claude-re-setup/CLAUDE.md

CLAUDE.md

Guidance for Claude Code when working in this repository.

Purpose

This repo provides a reproducible, Docker-managed reverse-engineering workstation on Linux, built around Claude Desktop with two MCP integrations:

1. Reverse Engineer Anything MCP: general-purpose RE tooling exposed to Claude over MCP.
2. Ghidra + GhidraMCP: Ghidra with the GhidraMCP plugin, so Claude can query and annotate an open program (functions, decompilation, xrefs, renames, comments).

The goal is that docker compose up gives you a working setup where Claude Desktop can drive both toolsets against binaries in a shared workspace, without installing Ghidra, a JDK or RE tooling on the host.

Status

Early stage. What exists: a single image (Dockerfile, launch-apps.sh) with Claude Desktop and Ghidra, started by run.sh; no compose setup yet. The layout below is the intended structure. Update this file when the real structure differs.

Intended layout

.
├── CLAUDE.md
├── README.md                 # user-facing setup and usage
├── docker-compose.yml        # orchestrates all services
├── .env.example              # versions, ports, UID/GID, display settings
├── claude-desktop/
│   ├── Dockerfile            # Claude Desktop (Linux build) + GUI deps
│   └── claude_desktop_config.json  # MCP server definitions (template)
├── ghidra/
│   ├── Dockerfile            # JDK + Ghidra + GhidraMCP plugin
│   └── scripts/              # plugin install / headless helpers
├── re-mcp/
│   └── Dockerfile            # Reverse Engineer Anything MCP server
├── scripts/                  # host helpers (xhost setup, start/stop, health checks)
└── workspace/                # shared, git-ignored: binaries + Ghidra projects

Architecture

• Claude Desktop and Ghidra share one container (the root Dockerfile, started by run.sh), at the user's request. Ghidra is the official GitHub release (version, build date and SHA-256 are build args), runs on Ubuntu's openjdk-25-jdk, lives in /opt/ghidra and starts together with Claude Desktop. The Developer plugin package is enabled in both the project window and the CodeBrowser. A bare <PACKAGE NAME="Developer" /> only adds the package's RELEASED plugins, so the STABLE ones are listed with <INCLUDE CLASS=...>. CodeBrowser: the build inserts ghidra/codebrowser-developer.xml into defaultTools/CodeBrowser.tool inside Public_Release.jar. Project window: it has no default to patch, so ghidra/FrontEndTool.xml is copied into the user settings, along with ghidra/preferences (USER_AGREEMENT=ACCEPT, because a pre-created settings dir otherwise makes Ghidra ask for its user agreement). To check a config really loaded, close Ghidra cleanly and see whether the plugins survive in the file it rewrites; Ghidra drops what it didn't load.

• Shared workspace volume. Every container mounts the workspace at /workspace, so a file path means the same thing to Claude, Ghidra and the RE MCP. run.sh asks for the host folder on each start in the desktop's folder picker (zenity, or kdialog on KDE; terminal prompt if neither exists), opening at the last folder used, else ./workspace. Skip it with --workspace DIR or WORKSPACE=DIR. It refuses / and $HOME. The image symlinks ~/workspace to /workspace for Claude Desktop's file picker.

• GUI forwarding. Claude Desktop and Ghidra are GUI apps. Default to X11 forwarding (/tmp/.X11-unix + DISPLAY). Support Wayland through XWayland. Keep a noVNC/VNC fallback in mind for headless hosts. Never solve display access with a blanket xhost +. Scope it (xhost +local:docker or +SI:localuser:...).

• GhidraMCP wiring. GhidraMCP has two parts:

  • a Ghidra plugin that runs an HTTP server inside Ghidra (default port 8080), and
  • a Python MCP bridge (bridge_mcp_ghidra.py) that speaks MCP to Claude and forwards calls to that HTTP server.

  The bridge is configured with the Ghidra server URL (e.g. http://ghidra:8080/). The plugin must be enabled in the CodeBrowser and a program must be open, or the bridge has nothing to talk to.

• Container lifetime follows the apps. The entrypoint launch-apps.sh starts Claude Desktop and Ghidra and stops both, ending the container, when either is closed. Ghidra counts as closed when its process exits (closing the project window quits it; CodeBrowser or Help windows don't). Claude Desktop's window only hides the app on close (GNOME shows no tray icon), so its X windows are watched: none open or minimized for ~3 s counts as closed. run.sh uses --init so signals and zombie processes are handled.

• MCP transport between containers. Claude Desktop starts local MCP servers as stdio subprocesses. Because the servers live in other containers, pick one approach and apply it consistently:

  • Preferred: run the MCP servers with an HTTP/SSE transport in their own containers. Bridge them into Claude Desktop's stdio config with a small proxy (e.g. mcp-remote or mcp-proxy) installed in the Claude Desktop image.
  • Alternative: install the bridges inside the Claude Desktop image and point them at the other containers over the network. This works well for the GhidraMCP bridge, which is just Python + HTTP.
  • Avoid mounting the Docker socket into the Claude Desktop container just to docker exec MCP servers.

Conventions

• Pin versions. Ghidra version, GhidraMCP release, JDK version, Claude Desktop build and RE MCP commit go in .env / build args, not latest. The GhidraMCP release must match the Ghidra version it was built for.
• Run as non-root inside containers. Map the host UID/GID (via .env) so files in workspace/ stay owned by the user.
• Persist state in named volumes or workspace/: Ghidra user settings and projects. Rebuilding an image must not lose analysis.
• Claude Desktop sign-in is not persisted. No keyring is installed and ~/.config/Claude is not mounted, so the user logs in on every start. Don't add a keyring or config volume back without being asked.
• No secrets in the repo. Credentials, session data and workspace/ contents are git-ignored. Ship .env.example, never .env.
• Untrusted binaries. Samples under analysis may be malicious. Never execute them on the host or in the Claude Desktop container. Containers that might run samples (dynamic analysis) should have no host mounts beyond workspace/ and should allow network isolation (network_mode: none or an internal-only network).
• Linux only. Target recent Docker Engine + Compose v2 (docker compose, not docker-compose). Make the setup work under both Docker and rootless Podman where practical. On SELinux hosts such as Fedora, bind mounts need :z/:Z.

Common commands

These are expected once the compose setup exists. Keep this list in sync with reality.

cp .env.example .env            # then adjust UID/GID, versions, DISPLAY
xhost +local:docker             # allow containers to use the X server
docker compose build
docker compose up -d
docker compose logs -f <service>
docker compose down

Things to verify, not assume

• Claude Desktop on Linux. Check whether an official Linux build is available at the time of work. If not, use a maintained community repackaging and document which one and why. Confirm the config path, usually ~/.config/Claude/claude_desktop_config.json.
• Reverse Engineer Anything MCP. Confirm the upstream repository, install method, runtime (Python/Node), required external tools and supported transports before writing its Dockerfile. Record the source URL in the README.
• GhidraMCP. Confirm the current release, its supported Ghidra version, the bridge's CLI flags and its default ports from the upstream README.

When making changes

• After changing a Dockerfile or compose file, run docker compose config to validate it, then build the affected service.
• When adding an MCP server, update claude-desktop/claude_desktop_config.json, docker-compose.yml, README.md and the Architecture section above together.