refactor(cli): remove deprecated Docker/Zep storage options (LISA-70)

CHANGELOG.md

@@ -9,6 +9,102 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+### Changed
+
+#### Remove Deprecated Docker/Zep Storage Options ([LISA-70](https://linear.app/tonycasey/issue/LISA-70))
+
+Simplified the CLI by removing deprecated storage options now that git-mem is the sole backend:
+
+- **Removed from `lisa init`**:
+  - Storage mode prompts (local Docker, Zep Cloud, skip)
+  - `--mode`, `--endpoint`, `--group` options
+  - `--zep-api-key`, `--zep-project-id` options
+  - Docker compose file scaffolding
+
+- **Removed commands**:
+  - `lisa up` - Docker Compose start
+  - `lisa down` - Docker Compose stop
+
+- **Simplified `lisa doctor`**:
+  - Removed Docker, Neo4j, and Zep connectivity checks
+  - Now checks: git repository, Lisa structure, Claude hooks, git-mem notes
+
+- **Cleaned up**:
+  - Deleted `docker.ts` module
+  - Deleted `.lisa/docker/` templates
+  - Simplified `.env.template` (removed STORAGE_MODE, GRAPHITI_ENDPOINT, NEO4J_* vars)
+  - Removed `DeploymentMode`, `IGraphitiConfig` types
+  - Removed `DEFAULT_ENDPOINT`, `ZEP_CLOUD_ENDPOINT` constants
+
+---
+
+## [2.27.0] - 2026-02-20
+
+### Changed
+
+#### Git-Mem: Replace All Memory Backends ([LISA-34](https://linear.app/tonycasey/issue/LISA-34))
+
+**Major architecture change**: Replaced all memory backends (MCP, Neo4j, Zep) with git-mem, a git-based memory system using git notes. This eliminates external database dependencies and simplifies the architecture.
+
+- All memory operations now use `refs/notes/mem` in the git repository
+- Repository provides natural scoping - no need for group IDs
+- Memories persist as git notes, visible via `git notes --ref=mem`
+- Removed MCP, Neo4j, and Zep repository implementations
+- Added `GitMemAdapter` and `GitMemTaskAdapter` for clean abstraction
+- Simplified DI container with fewer backends to manage
+
+#### Remove Group ID System ([LISA-59](https://linear.app/tonycasey/issue/LISA-59))
+
+Removed the group ID system (~630 lines deleted). The git repository itself now provides scoping - memories are stored in `refs/notes/mem` which is repo-specific.
+
+- Removed `group:${groupId}` tagging from all storage services
+- Removed `groupIds`/`groupId` parameters from method signatures
+- Deleted `src/lib/skills/common/group-id.ts` (~163 lines)
+- Deleted `src/lib/skills/shared/utils/group-id.ts` (~183 lines)
+- Simplified interfaces: `IMemoryService`, `ITaskService`, `ISkillMemoryService`, `ISkillTaskService`
+- Backward compatible: existing memories with `group:` tags remain stored
+
+#### Consolidate Skills Service Factories ([LISA-58](https://linear.app/tonycasey/issue/LISA-58))
+
+Consolidated skills service factory patterns for cleaner dependency injection.
+
+#### Consolidate Git into GitHub Skill ([LISA-19](https://linear.app/tonycasey/issue/LISA-19), [LISA-33](https://linear.app/tonycasey/issue/LISA-33))
+
+- Merged `/git` skill into `/github` skill
+- Renamed `/init-review` to `/review`
+- Single skill for all GitHub and git workflow operations
+
+### Added
+
+#### Repo Profile Generation Service ([LISA-11](https://linear.app/tonycasey/issue/LISA-11))
+
+Added `RepoProfileService` for generating repository profiles with project metadata and structure analysis.
+
+#### Git-Powered Memory: Phase 4 Indexing ([LISA-10](https://linear.app/tonycasey/issue/LISA-10))
+
+Added `GitIndexingService` for indexing git history into memory. Completes the git-powered memory feature.
+
+- Indexes commits, branches, tags, and file history
+- Extracts facts from commit messages and diffs
+- Supports incremental indexing (only new commits)
+
+#### Git-Powered Memory: Phase 3 Heuristic Extraction ([LISA-9](https://linear.app/tonycasey/issue/LISA-9))
+
+Added heuristic extraction for git-powered memory without LLM dependency.
+
+- Pattern-based extraction from commit messages
+- Detects decisions, conventions, and architectural changes
+- Fast local processing without API calls
+
+#### LLM Environment Variable Support ([LISA-16](https://linear.app/tonycasey/issue/LISA-16))
+
+Added environment variable support for LLM feature toggles and budget controls.
+
+- `LISA_LLM_ENABLED` - Master switch for LLM features
+- `LISA_LLM_BUDGET` - Monthly token budget
+- `LISA_LLM_FEATURES` - Comma-separated list of enabled features
+- Environment variables override preference store settings
+
 ### Fixed
 
 #### Neo4j Write Fallback for Memory ([LISA-17](https://linear.app/tonycasey/issue/LISA-17))

package.json

@@ -1,6 +1,6 @@
 {
   "name": "@tonycasey/lisa",
-  "version": "2.26.0",
+  "version": "2.27.0",
   "description": "Long-term memory for AI coding assistants. Automatic context persistence, task tracking, and knowledge capture across coding sessions. Supports Claude Code and OpenCode.",
   "bin": {
     "lisa": "dist/lib/cli.js",

src/lib/cli.ts

@@ -11,18 +11,14 @@ import {
   doctorCommand,
   initCommand,
   cleanupPreviousInstall,
-  upCommand,
-  downCommand,
   registerHookCommands,
   registerKnowledgeCommands,
   registerSkillCommands,
   registerIssueCommands,
   registerPrCommands,
   TEMPLATE_ROOT,
   VERSION,
-  DEFAULT_ENDPOINT,
   DEFAULT_GROUP,
-  type DeploymentMode,
   type CliSupport,
 } from './commands';
 
@@ -50,13 +46,8 @@ program
 
 program
   .command('init')
-  .description('Scaffold .lisa, .claude/.opencode, and Docker assets')
-  .option('-e, --endpoint <url>', 'MCP endpoint')
-  .option('-g, --group <id>', 'Default group id')
+  .description('Scaffold .lisa and .claude/.opencode directories')
   .option('-f, --force', 'Overwrite existing files')
-  .option('-m, --mode <mode>', 'Deployment mode: local or zep-cloud')
-  .option('--zep-api-key <key>', 'Zep API key (for zep-cloud mode)')
-  .option('--zep-project-id <id>', 'Zep project ID (for zep-cloud mode)')
   .option('-y, --yes', 'Skip prompts, use defaults')
   .option('--isolated', 'Install to .claude/lib for non-npm projects (Python, Go, etc.)')
   .option('--claude-only', 'Only scaffold for Claude Code')
@@ -71,7 +62,6 @@ program
       const log = cliLogger.child({ command: 'init' });
       const verbose = cmd.verbose && !cmd.quiet;
       log.info('Starting init command', {
-        mode: cmd.mode,
         claudeOnly: cmd.claudeOnly,
         opencodeOnly: cmd.opencodeOnly,
         verbose,
@@ -91,14 +81,8 @@ program
       // If neither flag is set, cliSupport remains undefined and prompts will be shown
 
       await initCommand({
-        endpoint: cmd.endpoint,
-        group: cmd.group,
         force: cmd.force,
         cwd: process.cwd(),
-        includeDocker: true,
-        mode: cmd.mode as DeploymentMode | undefined,
-        zepApiKey: cmd.zepApiKey,
-        zepProjectId: cmd.zepProjectId,
         yes: cmd.yes,
         isolated: cmd.isolated,
         cliSupport,
@@ -114,13 +98,8 @@ program
 
 program
   .command('setup')
-  .description('Scaffold .lisa and .claude/.opencode only (no Docker assets)')
-  .option('-e, --endpoint <url>', 'MCP endpoint')
-  .option('-g, --group <id>', 'Default group id')
+  .description('Alias for init - scaffold .lisa and .claude/.opencode directories')
   .option('-f, --force', 'Overwrite existing files')
-  .option('-m, --mode <mode>', 'Deployment mode: local or zep-cloud')
-  .option('--zep-api-key <key>', 'Zep API key (for zep-cloud mode)')
-  .option('--zep-project-id <id>', 'Zep project ID (for zep-cloud mode)')
   .option('-y, --yes', 'Skip prompts, use defaults')
   .option('--isolated', 'Install to .claude/lib for non-npm projects (Python, Go, etc.)')
   .option('--claude-only', 'Only scaffold for Claude Code')
@@ -145,14 +124,8 @@ program
     }
 
     await initCommand({
-      endpoint: cmd.endpoint,
-      group: cmd.group,
       force: cmd.force,
       cwd: process.cwd(),
-      includeDocker: false,
-      mode: cmd.mode as DeploymentMode | undefined,
-      zepApiKey: cmd.zepApiKey,
-      zepProjectId: cmd.zepProjectId,
       yes: cmd.yes,
       isolated: cmd.isolated,
       cliSupport,
@@ -163,39 +136,15 @@ program
     }, services);
   });
 
-program
-  .command('up')
-  .description('Start Neo4j/Graph/graphiti-mcp via docker compose')
-  .option('-c, --compose <file>', 'Compose file', 'docker-compose.graphiti.yml')
-  .action(async (cmd) => {
-    const composeFile = path.resolve(process.cwd(), cmd.compose);
-    const services = createCliServices(TEMPLATE_ROOT);
-    await upCommand({ composeFile }, services);
-  });
-
-program
-  .command('down')
-  .description('Stop Neo4j/Graph/graphiti-mcp via docker compose')
-  .option('-c, --compose <file>', 'Compose file', 'docker-compose.graphiti.yml')
-  .action(async (cmd) => {
-    const composeFile = path.resolve(process.cwd(), cmd.compose);
-    const services = createCliServices(TEMPLATE_ROOT);
-    await downCommand({ composeFile }, services);
-  });
-
 program
   .command('doctor')
-  .description('Validate Lisa configuration and backend connectivity')
-  .option('-c, --compose <file>', 'Compose file', 'docker-compose.graphiti.yml')
-  .option('-e, --endpoint <url>', 'MCP endpoint override')
+  .description('Validate Lisa configuration and setup')
   .option('-v, --verbose', 'Show detailed diagnostics')
   .option('--json', 'Output results as JSON')
   .action(async (cmd) => {
     const services = createCliServices(TEMPLATE_ROOT);
     await doctorCommand({
       cwd: process.cwd(),
-      compose: cmd.compose,
-      endpoint: cmd.endpoint,
       verbose: cmd.verbose,
       json: cmd.json,
     }, services);
@@ -319,10 +268,7 @@ if (require.main === module) {
 export {
   initCommand,
   doctorCommand,
-  upCommand,
-  downCommand,
   cleanupPreviousInstall,
-  DEFAULT_ENDPOINT,
   DEFAULT_GROUP,
   TEMPLATE_ROOT,
   runScan,