Add internal-docs as private submodule

Author: PatrickSys

.gitignore

@@ -10,6 +10,4 @@ dist/
 *.swo
 *~
 .claude
-internal-docs/
-internal-docs.zip
 .codebase-intelligence.json

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "internal-docs"]
+	path = internal-docs
+	url = https://github.com/PatrickSys/codebase-context-mcp-internal.git

AGENTS.md

@@ -0,0 +1,60 @@
+# Agent Instructions
+
+## Internal Documentation
+
+This repository uses a **git submodule** for internal documentation:
+
+- **Submodule path**: `internal-docs/`
+- **Private repository**: `PatrickSys/codebase-context-mcp-internal`
+- **Purpose**: Store internal research, strategies, and private development notes
+
+### Initial Setup (New Machine)
+
+When cloning this repository for the first time:
+
+```bash
+git clone https://github.com/PatrickSys/codebase-context-mcp.git
+cd codebase-context-mcp
+git submodule init
+git submodule update
+```
+
+Or use the shorthand:
+
+```bash
+git clone --recurse-submodules https://github.com/PatrickSys/codebase-context-mcp.git
+```
+
+### Authentication
+
+The submodule repository is **private**. Ensure you have:
+- A valid GitHub Personal Access Token (PAT) with `repo` scope, OR
+- SSH keys configured for GitHub access
+
+### Syncing Changes
+
+To pull latest changes from both main and submodule repositories:
+
+```bash
+git pull
+git submodule update --remote
+```
+
+To commit changes in the submodule:
+
+```bash
+cd internal-docs
+git add .
+git commit -m "your message"
+git push origin main
+cd ..
+git add internal-docs
+git commit -m "Update submodule reference"
+```
+
+### Why a Submodule?
+
+- **Privacy**: Keeps internal docs in a separate private repository
+- **Sync**: Enables synchronization across multiple machines
+- **Version Control**: Tracks internal docs alongside public code
+- **Security**: CrowdStrike restrictions prevent USB transfers; GitHub provides secure cloud sync