The MCP configuration is already handled by the Dockerfile using
claude mcp add-json command. The template file was unnecessary and
could cause confusion.
This template provides instructions for Claude when running in the Docker
container, including task execution workflow, coding standards, and
Twilio notification requirements.
Implemented SYSTEM_PACKAGES environment variable for flexible system library installation:
Key Features:
- Users specify packages in .env: SYSTEM_PACKAGES="libopenslide0 libgdal-dev"
- Packages installed during Docker build (secure, no runtime mounting)
- Automatic rebuild detection when packages change
- Documentation with common scientific computing packages
Technical Implementation:
- ARG SYSTEM_PACKAGES in Dockerfile with conditional apt-get install
- Build argument passed from claude-docker.sh script
- Clean package management with cache cleanup
Benefits:
- Secure: No system directory mounting required
- Flexible: Users choose exactly what they need
- Documented: Common packages listed in README
- Clean: Packages baked into image, not mounted at runtime
Tested successfully with OpenSlide: conda run -n prism python -c "import openslide"
Added CONDA_PKGS_DIRS environment variable setting to ensure conda
looks in the correct package cache directories inside the container.
This matches the pattern used for CONDA_ENVS_DIRS.
Enhanced conda support to handle custom environment and package directories:
Key Changes:
- Mount conda installation at original path (not /opt/miniconda3)
- Add CONDA_EXTRA_DIRS for mounting additional search paths
- Mount all conda-configured directories to preserve existing setup
- Update CLAUDE.md to use ${CONDA_EXE} environment variable
Technical Details:
- Preserves original conda paths so existing configuration works
- Handles multiple envs_dirs and pkgs_dirs automatically
- Provides feedback about which directories are mounted
- Falls back gracefully for missing directories
Example usage: CONDA_EXTRA_DIRS="/vol/path/.conda/envs /vol/path/conda_envs /vol/path/.conda/pkgs"
Result: All conda environments and packages accessible in container.
Major breakthrough solving the authentication chicken-and-egg problem:
Key Changes:
- Copy ~/.claude.json and ~/.claude/ during Docker build for baked-in auth
- Add -s user flag to claude mcp add-json for persistent MCP servers
- Simplify rebuild logic to prevent unnecessary rebuilds
- Update documentation with rebuild instructions
Technical Details:
- Authentication files placed before USER switch in Dockerfile
- MCP configuration now persists across all sessions
- Rebuild only occurs when image doesn't exist
- Clean separation of build vs runtime concerns
Result: Users authenticate once on host, then zero login prompts forever.
SMS notifications ready immediately on container start.
- Replace API Key/Secret auth with Account SID/Auth Token
- Configure MCP during Docker build instead of runtime
- Remove mcp-config.json and config directory
- Simplify startup script by removing MCP configuration logic
- Update documentation and test scripts for new auth method
The MCP server is now configured directly in the Dockerfile using
'claude mcp add-json' command, making the setup more reliable and
eliminating runtime configuration complexity.
- Add proper type and env sections to mcp-config.json
- Remove dynamic MCP add command, use pre-configured MCP
- Bake .env credentials into Docker image at build time
- Remove runtime .env volume mount - true one-time setup
- Auto-rebuild image when .env file changes
- Export Twilio env vars for MCP server subprocess
- Remove conflicting .mcp.json file
- Add authentication persistence to features section
- Update configuration section with claude-home directory
- Clarify what files go where in the setup
- Add persistent volume mount for Claude home directory (~/.claude)
- Create non-root user in Docker container for better security
- Mount host ~/.claude-docker/claude-home to container ~/.claude
- Update install script to create claude-home directory
- Check for existing credentials on startup
- Authentication tokens now persist across container restarts
- Container launches successfully after fixes
- Next priorities: auth persistence, firewall, command history
- Need to study Anthropic dev container implementation
- Change executable from claude-code to claude in startup.sh
- Fix .env parsing to handle comments using set -a/source
- Add explicit PATH for npm global binaries in Dockerfile
- Update scratchpad.md with fix documentation
- Update scratchpad with completed MVP status and Phase 2 roadmap
- Rewrite README with comprehensive setup instructions and feature overview
- Document next steps: firewall security and shell history persistence
- Dockerfile with Claude Code and Twilio MCP integration
- Wrapper script for easy invocation from anywhere
- Auto-setup of .claude directory in projects
- SMS notifications via Twilio when tasks complete
- Installation script for zshrc alias
- Full autonomous permissions with --dangerously-skip-permissions
- Context persistence via scratchpad.md
