codebase-memory-mcp

The fastest and most efficient code intelligence engine for AI coding agents. Full-indexes an average repository in milliseconds, the Linux kernel (28M LOC, 75K files) in 3 minutes. Answers structural queries in under 1ms. Ships as a single static binary for macOS, Linux, and Windows — download, run install, done.

High-quality parsing through tree-sitter AST analysis across all 66 languages, enhanced with LSP-style hybrid type resolution for Go, C, and C++ (more languages coming soon) — producing a persistent knowledge graph of functions, classes, call chains, HTTP routes, and cross-service links. 14 MCP tools. Zero dependencies. Plug and play across 10 coding agents.

Why codebase-memory-mcp

• Extreme indexing speed — Linux kernel (28M LOC, 75K files) in 3 minutes. RAM-first pipeline: LZ4 compression, in-memory SQLite, fused Aho-Corasick pattern matching. Memory released after indexing.
• Plug and play — single static binary for macOS (arm64/amd64), Linux (arm64/amd64), and Windows (amd64). No Docker, no runtime dependencies, no API keys. Download → install → restart agent → done.
• 66 languages — vendored tree-sitter grammars compiled into the binary. Nothing to install, nothing that breaks.
• 120x fewer tokens — 5 structural queries: ~3,400 tokens vs ~412,000 via file-by-file search. One graph query replaces dozens of grep/read cycles.
• 10 agents, one command — install auto-detects Claude Code, Codex CLI, Gemini CLI, Zed, OpenCode, Antigravity, Aider, KiloCode, VS Code, and OpenClaw — configures MCP entries, instruction files, and pre-tool hooks for each.
• Built-in graph visualization — 3D interactive UI at localhost:9749 (optional UI binary variant).
• Infrastructure-as-code indexing — Dockerfiles, Kubernetes manifests, and Kustomize overlays indexed as graph nodes with cross-references. Resource nodes for K8s kinds, Module nodes for Kustomize overlays with IMPORTS edges to referenced resources.
• 14 MCP tools — search, trace, architecture, impact analysis, Cypher queries, dead code detection, cross-service HTTP linking, ADR management, and more.

Quick Start

One-line install (macOS / Linux):

curl -fsSL https://raw.githubusercontent.com/DeusData/codebase-memory-mcp/main/install.sh | bash

With graph visualization UI:

curl -fsSL https://raw.githubusercontent.com/DeusData/codebase-memory-mcp/main/install.sh | bash -s -- --ui

Windows (PowerShell):

powershell -ExecutionPolicy ByPass -c "irm https://raw.githubusercontent.com/DeusData/codebase-memory-mcp/main/install.ps1 | iex"

Options: --ui (graph visualization), --skip-config (binary only, no agent setup), --dir=<path> (custom location).

Restart your coding agent. Say "Index this project" — done.

1. Download the archive for your platform from the latest release:

   • codebase-memory-mcp-<os>-<arch>.tar.gz (macOS/Linux) or .zip (Windows) — standard
   • codebase-memory-mcp-ui-<os>-<arch>.tar.gz / .zip — with graph visualization

2. Extract and install (each archive includes install.sh or install.ps1):

   macOS / Linux:

   bash

   tar xzf codebase-memory-mcp-*.tar.gz
   ./install.sh
   

   Windows (PowerShell):

   powershell

   Expand-Archive codebase-memory-mcp-windows-amd64.zip -DestinationPath .
   .\install.ps1
   

3. Restart your coding agent.

The install command automatically strips macOS quarantine attributes and ad-hoc signs the binary — no manual xattr/codesign needed.

The install command auto-detects all installed coding agents and configures MCP server entries, instruction files, skills, and pre-tool hooks for each.

Graph Visualization UI

If you downloaded the ui variant:

codebase-memory-mcp --ui=true --port=9749

Open http://localhost:9749 in your browser. The UI runs as a background thread alongside the MCP server — it's available whenever your agent is connected.

Auto-Index

Enable automatic indexing on MCP session start:

codebase-memory-mcp config set auto_index true

When enabled, new projects are indexed automatically on first connection. Previously-indexed projects are registered with the background watcher for ongoing git-based change detection. Configurable file limit: config set auto_index_limit 50000.

Keeping Up to Date

codebase-memory-mcp update

The MCP server also checks for updates on startup and notifies on the first tool call if a newer release is available.

Uninstall

codebase-memory-mcp uninstall

Removes all agent configs, skills, hooks, and instructions. Does not remove the binary or SQLite databases.

Features

• Architecture overview: get_architecture returns languages, packages, entry points, routes, hotspots, boundaries, layers, and clusters in a single call
• Architecture Decision Records: manage_adr persists architectural decisions across sessions
• Louvain community detection: Discovers functional modules by clustering call edges
• Git diff impact mapping: detect_changes maps uncommitted changes to affected symbols with risk classification
• Call graph: Resolves function calls across files and packages (import-aware, type-inferred)
• Cross-service HTTP linking: Discovers REST routes and matches them to HTTP call sites with confidence scoring
• Auto-sync: Background watcher detects file changes and re-indexes automatically
• Cypher-like queries: MATCH (f:Function)-[:CALLS]->(g) WHERE f.name = 'main' RETURN g.name
• Dead code detection: Finds functions with zero callers, excluding entry points
• Route nodes: REST endpoints are first-class graph entities
• CLI mode: codebase-memory-mcp cli search_graph '{"name_pattern": ".*Handler.*"}'
• Single binary, zero infrastructure: SQLite-backed, persists to ~/.cache/codebase-memory-mcp/

How It Works

codebase-memory-mcp is a structural analysis backend — it builds and queries the knowledge graph. It does not include an LLM. Instead, it relies on your MCP client (Claude Code, or any MCP-compatible agent) to be the intelligence layer.

You: "what calls ProcessOrder?"

Agent calls: trace_call_path(function_name="ProcessOrder", direction="inbound")

codebase-memory-mcp: executes graph query, returns structured results

Agent: presents the call chain in plain English

Why no built-in LLM? Other code graph tools embed an LLM for natural language → graph query translation. This means extra API keys, extra cost, and another model to configure. With MCP, the agent you're already talking to is the query translator.

Performance

Benchmarked on Apple M3 Pro:

RAM-first pipeline: All indexing runs in memory (LZ4 HC compressed read, in-memory SQLite, single dump at end). Memory is released back to the OS after indexing completes.

Token efficiency: Five structural queries consumed ~3,400 tokens via codebase-memory-mcp versus ~412,000 tokens via file-by-file grep exploration — a 99.2% reduction.

Installation

Pre-built Binaries

Every release includes checksums.txt with SHA-256 hashes. All binaries are statically linked — no shared library dependencies.

Windows note: SmartScreen may show a warning for unsigned software. Click "More info" → "Run anyway". Verify integrity with checksums.txt.

Setup Scripts

macOS / Linux:

curl -fsSL https://raw.githubusercontent.com/DeusData/codebase-memory-mcp/main/scripts/setup.sh | bash

Windows (PowerShell):

irm https://raw.githubusercontent.com/DeusData/codebase-memory-mcp/main/scripts/setup-windows.ps1 | iex

Install via Claude Code

You: "Install this MCP server: https://github.com/DeusData/codebase-memory-mcp"

Build from Source

git clone https://github.com/DeusData/codebase-memory-mcp.git
cd codebase-memory-mcp
scripts/build.sh                    # standard binary
scripts/build.sh --with-ui          # with graph visualization
# Binary at: build/c/codebase-memory-mcp

Manual MCP Configuration

Add to ~/.claude/.mcp.json (global) or project .mcp.json:

{
  "mcpServers": {
    "codebase-memory-mcp": {
      "command": "/path/to/codebase-memory-mcp",
      "args": []
    }
  }
}

Restart your agent. Verify with /mcp — you should see codebase-memory-mcp with 14 tools.

Multi-Agent Support

install auto-detects and configures all installed agents:

Hooks are advisory (exit code 0) — they remind agents to prefer MCP graph tools when they reach for grep/glob/read, without blocking the tool call.

CLI Mode

Every MCP tool can be invoked from the command line:

codebase-memory-mcp cli index_repository '{"repo_path": "/path/to/repo"}'
codebase-memory-mcp cli search_graph '{"name_pattern": ".*Handler.*", "label": "Function"}'
codebase-memory-mcp cli trace_call_path '{"function_name": "Search", "direction": "both"}'
codebase-memory-mcp cli query_graph '{"query": "MATCH (f:Function) RETURN f.name LIMIT 5"}'
codebase-memory-mcp cli list_projects
codebase-memory-mcp cli --raw search_graph '{"label": "Function"}' | jq '.results[].name'

MCP Tools

Indexing

Querying

Graph Data Model

Node Labels

Project, Package, Folder, File, Module, Class, Function, Method, Interface, Enum, Type, Route, Resource

Edge Types

CONTAINS_PACKAGE, CONTAINS_FOLDER, CONTAINS_FILE, DEFINES, DEFINES_METHOD, IMPORTS, CALLS, HTTP_CALLS, ASYNC_CALLS, IMPLEMENTS, HANDLES, USAGE, CONFIGURES, WRITES, MEMBER_OF, TESTS, USES_TYPE, FILE_CHANGES_WITH

Qualified Names

get_code_snippet uses qualified names: <project>.<path_parts>.<name>. Use search_graph to discover them first.

Supported Cypher Subset

query_graph supports: MATCH with labels and relationship types, variable-length paths, WHERE with comparisons/regex/CONTAINS, RETURN with property access and COUNT/DISTINCT, ORDER BY, LIMIT. Not supported: WITH, COLLECT, OPTIONAL MATCH, mutations.

Ignoring Files

Layered: hardcoded patterns (.git, node_modules, etc.) → .gitignore hierarchy → .cbmignore (project-specific, gitignore syntax). Symlinks are always skipped.

Configuration

codebase-memory-mcp config list                          # show all settings
codebase-memory-mcp config set auto_index true           # auto-index on session start
codebase-memory-mcp config set auto_index_limit 50000    # max files for auto-index
codebase-memory-mcp config reset auto_index              # reset to default

Environment Variables

# Store indexes in a custom directory
export CBM_CACHE_DIR=~/my-projects/cbm-data

Custom File Extensions

Map additional file extensions to supported languages via JSON config files. Useful for framework-specific extensions like .blade.php (Laravel) or .mjs (ES modules).

Per-project (in your repo root):

// .codebase-memory.json
{"extra_extensions": {".blade.php": "php", ".mjs": "javascript"}}

Global (applies to all projects):

// ~/.config/codebase-memory-mcp/config.json  (or $XDG_CONFIG_HOME/...)
{"extra_extensions": {".twig": "html", ".phtml": "php"}}

Project config overrides global for conflicting extensions. Unknown language values are silently skipped. Missing config files are ignored.

Persistence

SQLite databases stored at ~/.cache/codebase-memory-mcp/. Persists across restarts (WAL mode, ACID-safe). To reset: rm -rf ~/.cache/codebase-memory-mcp/.

Troubleshooting

Language Support

66 languages. Benchmarked against 64 real open-source repositories (78 to 49K nodes):

Plus: Clojure, F#, Julia, Vim Script, Nix, Common Lisp, Elm, Fortran, CUDA, COBOL, Verilog, Emacs Lisp, MATLAB, Lean 4, FORM, Magma, Wolfram, JSON, XML, Markdown, Makefile, CMake, Protobuf, GraphQL, Vue, Svelte, Meson, GLSL, INI.

Architecture

src/
  main.c              Entry point (MCP stdio server + CLI + install/update/config)
  mcp/                MCP server (14 tools, JSON-RPC 2.0, session detection, auto-index)
  cli/                Install/uninstall/update/config (10 agents, hooks, instructions)
  store/              SQLite graph storage (nodes, edges, traversal, search, Louvain)
  pipeline/           Multi-pass indexing (structure → definitions → calls → HTTP links → config → tests)
  cypher/             Cypher query lexer, parser, planner, executor
  discover/           File discovery (.gitignore, .cbmignore, symlink handling)
  watcher/            Background auto-sync (git polling, adaptive intervals)
  traces/             Runtime trace ingestion
  ui/                 Embedded HTTP server + 3D graph visualization
  foundation/         Platform abstractions (threads, filesystem, logging, memory)
internal/cbm/         Vendored tree-sitter grammars (66 languages) + AST extraction engine

License

MIT