrowse/core": "npm:^4.1.1"
     "@jbrowse/development-tools": "npm:^2.2.1"
-    "@jbrowse/plugin-authentication": "npm:^3.6.5"
-    "@jbrowse/plugin-linear-genome-view": "npm:^3.6.5"
+    "@jbrowse/mobx-state-tree": "npm:^5.5.0"
+    "@jbrowse/plugin-authentication": "npm:^4.1.1"
+    "@jbrowse/plugin-linear-genome-view": "npm:^4.1.1"
     "@jest/globals": "npm:^29.0.3"
-    "@mui/icons-material": "npm:^6.5.0"
-    "@mui/material": "npm:^7.0.0"
+    "@mui/icons-material": "npm:^7.3.7"
+    "@mui/material": "npm:^7.3.7"
     "@mui/x-data-grid": "npm:^8.0.0"
+    "@rollup/plugin-babel": "npm:^6.1.0"
+    "@rollup/plugin-commonjs": "npm:^29.0.0"
+    "@rollup/plugin-json": "npm:^6.1.0"
+    "@rollup/plugin-node-resolve": "npm:^16.0.3"
+    "@rollup/plugin-typescript": "npm:^12.3.0"
     "@types/autosuggest-highlight": "npm:^3"
+    "@types/babel-plugin-macros": "npm:^3"
+    "@types/babel__core": "npm:^7"
+    "@types/babel__preset-env": "npm:^7"
     "@types/file-saver": "npm:^2"
     "@types/jsonpath": "npm:^0.2.0"
-    "@types/node": "npm:^20.19.15"
+    "@types/lodash.merge": "npm:^4"
+    "@types/node": "npm:^24.10.9"
     "@types/prop-types": "npm:^15"
     "@types/react": "npm:^18.3.4"
     "@types/react-dom": "npm:^18"
     autosuggest-highlight: "npm:^3.3.4"
+    babel-plugin-annotate-pure-calls: "npm:^0.5.0"
+    babel-plugin-dev-expression: "npm:^0.2.3"
+    babel-plugin-macros: "npm:^3.1.0"
+    babel-plugin-polyfill-regenerator: "npm:^0.6.6"
+    babel-plugin-transform-rename-import: "npm:^2.3.0"
     bson-objectid: "npm:^2.0.4"
+    builtin-modules: "npm:^5.0.0"
+    chalk: "npm:^5.6.2"
     clsx: "npm:^1.1.1"
     cypress: "npm:12.17.3"
     cypress-image-diff-html-report: "npm:^2.2.0"
@@ -520,34 +537,39 @@ __metadata:
     idb: "npm:^7.1.1"
     jest: "npm:^29.6.2"
     jest-fetch-mock: "npm:^3.0.3"
+    jest-util: "npm:^30.2.0"
     jsonpath: "npm:^1.1.1"
     librpc-web-mod: "npm:^1.1.9"
+    lodash.merge: "npm:^4.6.2"
     mobx: "npm:^6.6.1"
     mobx-react: "npm:^7.2.1"
-    mobx-state-tree: "npm:^5.4.0"
     nanoid: "npm:^4.0.2"
     npm-run-all: "npm:^4.1.5"
     prop-types: "npm:^15.8.1"
     react: "npm:^18.2.0"
     react-dom: "npm:^18.2.0"
     rimraf: "npm:^3.0.2"
-    rollup: "npm:^2.79.2"
+    rollup: "npm:^4.57.0"
+    rollup-plugin-external-globals: "npm:^0.13.0"
+    rollup-plugin-polyfill-node: "npm:^0.13.0"
+    rollup-plugin-sourcemaps: "npm:^0.6.3"
+    rollup-plugin-terser: "npm:^7.0.2"
     rxjs: "npm:^7.4.0"
     serve: "npm:^14.0.1"
     shx: "npm:^0.3.3"
     socket.io-client: "npm:^4.5.4"
     start-server-and-test: "npm:^1.11.7"
-    ts-jest: "npm:^29.1.1"
+    ts-jest: "npm:^29.4.6"
     ts-node: "npm:^10.3.0"
     tslib: "npm:^2.3.1"
     tss-react: "npm:^4.6.1"
     typescript: "npm:^5.5.3"
   peerDependencies:
-    "@jbrowse/core": ^3.0.1
-    "@mui/material": ^7.0.0
+    "@jbrowse/core": ^4.1.1
+    "@jbrowse/mobx-state-tree": ^5.5.0
+    "@mui/material": ^7.3.7
     mobx: ^6.6.1
     mobx-react: ^9.0.0
-    mobx-state-tree: ^5.4.0
     prop-types: ^15.8.1
     react: ^18.2.0
     react-dom: ^18.2.0
@@ -560,9 +582,9 @@ __metadata:
   version: 0.0.0-use.local
   resolution: "@apollo-annotation/mst@workspace:packages/apollo-mst"
   dependencies:
-    "@jbrowse/core": "npm:^3.6.5"
+    "@jbrowse/core": "npm:^4.1.1"
+    "@jbrowse/mobx-state-tree": "npm:^5.5.0"
     mobx: "npm:^6.6.1"
-    mobx-state-tree: "npm:^5.4.0"
     react-dom: "npm:^18.2.0"
     rxjs: "npm:^7.4.0"
     tslib: "npm:^2.3.1"
@@ -578,7 +600,7 @@ __metadata:
     "@nestjs/common": "npm:^10.1.0"
     "@nestjs/core": "npm:^10.1.0"
     "@nestjs/mongoose": "npm:^10.0.0"
-    "@types/node": "npm:^20.19.15"
+    "@types/node": "npm:^24.10.9"
     mongoose: "npm:^6.12.0"
     reflect-metadata: "npm:^0.1.13"
     rxjs: "npm:^7.4.0"
@@ -596,11 +618,12 @@ __metadata:
     "@apollo-annotation/schemas": "workspace:^"
     "@gmod/gff": "npm:^2.0.0"
     "@gmod/indexedfasta": "npm:^2.0.4"
-    "@jbrowse/core": "npm:^3.6.5"
+    "@jbrowse/core": "npm:^4.1.1"
+    "@jbrowse/mobx-state-tree": "npm:^5.5.0"
     "@nestjs/common": "npm:^10.1.0"
     "@nestjs/core": "npm:^10.1.0"
     "@types/chai": "npm:^4.3.19"
-    "@types/node": "npm:^20.19.15"
+    "@types/node": "npm:^24.10.9"
     bson-objectid: "npm:^2.0.4"
     chai: "npm:^5.1.1"
     chai-exclude: "npm:^3.0.0"
@@ -608,7 +631,6 @@ __metadata:
     glob: "npm:^11.0.0"
     jwt-decode: "npm:^3.1.2"
     mobx: "npm:^6.6.1"
-    mobx-state-tree: "npm:^5.4.0"
     mongoose: "npm:^6.12.0"
     react-dom: "npm:^18.2.0"
     rimraf: "npm:^3.0.2"
@@ -617,14 +639,15 @@ __metadata:
     tsx: "npm:^4.6.2"
     typescript: "npm:^5.5.3"
   peerDependencies:
-    "@mui/material": ^7.0.0
+    "@jbrowse/mobx-state-tree": ^5.5.0
+    "@mui/material": ^7.3.7
     "@mui/x-data-grid": ^8.0.0
     mobx: ^6.6.1
     mobx-react: ^7.2.1
-    mobx-state-tree: ^5.4.0
     prop-types: ^15.8.1
     react: ^18.2.0
     react-dom: ^18.2.0
+    reflect-metadata: ^0.1.13
     rxjs: ^7.4.0
   languageName: unknown
   linkType: soft
@@ -641,7 +664,7 @@ __metadata:
     "@docusaurus/tsconfig": "npm:^3.5.2"
     "@docusaurus/types": "npm:^3.5.2"
     "@mdx-js/react": "npm:^3.0.0"
-    "@types/node": "npm:^20.19.15"
+    "@types/node": "npm:^24.10.9"
     "@types/react": "npm:^18.3.4"
     clsx: "npm:^1.1.1"
     prism-react-renderer: "npm:^2.3.0"
@@ -1899,6 +1922,17 @@ __metadata:
   languageName: node
   linkType: hard
 
+"@babel/code-frame@npm:^7.28.6":
+  version: 7.28.6
+  resolution: "@babel/code-frame@npm:7.28.6"
+  dependencies:
+    "@babel/helper-validator-identifier": "npm:^7.28.5"
+    js-tokens: "npm:^4.0.0"
+    picocolors: "npm:^1.1.1"
+  checksum: 10c0/ed5d57f99455e3b1c23e75ebb8430c6b9800b4ecd0121b4348b97cecb65406a47778d6db61f0d538a4958bb01b4b277e90348a68d39bd3beff1d7c940ed6dd66
+  languageName: node
+  linkType: hard
+
 "@babel/compat-data@npm:^7.22.20, @babel/compat-data@npm:^7.22.6, @babel/compat-data@npm:^7.22.9":
   version: 7.22.20
   resolution: "@babel/compat-data@npm:7.22.20"
@@ -1927,6 +1961,13 @@ __metadata:
   languageName: node
   linkType: hard
 
+"@babel/compat-data@npm:^7.28.6":
+  version: 7.28.6
+  resolution: "@babel/compat-data@npm:7.28.6"
+  checksum: 10c0/2d047431041281eaf33e9943d1a269d3374dbc9b498cafe6a18f5ee9aee7bb96f7f6cac0304eab4d13c41fc4db00fe4ca16c7aa44469ca6a211b8b6343b78fc4
+  languageName: node
+  linkType: hard
+
 "@babel/core@npm:^7.11.6, @babel/core@npm:^7.12.3, @babel/core@npm:^7.16.0":
   version: 7.23.0
   resolution: "@babel/core@npm:7.23.0"
@@ -1996,6 +2037,29 @@ __metadata:
   languageName: node
   linkType: hard
 
+"@babel/core@npm:^7.28.6":
+  version: 7.28.6
+  resolution: "@babel/core@npm:7.28.6"
+  dependencies:
+    "@babel/code-frame": "npm:^7.28.6"
+    "@babel/generator": "npm:^7.28.6"
+    "@babel/helper-compilation-targets": "npm:^7.28.6"
+    "@babel/helper-module-transforms": "npm:^7.28.6"
+    "@babel/helpers": "npm:^7.28.6"
+    "@babel/parser": "npm:^7.28.6"
+    "@babel/template": "npm:^7.28.6"
+    "@babel/traverse": "npm:^7.28.6"
+    "@babel/types": "npm:^7.28.6"
+    "@jridgewell/remapping": "npm:^2.3.5"
+    convert-source-map: "npm:^2.0.0"
+    debug: "npm:^4.1.0"
+    gensync: "npm:^1.0.0-beta.2"
+    json5: "npm:^2.2.3"
+    semver: "npm:^6.3.1"
+  checksum: 10c0/716b88b1ab057aa53ffa40f2b2fb7e4ab7a35cd6a065fa60e55ca13d2a666672592329f7ea9269aec17e90cc7ce29f42eda566d07859bfd998329a9f283faadb
+  languageName: node
+  linkType: hard
+
 "@babel/core@npm:^7.7.5, @babel/core@npm:^7.8.7":
   version: 7.23.6
   resolution: "@babel/core@npm:7.23.6"
@@ -2068,6 +2132,19 @@ __metadata:
   languageName: node
   linkType: hard
 
+"@babel/generator@npm:^7.28.6":
+  version: 7.28.6
+  resolution: "@babel/generator@npm:7.28.6"
+  dependencies:
+    "@babel/parser": "npm:^7.28.6"
+    "@babel/types": "npm:^7.28.6"
+    "@jridgewell/gen-mapping": "npm:^0.3.12"
+    "@jridgewell/trace-mapping": "npm:^0.3.28"
+    jsesc: "npm:^3.0.2"
+  checksum: 10c0/162fa358484a9a18e8da1235d998f10ea77c63bab408c8d3e327d5833f120631a77ff022c5ed1d838ee00523f8bb75df1f08196d3657d0bca9f2cfeb8503cc12
+  languageName: node
+  linkType: hard
+
 "@babel/helper-annotate-as-pure@npm:^7.22.5":
   version: 7.22.5
   resolution: "@babel/helper-annotate-as-pure@npm:7.22.5"
@@ -2086,6 +2163,15 @@ __metadata:
   languageName: node
   linkType: hard
 
+"@babel/helper-annotate-as-pure@npm:^7.27.1, @babel/helper-annotate-as-pure@npm:^7.27.3":
+  version: 7.27.3
+  resolution: "@babel/helper-annotate-as-pure@npm:7.27.3"
+  dependencies:
+    "@babel/types": "npm:^7.27.3"
+  checksum: 10c0/94996ce0a05b7229f956033e6dcd69393db2b0886d0db6aff41e704390402b8cdcca11f61449cb4f86cfd9e61b5ad3a73e4fa661eeed7846b125bd1c33dbc633
+  languageName: node
+  linkType: hard
+
 "@babel/helper-builder-binary-assignment-operator-visitor@npm:^7.22.5":
   version: 7.22.15
   resolution: "@babel/helper-builder-binary-assignment-operator-visitor@npm:7.22.15"
@@ -2144,6 +2230,19 @@ __metadata:
   languageName: node
   linkType: hard
 
+"@babel/helper-compilation-targets@npm:^7.27.1, @babel/helper-compilation-targets@npm:^7.28.6":
+  version: 7.28.6
+  resolution: "@babel/helper-compilation-targets@npm:7.28.6"
+  dependencies:
+    "@babel/compat-data": "npm:^7.28.6"
+    "@babel/helper-validator-option": "npm:^7.27.1"
+    browserslist: "npm:^4.24.0"
+    lru-cache: "npm:^5.1.1"
+    semver: "npm:^6.3.1"
+  checksum: 10c0/3fcdf3b1b857a1578e99d20508859dbd3f22f3c87b8a0f3dc540627b4be539bae7f6e61e49d931542fe5b557545347272bbdacd7f58a5c77025a18b745593a50
+  languageName: node
+  linkType: hard
+
 "@babel/helper-compilation-targets@npm:^7.27.2":
   version: 7.27.2
   resolution: "@babel/helper-compilation-targets@npm:7.27.2"
@@ -2193,6 +2292,23 @@ __metadata:
   languageName: node
   linkType: hard
 
+"@babel/helper-create-class-features-plugin@npm:^7.28.6":
+  version: 7.28.6
+  resolution: "@babel/helper-create-class-features-plugin@npm:7.28.6"
+  dependencies:
+    "@babel/helper-annotate-as-pure": "npm:^7.27.3"
+    "@babel/helper-member-expression-to-functions": "npm:^7.28.5"
+    "@babel/helper-optimise-call-expression": "npm:^7.27.1"
+    "@babel/helper-replace-supers": "npm:^7.28.6"
+    "@babel/helper-skip-transparent-expression-wrappers": "npm:^7.27.1"
+    "@babel/traverse": "npm:^7.28.6"
+    semver: "npm:^6.3.1"
+  peerDependencies:
+    "@babel/core": ^7.0.0
+  checksum: 10c0/0b62b46717891f4366006b88c9b7f277980d4f578c4c3789b7a4f5a2e09e121de4cda9a414ab403986745cd3ad1af3fe2d948c9f78ab80d4dc085afc9602af50
+  languageName: node
+  linkType: hard
+
 "@babel/helper-create-regexp-features-plugin@npm:^7.18.6, @babel/helper-create-regexp-features-plugin@npm:^7.22.5":
   version: 7.22.15
   resolution: "@babel/helper-create-regexp-features-plugin@npm:7.22.15"
@@ -2219,6 +2335,19 @@ __metadata:
   languageName: node
   linkType: hard
 
+"@babel/helper-create-regexp-features-plugin@npm:^7.27.1, @babel/helper-create-regexp-features-plugin@npm:^7.28.5":
+  version: 7.28.5
+  resolution: "@babel/helper-create-regexp-features-plugin@npm:7.28.5"
+  dependencies:
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+  resolution: "@babel/plugin-bugfix-firefox-class-in-computed-class-key@npm:7.28.5"
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+  resolution: "@babel/plugin-bugfix-safari-class-field-initializer-scope@npm:7.27.1"
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+  resolution: "@babel/plugin-bugfix-v8-spread-parameters-in-optional-chaining@npm:7.27.1"
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+  resolution: "@babel/plugin-syntax-import-assertions@npm:7.28.6"
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-  resolution: "@jbrowse/cli@npm:3.6.5"
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+  resolution: "@jbrowse/cli@npm:4.1.3"
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-    decompress: "npm:^4.0.0"
-    express: "npm:^5.1.0"
-    ixixx: "npm:^2.0.1"
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+  resolution: "@jbrowse/text-indexing-core@npm:4.1.3"
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+  resolution: "@jest/diff-sequences@npm:30.0.1"
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   resolution: "@jest/environment@npm:29.7.0"
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@@ -6518,6 +7754,13 @@ __metadata:
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   resolution: "@jest/globals@npm:29.7.0"
@@ -6530,6 +7773,16 @@ __metadata:
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+  version: 30.0.1
+  resolution: "@jest/pattern@npm:30.0.1"
+  dependencies:
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+    jest-regex-util: "npm:30.0.1"
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   resolution: "@jest/reporters@npm:29.7.0"
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+"@jest/schemas@npm:30.0.5":
+  version: 30.0.5
+  resolution: "@jest/schemas@npm:30.0.5"
+  dependencies:
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+  languageName: node
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+
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   resolution: "@jest/schemas@npm:29.6.3"
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+  version: 30.2.0
+  resolution: "@jest/types@npm:30.2.0"
+  dependencies:
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+    "@jest/schemas": "npm:30.0.5"
+    "@types/istanbul-lib-coverage": "npm:^2.0.6"
+    "@types/istanbul-reports": "npm:^3.0.4"
+    "@types/node": "npm:*"
+    "@types/yargs": "npm:^17.0.33"
+    chalk: "npm:^4.1.2"
+  checksum: 10c0/ae121f6963bd9ed1cd9651db7be91bf14c05bff0d0eec4fca9fecf586bea4005e8f1de8cc9b8ef72e424ea96a309d123bef510b55a6a17a3b4b91a39d775e5cd
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-  languageName: node
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-  peerDependenciesMeta:
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+  languageName: node
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+  languageName: node
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+  languageName: node
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-  resolution: "@types/multer@npm:1.4.8"
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-  resolution: "dompurify@npm:3.2.4"
+"dompurify@npm:^3.3.1":
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+  resolution: "dompurify@npm:3.3.1"
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   dependenciesMeta:
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+  resolution: "electron-to-chromium@npm:1.5.279"
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+
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-  resolution: "express@npm:5.1.0"
+"express@npm:^5.2.1":
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+  resolution: "express@npm:5.2.1"
   dependencies:
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-    body-parser: "npm:^2.2.0"
+    body-parser: "npm:^2.2.1"
     content-disposition: "npm:^1.0.0"
     content-type: "npm:^1.0.5"
     cookie: "npm:^0.7.1"
     cookie-signature: "npm:^1.2.1"
     debug: "npm:^4.4.0"
+    depd: "npm:^2.0.0"
     encodeurl: "npm:^2.0.0"
     escape-html: "npm:^1.0.3"
     etag: "npm:^1.8.1"
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-"file-saver@npm:^2.0.0, file-saver@npm:^2.0.5":
+"file-saver-es@npm:^2.0.5":
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+  resolution: "file-saver-es@npm:2.0.5"
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+  languageName: node
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+"find-up@npm:^5.0.0":
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+  resolution: "find-up@npm:5.0.0"
+  dependencies:
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+  languageName: node
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+
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+"generic-filehandle2@npm:^2.0.18":
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+  resolution: "generic-filehandle2@npm:2.0.18"
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+  resolution: "http-errors@npm:2.0.1"
+  dependencies:
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+    setprototypeof: "npm:~1.2.0"
+    statuses: "npm:~2.0.2"
+    toidentifier: "npm:~1.0.1"
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+  languageName: node
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+
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   resolution: "http-parser-js@npm:0.5.8"
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-  version: 0.7.0
-  resolution: "iconv-lite@npm:0.7.0"
+"iconv-lite@npm:^0.6.2":
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+  resolution: "iconv-lite@npm:0.6.3"
   dependencies:
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-  resolution: "iconv-lite@npm:0.6.3"
+"iconv-lite@npm:^0.7.0, iconv-lite@npm:~0.7.0":
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+"idb@npm:^8.0.3":
+  version: 8.0.3
+  resolution: "idb@npm:8.0.3"
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+  languageName: node
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+
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@@ -20270,6 +22058,15 @@ __metadata:
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+"is-core-module@npm:^2.16.1":
+  version: 2.16.1
+  resolution: "is-core-module@npm:2.16.1"
+  dependencies:
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+  languageName: node
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+
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   resolution: "is-core-module@npm:2.13.1"
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-"is-plain-obj@npm:^2.0.0, is-plain-obj@npm:^2.1.0":
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+"is-reference@npm:^3.0.2":
+  version: 3.0.3
+  resolution: "is-reference@npm:3.0.3"
+  dependencies:
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+  languageName: node
+  linkType: hard
+
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   resolution: "is-regex@npm:1.1.4"
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-"ixixx@npm:^2.0.1":
-  version: 2.2.2
-  resolution: "ixixx@npm:2.2.2"
+"ixixx@npm:^3.0.3":
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+  resolution: "ixixx@npm:3.0.3"
   dependencies:
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-    external-sorting: "npm:^1.3.1"
     split2: "npm:^4.1.0"
     tmp: "npm:^0.2.1"
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-  resolution: "jest-diff@npm:27.5.1"
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+  resolution: "jest-diff@npm:30.2.0"
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+    chalk: "npm:^4.1.2"
+    pretty-format: "npm:30.2.0"
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-  resolution: "jest-matcher-utils@npm:27.5.1"
+"jest-matcher-utils@npm:30.2.0":
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   dependencies:
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-    jest-diff: "npm:^27.5.1"
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+    jest-diff: "npm:30.2.0"
+    pretty-format: "npm:30.2.0"
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+  version: 30.2.0
+  resolution: "jest-message-util@npm:30.2.0"
+  dependencies:
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+    "@jest/types": "npm:30.2.0"
+    "@types/stack-utils": "npm:^2.0.3"
+    chalk: "npm:^4.1.2"
+    graceful-fs: "npm:^4.2.11"
+    micromatch: "npm:^4.0.8"
+    pretty-format: "npm:30.2.0"
+    slash: "npm:^3.0.0"
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+  languageName: node
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+
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   resolution: "jest-message-util@npm:29.7.0"
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+  resolution: "jest-mock@npm:30.2.0"
+  dependencies:
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+    "@types/node": "npm:*"
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+  languageName: node
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   resolution: "jest-mock@npm:29.7.0"
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+  resolution: "jest-regex-util@npm:30.0.1"
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+  languageName: node
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+
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-"jest-util@npm:^29.0.0, jest-util@npm:^29.7.0":
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+  resolution: "jest-util@npm:30.2.0"
+  dependencies:
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+    "@types/node": "npm:*"
+    chalk: "npm:^4.1.2"
+    ci-info: "npm:^4.2.0"
+    graceful-fs: "npm:^4.2.11"
+    picomatch: "npm:^4.0.2"
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+  languageName: node
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-  languageName: node
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+"js-yaml@npm:^4.1.0":
+  version: 4.1.0
+  resolution: "js-yaml@npm:4.1.0"
+  dependencies:
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+  bin:
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+  languageName: node
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+
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   resolution: "jsbn@npm:0.1.1"
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+"librpc-web-mod@npm:^2.1.1":
+  version: 2.1.1
+  resolution: "librpc-web-mod@npm:2.1.1"
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+  languageName: node
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+
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   resolution: "lilconfig@npm:3.0.0"
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   dependencies:
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+"magic-string@npm:^0.30.10":
+  version: 0.30.21
+  resolution: "magic-string@npm:0.30.21"
+  dependencies:
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+  languageName: node
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+
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   resolution: "magic-string@npm:0.30.19"
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-"make-error@npm:1.x, make-error@npm:^1.1.1":
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-  resolution: "minimatch@npm:5.0.1"
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-"mkdirp@npm:^0.5.4":
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-"mobx-react-lite@npm:^4.1.0":
-  version: 4.1.0
-  resolution: "mobx-react-lite@npm:4.1.0"
+"mobx-react-lite@npm:^4.1.1":
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+  resolution: "mobx-react-lite@npm:4.1.1"
   dependencies:
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     react-native:
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-"mobx-react@npm:^9.0.0":
-  version: 9.2.0
-  resolution: "mobx-react@npm:9.2.0"
+"mobx-react@npm:^9.2.1":
+  version: 9.2.1
+  resolution: "mobx-react@npm:9.2.1"
   dependencies:
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+    mobx-react-lite: "npm:^4.1.1"
   peerDependencies:
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     react: ^16.8.0 || ^17 || ^18 || ^19
@@ -24086,23 +25924,14 @@ __metadata:
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     react-native:
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-  checksum: 10c0/253410a3a4d5005d6f8ec5ed8e6c9696381e65ffe03b072ee6baa7bb5973eaaa0b51f10c83849a94a1b03011538c76b80af26c6230808bd99fb3dfd130ac1845
-  languageName: node
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-"mobx-state-tree@npm:^5.0.0, mobx-state-tree@npm:^5.4.0":
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+"mobx@npm:^6.15.0":
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+  resolution: "mobx@npm:6.15.0"
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-    nanoid: "npm:3.3.3"
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-    yargs-unparser: "npm:2.0.0"
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-    mocha: bin/mocha.js
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-  languageName: node
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-  version: 1.4.5-lts.1
-  resolution: "multer@npm:1.4.5-lts.1"
+"multer@npm:^2.0.2":
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+  resolution: "multer@npm:2.0.2"
   dependencies:
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-    busboy: "npm:^1.0.0"
-    concat-stream: "npm:^1.5.2"
-    mkdirp: "npm:^0.5.4"
+    busboy: "npm:^1.6.0"
+    concat-stream: "npm:^2.0.0"
+    mkdirp: "npm:^0.5.6"
     object-assign: "npm:^4.1.1"
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-    xtend: "npm:^4.0.0"
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+    type-is: "npm:^1.6.18"
+    xtend: "npm:^4.0.2"
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-  languageName: node
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-  languageName: node
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-"node-fetch@npm:^2.6.1, node-fetch@npm:^2.6.12, node-fetch@npm:^2.6.7":
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   dependencies:
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+"node-releases@npm:^2.0.27":
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+  resolution: "node-releases@npm:2.0.27"
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+  languageName: node
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+
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   resolution: "nopt@npm:5.0.0"
@@ -25617,6 +27405,13 @@ __metadata:
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+"pako-esm2@npm:^2.0.2":
+  version: 2.0.2
+  resolution: "pako-esm2@npm:2.0.2"
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+  languageName: node
+  linkType: hard
+
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   resolution: "pako@npm:1.0.11"
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-  resolution: "pretty-format@npm:27.5.1"
+"pretty-format@npm:30.2.0, pretty-format@npm:^30.0.0":
+  version: 30.2.0
+  resolution: "pretty-format@npm:30.2.0"
   dependencies:
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-    ansi-styles: "npm:^5.0.0"
-    react-is: "npm:^17.0.1"
-  checksum: 10c0/0cbda1031aa30c659e10921fa94e0dd3f903ecbbbe7184a729ad66f2b6e7f17891e8c7d7654c458fa4ccb1a411ffb695b4f17bbcd3fe075fabe181027c4040ed
+    "@jest/schemas": "npm:30.0.5"
+    ansi-styles: "npm:^5.2.0"
+    react-is: "npm:^18.3.1"
+  checksum: 10c0/8fdacfd281aa98124e5df80b2c17223fdcb84433876422b54863a6849381b3059eb42b9806d92d2853826bcb966bcb98d499bea5b1e912d869a3c3107fd38d35
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+"qs@npm:^6.14.1":
+  version: 6.14.1
+  resolution: "qs@npm:6.14.1"
+  dependencies:
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+  checksum: 10c0/0e3b22dc451f48ce5940cbbc7c7d9068d895074f8c969c0801ac15c1313d1859c4d738e46dc4da2f498f41a9ffd8c201bd9fb12df67799b827db94cc373d2613
+  languageName: node
+  linkType: hard
+
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   resolution: "qs@npm:6.10.4"
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-  resolution: "quick-lru@npm:4.0.1"
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-  languageName: node
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-
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   resolution: "quick-lru@npm:5.1.1"
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-  resolution: "quickselect@npm:2.0.0"
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-  languageName: node
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   resolution: "random-bytes@npm:1.0.0"
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-  resolution: "raw-body@npm:3.0.1"
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-    http-errors: "npm:2.0.0"
-    iconv-lite: "npm:0.7.0"
-    unpipe: "npm:1.0.0"
-  checksum: 10c0/892f4fbd21ecab7e2fed0f045f7af9e16df7e8050879639d4e482784a2f4640aaaa33d916a0e98013f23acb82e09c2e3c57f84ab97104449f728d22f65a7d79a
-  languageName: node
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-
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-  version: 3.0.1
-  resolution: "rbush@npm:3.0.1"
+"raw-body@npm:^3.0.1":
+  version: 3.0.2
+  resolution: "raw-body@npm:3.0.2"
   dependencies:
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-  checksum: 10c0/55311586c30cdedaa2220de6f1da45fe1fa806263afbf7b6f4c0078983830c2abc7771187896d68bfc9078cb279079fb4c84971831da4b74384aab2c2c417758
+    bytes: "npm:~3.1.2"
+    http-errors: "npm:~2.0.1"
+    iconv-lite: "npm:~0.7.0"
+    unpipe: "npm:~1.0.0"
+  checksum: 10c0/d266678d08e1e7abea62c0ce5864344e980fa81c64f6b481e9842c5beaed2cdcf975f658a3ccd67ad35fc919c1f6664ccc106067801850286a6cbe101de89f29
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-"react-draggable@npm:^4.4.5":
-  version: 4.4.6
-  resolution: "react-draggable@npm:4.4.6"
+"react-draggable@npm:^4.5.0":
+  version: 4.5.0
+  resolution: "react-draggable@npm:4.5.0"
   dependencies:
-    clsx: "npm:^1.1.1"
+    clsx: "npm:^2.1.1"
     prop-types: "npm:^15.8.1"
   peerDependencies:
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     react-dom: ">= 16.3.0"
-  checksum: 10c0/1e8cf47414a8554caa68447e5f27749bc40e1eabb4806e2dadcb39ab081d263f517d6aaec5231677e6b425603037c7e3386d1549898f9ffcc98a86cabafb2b9a
+  checksum: 10c0/6f7591fe450555218bf0d9e31984be02451bf3f678fb121f51ac0a0a645d01a1b5ea8248ef9afddcd24239028911fd88032194b9c00b30ad5ece76ea13397fc3
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-  resolution: "react-is@npm:16.13.1"
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-  languageName: node
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-  version: 17.0.2
-  resolution: "react-is@npm:17.0.2"
-  checksum: 10c0/2bdb6b93fbb1820b024b496042cce405c57e2f85e777c9aabd55f9b26d145408f9f74f5934676ffdc46f3dcff656d78413a6e43968e7b3f92eea35b3052e9053
+  version: 16.13.1
+  resolution: "react-is@npm:16.13.1"
+  checksum: 10c0/33977da7a5f1a287936a0c85639fec6ca74f4f15ef1e59a6bc20338fc73dc69555381e211f7a3529b8150a1f71e4225525b41b60b52965bda53ce7d47377ada1
   languageName: node
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+"react-is@npm:^18.3.1":
+  version: 18.3.1
+  resolution: "react-is@npm:18.3.1"
+  checksum: 10c0/f2f1e60010c683479e74c63f96b09fb41603527cd131a9959e2aee1e5a8b0caf270b365e5ca77d4a6b18aae659b60a86150bb3979073528877029b35aecd2072
+  languageName: node
+  linkType: hard
+
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   resolution: "react-is@npm:19.1.1"
@@ -27279,6 +29060,13 @@ __metadata:
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+"react-is@npm:^19.2.3":
+  version: 19.2.4
+  resolution: "react-is@npm:19.2.4"
+  checksum: 10c0/477a7cfc900f24194606e315fa353856a3a13487ea8eca841678817cad4daef64339ea0d1e84e58459fc75dbe0d9ba00bb0cc626db3d07e0cf31edc64cb4fa37
+  languageName: node
+  linkType: hard
+
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   resolution: "react-json-view-lite@npm:1.4.0"
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-"readable-stream@npm:^3.0.6, readable-stream@npm:^3.4.0, readable-stream@npm:^3.6.0":
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   dependencies:
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+"regenerate-unicode-properties@npm:^10.2.2":
+  version: 10.2.2
+  resolution: "regenerate-unicode-properties@npm:10.2.2"
+  dependencies:
+    regenerate: "npm:^1.4.2"
+  checksum: 10c0/66a1d6a1dbacdfc49afd88f20b2319a4c33cee56d245163e4d8f5f283e0f45d1085a78f7f7406dd19ea3a5dd7a7799cd020cd817c97464a7507f9d10fbdce87c
+  languageName: node
+  linkType: hard
+
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   version: 1.4.2
   resolution: "regenerate@npm:1.4.2"
@@ -27686,6 +29483,20 @@ __metadata:
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+"regexpu-core@npm:^6.3.1":
+  version: 6.4.0
+  resolution: "regexpu-core@npm:6.4.0"
+  dependencies:
+    regenerate: "npm:^1.4.2"
+    regenerate-unicode-properties: "npm:^10.2.2"
+    regjsgen: "npm:^0.8.0"
+    regjsparser: "npm:^0.13.0"
+    unicode-match-property-ecmascript: "npm:^2.0.0"
+    unicode-match-property-value-ecmascript: "npm:^2.2.1"
+  checksum: 10c0/1eed9783c023dd06fb1f3ce4b6e3fdf0bc1e30cb036f30aeb2019b351e5e0b74355b40462282ea5db092c79a79331c374c7e9897e44a5ca4509e9f0b570263de
+  languageName: node
+  linkType: hard
+
 "registry-auth-token@npm:3.3.2":
   version: 3.3.2
   resolution: "registry-auth-token@npm:3.3.2"
@@ -27723,6 +29534,13 @@ __metadata:
   languageName: node
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+"regjsgen@npm:^0.8.0":
+  version: 0.8.0
+  resolution: "regjsgen@npm:0.8.0"
+  checksum: 10c0/44f526c4fdbf0b29286101a282189e4dbb303f4013cf3fea058668d96d113b9180d3d03d1e13f6d4cbde38b7728bf951aecd9dc199938c080093a9a6f0d7a6bd
+  languageName: node
+  linkType: hard
+
 "regjsparser@npm:^0.12.0":
   version: 0.12.0
   resolution: "regjsparser@npm:0.12.0"
@@ -27734,6 +29552,17 @@ __metadata:
   languageName: node
   linkType: hard
 
+"regjsparser@npm:^0.13.0":
+  version: 0.13.0
+  resolution: "regjsparser@npm:0.13.0"
+  dependencies:
+    jsesc: "npm:~3.1.0"
+  bin:
+    regjsparser: bin/parser
+  checksum: 10c0/4702f85cda09f67747c1b2fb673a0f0e5d1ba39d55f177632265a0be471ba59e3f320623f411649141f752b126b8126eac3ff4c62d317921e430b0472bfc6071
+  languageName: node
+  linkType: hard
+
 "regjsparser@npm:^0.9.1":
   version: 0.9.1
   resolution: "regjsparser@npm:0.9.1"
@@ -28025,6 +29854,19 @@ __metadata:
   languageName: node
   linkType: hard
 
+"resolve@npm:^1.22.1, resolve@npm:^1.22.11":
+  version: 1.22.11
+  resolution: "resolve@npm:1.22.11"
+  dependencies:
+    is-core-module: "npm:^2.16.1"
+    path-parse: "npm:^1.0.7"
+    supports-preserve-symlinks-flag: "npm:^1.0.0"
+  bin:
+    resolve: bin/resolve
+  checksum: 10c0/f657191507530f2cbecb5815b1ee99b20741ea6ee02a59c57028e9ec4c2c8d7681afcc35febbd554ac0ded459db6f2d8153382c53a2f266cee2575e512674409
+  languageName: node
+  linkType: hard
+
 "resolve@npm:^2.0.0-next.5":
   version: 2.0.0-next.5
   resolution: "resolve@npm:2.0.0-next.5"
@@ -28051,6 +29893,19 @@ __metadata:
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   linkType: hard
 
+"resolve@patch:resolve@npm%3A^1.22.1#optional!builtin<compat/resolve>, resolve@patch:resolve@npm%3A^1.22.11#optional!builtin<compat/resolve>":
+  version: 1.22.11
+  resolution: "resolve@patch:resolve@npm%3A1.22.11#optional!builtin<compat/resolve>::version=1.22.11&hash=c3c19d"
+  dependencies:
+    is-core-module: "npm:^2.16.1"
+    path-parse: "npm:^1.0.7"
+    supports-preserve-symlinks-flag: "npm:^1.0.0"
+  bin:
+    resolve: bin/resolve
+  checksum: 10c0/ee5b182f2e37cb1165465e58c6abc797fec0a80b5ba3231607beb4677db0c9291ac010c47cf092b6daa2b7f518d69a0e21888e7e2b633f68d501a874212a8c63
+  languageName: node
+  linkType: hard
+
 "resolve@patch:resolve@npm%3A^2.0.0-next.5#optional!builtin<compat/resolve>":
   version: 2.0.0-next.5
   resolution: "resolve@patch:resolve@npm%3A2.0.0-next.5#optional!builtin<compat/resolve>::version=2.0.0-next.5&hash=c3c19d"
@@ -28163,6 +30018,20 @@ __metadata:
   languageName: node
   linkType: hard
 
+"rollup-plugin-external-globals@npm:^0.13.0":
+  version: 0.13.0
+  resolution: "rollup-plugin-external-globals@npm:0.13.0"
+  dependencies:
+    "@rollup/pluginutils": "npm:^5.1.0"
+    estree-walker: "npm:^3.0.3"
+    is-reference: "npm:^3.0.2"
+    magic-string: "npm:^0.30.10"
+  peerDependencies:
+    rollup: ^2.25.0 || ^3.3.0 || ^4.1.4
+  checksum: 10c0/c80be4b2c27ba33a4780ef70d39c1047f98da7322ce62a3877de06c3afdcb5fd213ad371f6c6eab5e5f7f711bad765999db43d44b2815236c62ff342a22ff328
+  languageName: node
+  linkType: hard
+
 "rollup-plugin-external-globals@npm:^0.6.1":
   version: 0.6.1
   resolution: "rollup-plugin-external-globals@npm:0.6.1"
@@ -28188,6 +30057,17 @@ __metadata:
   languageName: node
   linkType: hard
 
+"rollup-plugin-polyfill-node@npm:^0.13.0":
+  version: 0.13.0
+  resolution: "rollup-plugin-polyfill-node@npm:0.13.0"
+  dependencies:
+    "@rollup/plugin-inject": "npm:^5.0.4"
+  peerDependencies:
+    rollup: ^1.20.0 || ^2.0.0 || ^3.0.0 || ^4.0.0
+  checksum: 10c0/a6d7746d73b48869c2650d733a4f1bf4cd8613669959811485e866c13b6462465b227f9923a21521013cfc85dd23c28b5ccee1c1359584f1ccf6320e7c823fb3
+  languageName: node
+  linkType: hard
+
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   version: 0.6.3
   resolution: "rollup-plugin-sourcemaps@npm:0.6.3"
@@ -28218,17 +30098,93 @@ __metadata:
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-"rollup@npm:^2.79.2":
-  version: 2.79.2
-  resolution: "rollup@npm:2.79.2"
-  dependencies:
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+  version: 4.57.0
+  resolution: "rollup@npm:4.57.0"
+  dependencies:
+    "@rollup/rollup-android-arm-eabi": "npm:4.57.0"
+    "@rollup/rollup-android-arm64": "npm:4.57.0"
+    "@rollup/rollup-darwin-arm64": "npm:4.57.0"
+    "@rollup/rollup-darwin-x64": "npm:4.57.0"
+    "@rollup/rollup-freebsd-arm64": "npm:4.57.0"
+    "@rollup/rollup-freebsd-x64": "npm:4.57.0"
+    "@rollup/rollup-linux-arm-gnueabihf": "npm:4.57.0"
+    "@rollup/rollup-linux-arm-musleabihf": "npm:4.57.0"
+    "@rollup/rollup-linux-arm64-gnu": "npm:4.57.0"
+    "@rollup/rollup-linux-arm64-musl": "npm:4.57.0"
+    "@rollup/rollup-linux-loong64-gnu": "npm:4.57.0"
+    "@rollup/rollup-linux-loong64-musl": "npm:4.57.0"
+    "@rollup/rollup-linux-ppc64-gnu": "npm:4.57.0"
+    "@rollup/rollup-linux-ppc64-musl": "npm:4.57.0"
+    "@rollup/rollup-linux-riscv64-gnu": "npm:4.57.0"
+    "@rollup/rollup-linux-riscv64-musl": "npm:4.57.0"
+    "@rollup/rollup-linux-s390x-gnu": "npm:4.57.0"
+    "@rollup/rollup-linux-x64-gnu": "npm:4.57.0"
+    "@rollup/rollup-linux-x64-musl": "npm:4.57.0"
+    "@rollup/rollup-openbsd-x64": "npm:4.57.0"
+    "@rollup/rollup-openharmony-arm64": "npm:4.57.0"
+    "@rollup/rollup-win32-arm64-msvc": "npm:4.57.0"
+    "@rollup/rollup-win32-ia32-msvc": "npm:4.57.0"
+    "@rollup/rollup-win32-x64-gnu": "npm:4.57.0"
+    "@rollup/rollup-win32-x64-msvc": "npm:4.57.0"
+    "@types/estree": "npm:1.0.8"
     fsevents: "npm:~2.3.2"
   dependenciesMeta:
+    "@rollup/rollup-android-arm-eabi":
+      optional: true
+    "@rollup/rollup-android-arm64":
+      optional: true
+    "@rollup/rollup-darwin-arm64":
+      optional: true
+    "@rollup/rollup-darwin-x64":
+      optional: true
+    "@rollup/rollup-freebsd-arm64":
+      optional: true
+    "@rollup/rollup-freebsd-x64":
+      optional: true
+    "@rollup/rollup-linux-arm-gnueabihf":
+      optional: true
+    "@rollup/rollup-linux-arm-musleabihf":
+      optional: true
+    "@rollup/rollup-linux-arm64-gnu":
+      optional: true
+    "@rollup/rollup-linux-arm64-musl":
+      optional: true
+    "@rollup/rollup-linux-loong64-gnu":
+      optional: true
+    "@rollup/rollup-linux-loong64-musl":
+      optional: true
+    "@rollup/rollup-linux-ppc64-gnu":
+      optional: true
+    "@rollup/rollup-linux-ppc64-musl":
+      optional: true
+    "@rollup/rollup-linux-riscv64-gnu":
+      optional: true
+    "@rollup/rollup-linux-riscv64-musl":
+      optional: true
+    "@rollup/rollup-linux-s390x-gnu":
+      optional: true
+    "@rollup/rollup-linux-x64-gnu":
+      optional: true
+    "@rollup/rollup-linux-x64-musl":
+      optional: true
+    "@rollup/rollup-openbsd-x64":
+      optional: true
+    "@rollup/rollup-openharmony-arm64":
+      optional: true
+    "@rollup/rollup-win32-arm64-msvc":
+      optional: true
+    "@rollup/rollup-win32-ia32-msvc":
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+    "@rollup/rollup-win32-x64-gnu":
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+  languageName: node
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-  resolution: "ts-jest@npm:29.1.1"
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-    fast-json-stable-stringify: "npm:2.x"
-    jest-util: "npm:^29.0.0"
+    bs-logger: "npm:^0.2.6"
+    fast-json-stable-stringify: "npm:^2.1.0"
+    handlebars: "npm:^4.7.8"
     json5: "npm:^2.2.3"
-    lodash.memoize: "npm:4.x"
-    make-error: "npm:1.x"
-    semver: "npm:^7.5.3"
-    yargs-parser: "npm:^21.0.1"
+    lodash.memoize: "npm:^4.1.2"
+    make-error: "npm:^1.3.6"
+    semver: "npm:^7.7.3"
+    type-fest: "npm:^4.41.0"
+    yargs-parser: "npm:^21.1.1"
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     typescript: ">=4.3 <6"
   peerDependenciesMeta:
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-    ts-node-esm: dist/bin-esm.js
-    ts-node-script: dist/bin-script.js
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-    react: ^16.8.0 || ^17.0.0 || ^18.0.0 || ^19.0.0
-  peerDependenciesMeta:
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+
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+"undici-types@npm:~7.16.0":
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+  languageName: node
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+    picocolors: "npm:^1.1.1"
+  peerDependencies:
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+  bin:
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+"use-sync-external-store@npm:^1.6.0":
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+  resolution: "use-sync-external-store@npm:1.6.0"
+  peerDependencies:
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+  checksum: 10c0/35e1179f872a53227bdf8a827f7911da4c37c0f4091c29b76b1e32473d1670ebe7bcd880b808b7549ba9a5605c233350f800ffab963ee4a4ee346ee983b6019b
+  languageName: node
+  linkType: hard
+
 "utf8-byte-length@npm:^1.0.1":
   version: 1.0.4
   resolution: "utf8-byte-length@npm:1.0.4"
@@ -32542,13 +34505,6 @@ __metadata:
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-"workerpool@npm:6.2.1":
-  version: 6.2.1
-  resolution: "workerpool@npm:6.2.1"
-  checksum: 10c0/f0efd2d74eafd58eaeb36d7d85837d080f75c52b64893cff317b66257dd308e5c9f85ef0b12904f6c7f24ed2365bc3cfeba1f1d16aa736d84d6ef8156ae37c80
-  languageName: node
-  linkType: hard
-
 "wrap-ansi-cjs@npm:wrap-ansi@^7.0.0, wrap-ansi@npm:^7.0.0":
   version: 7.0.0
   resolution: "wrap-ansi@npm:7.0.0"
@@ -32692,7 +34648,7 @@ __metadata:
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-"xtend@npm:^4.0.0":
+"xtend@npm:^4.0.0, xtend@npm:^4.0.2":
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   resolution: "xtend@npm:4.0.2"
   checksum: 10c0/366ae4783eec6100f8a02dff02ac907bf29f9a00b82ac0264b4d8b832ead18306797e283cf19de776538babfdcb2101375ec5646b59f08c52128ac4ab812ed0e
@@ -32741,14 +34697,7 @@ __metadata:
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-"yargs-parser@npm:20.2.4":
-  version: 20.2.4
-  resolution: "yargs-parser@npm:20.2.4"
-  checksum: 10c0/08dc341f0b9f940c2fffc1d1decf3be00e28cabd2b578a694901eccc7dcd10577f10c6aa1b040fdd9a68b2042515a60f18476543bccacf9f3ce2c8534cd87435
-  languageName: node
-  linkType: hard
-
-"yargs-parser@npm:21.1.1, yargs-parser@npm:^21.0.1, yargs-parser@npm:^21.1.1":
+"yargs-parser@npm:21.1.1, yargs-parser@npm:^21.1.1":
   version: 21.1.1
   resolution: "yargs-parser@npm:21.1.1"
   checksum: 10c0/f84b5e48169479d2f402239c59f084cfd1c3acc197a05c59b98bab067452e6b3ea46d4dd8ba2985ba7b3d32a343d77df0debd6b343e5dae3da2aab2cdf5886b2
@@ -32765,40 +34714,6 @@ __metadata:
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-"yargs-parser@npm:^20.2.2":
-  version: 20.2.9
-  resolution: "yargs-parser@npm:20.2.9"
-  checksum: 10c0/0685a8e58bbfb57fab6aefe03c6da904a59769bd803a722bb098bd5b0f29d274a1357762c7258fb487512811b8063fb5d2824a3415a0a4540598335b3b086c72
-  languageName: node
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-
-"yargs-unparser@npm:2.0.0":
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-  resolution: "yargs-unparser@npm:2.0.0"
-  dependencies:
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-    decamelize: "npm:^4.0.0"
-    flat: "npm:^5.0.2"
-    is-plain-obj: "npm:^2.1.0"
-  checksum: 10c0/a5a7d6dc157efa95122e16780c019f40ed91d4af6d2bac066db8194ed0ec5c330abb115daa5a79ff07a9b80b8ea80c925baacf354c4c12edd878c0529927ff03
-  languageName: node
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-"yargs@npm:16.2.0":
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-  resolution: "yargs@npm:16.2.0"
-  dependencies:
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-    escalade: "npm:^3.1.1"
-    get-caller-file: "npm:^2.0.5"
-    require-directory: "npm:^2.1.1"
-    string-width: "npm:^4.2.0"
-    y18n: "npm:^5.0.5"
-    yargs-parser: "npm:^20.2.2"
-  checksum: 10c0/b1dbfefa679848442454b60053a6c95d62f2d2e21dd28def92b647587f415969173c6e99a0f3bab4f1b67ee8283bf735ebe3544013f09491186ba9e8a9a2b651
-  languageName: node
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-
 "yargs@npm:^15.0.2":
   version: 15.4.1
   resolution: "yargs@npm:15.4.1"