ML Jupyter MCP

# Setup Module TODO ## Project Setup Functionality ### Core Implementation - [ ] Create `project_setup.py` with main setup logic - [ ] Create `templates.py` to store default `.mcp.json` and `CLAUDE.md` templates - [ ] Implement smart merge functionality for existing `.mcp.json` files - [ ] Implement append functionality for existing `CLAUDE.md` files ### File Handlers - [ ] `.mcp.json` handler: - Detect existing file - Merge jupyter-executor config without duplication - Preserve existing user configurations - Handle nested JSON structures properly - [ ] `CLAUDE.md` handler: - Detect existing file - Append jupyter-specific instructions if not present - Avoid duplicate sections - Maintain markdown formatting ### MCP Tool Integration - [ ] Create `jupyter_setup_project()` tool - [ ] Add parameters: - `project_path` (default: current directory) - `override_existing` (default: False) - `custom_config` (optional: Dict for custom settings) - [ ] Return setup status and warnings ### CLI Integration - [ ] Add CLI command: `ml-jupyter-mcp setup [path]` - [ ] Add `--force` flag for overwriting - [ ] Add `--check` flag to verify setup without changes ### Templates - [ ] Default `.mcp.json` template with: - jupyter-executor configuration - Workflow instructions - Cell execution patterns - Error handling rules - [ ] Default `CLAUDE.md` template with: - Jupyter workflow instructions - Cell execution patterns - Package management guidelines - Error handling procedures ### Testing - [ ] Test fresh setup in empty project - [ ] Test merging with existing `.mcp.json` - [ ] Test appending to existing `CLAUDE.md` - [ ] Test duplicate prevention - [ ] Test CLI commands - [ ] Test MCP tool usage ### Documentation - [ ] Update README with setup instructions - [ ] Add docstrings to all functions - [ ] Create setup examples - [ ] Document merge behavior ### Edge Cases - [ ] Handle malformed existing JSON - [ ] Handle read-only files - [ ] Handle missing permissions - [ ] Handle symbolic links - [ ] Handle very large existing files ## Implementation Priority 1. Basic file creation for new projects 2. Smart merge for `.mcp.json` 3. Smart append for `CLAUDE.md` 4. MCP tool integration 5. CLI command 6. Testing 7. Documentation