chore: remove .claude submodule and investigations tool references

.gitignore

@@ -8,8 +8,8 @@
 .DS_Store
 Thumbs.db
 
-# Local settings
-.claude/settings.local.json
+# Local settings (clone opentrace/.claude here for shared agents/commands)
+.claude/
 
 # Environment files
 .env

CLAUDE.md

@@ -8,18 +8,12 @@ This is the **OpenTrace Claude Code Plugin** — a Claude Code plugin that conne
 
 ## Architecture
 
-The repository has two layers:
-
-1. **Plugin layer** (this repo) — Contains the plugin manifest, MCP server configuration, and plugin-specific hooks. This is what gets installed via `claude plugin install`.
-2. **Shared `.claude` submodule** — A git submodule (`opentrace/.claude`) containing shared agents, commands, hooks, and settings used across OpenTrace projects. Changes to shared settings must be submitted to the [.claude repository](https://github.com/opentrace/.claude) separately.
-
 ### Key Files
 
 - `.claude-plugin/plugin.json` — Plugin manifest: name, version, MCP server references, and hook definitions
 - `.claude-plugin/marketplace.json` — Marketplace metadata for plugin discovery
 - `mcp-servers/opentrace.json` — MCP server configuration pointing to `https://api.opentrace.ai/mcp/v1`
 - `hooks/` — Plugin hooks (see below)
-- `.claude/` — Git submodule with shared agents, commands, and settings (do not edit directly in this repo)
 
 ### Plugin Hooks
 
@@ -57,14 +51,12 @@ The standard development cycle is: edit files → `make dev` → restart Claude
 ### First-Time Setup
 
 ```bash
-git clone --recurse-submodules git@github.com:opentrace/claude-code.git
+git clone git@github.com:opentrace/claude-code.git
 cd claude-code
 make marketplace-add
 make install
 ```
 
-If cloned without submodules: `git submodule update --init --recursive`
-
 ### Testing Changes
 
 There is no automated test suite. Testing is manual:

CONTRIBUTING.md

@@ -2,14 +2,9 @@
 
 ## Local Development Setup
 
-1. **Clone the repository** (with submodules):
+1. **Clone the repository**:
    ```bash
-   git clone --recurse-submodules git@github.com:opentrace/claude-code.git
-   ```
-
-   If you already cloned without submodules:
-   ```bash
-   git submodule update --init --recursive
+   git clone git@github.com:opentrace/claude-code.git
    ```
 
 2. **Add the local repository as a marketplace**:
@@ -34,7 +29,6 @@ claude plugin install opentrace
 ## Project Structure
 
 ```
-.claude/             # Shared Claude Code settings (git submodule)
 hooks/
   session-start      # Hook that runs when a Claude Code session starts
 mcp-servers/
@@ -47,7 +41,7 @@ CONTRIBUTING.md
 
 - **Hooks** live in `hooks/`. Changes are picked up on the next Claude Code session.
 - **MCP server config** lives in `mcp-servers/opentrace.json`. Restart Claude Code after changes.
-- **Shared settings** are in the `.claude` submodule. If you need to modify shared settings, submit changes to the [.claude repository](https://github.com/opentrace/.claude) separately.
+- **Shared settings** (optional): OpenTrace developers can clone [opentrace/.claude](https://github.com/opentrace/.claude) into `.claude/` for shared agents and commands. This directory is gitignored.
 
 ## Submitting Changes
 

README.md

@@ -62,7 +62,6 @@ Identifies all dependent components and highlights critical paths.
 | **Discovery** | `search_nodes`, `query_nodes`, `get_node`, `find_similar_nodes` |
 | **Traversal** | `traverse_dependencies`, `traverse_incoming`, `traverse_outgoing`, `get_neighbors` |
 | **Analysis** | `find_path`, `get_node_statistics` |
-| **Investigations** | `list_investigations`, `get_investigation` |
 | **Source** | `load_source` (GitHub/GitLab integration) |
 
 **Analysis Prompts**: `discover_architecture`, `impact_analysis`, `dependency_analysis`

cspell.json

@@ -11,8 +11,6 @@
   "words": [
     "opentrace",
     "codebase",
-    "submodule",
-    "submodules",
     "guardrail",
     "guardrails",
     "hookSpecificOutput",