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11 changes: 6 additions & 5 deletions README.md
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[![Tests](https://img.shields.io/badge/tests-8050_passing-brightgreen)](https://github.com/DeusData/codebase-memory-mcp)
[![Languages](https://img.shields.io/badge/languages-162-orange)](https://github.com/DeusData/codebase-memory-mcp)
[![Hybrid LSP](https://img.shields.io/badge/Hybrid_LSP-10_languages-blue)](#hybrid-lsp)
[![Agents](https://img.shields.io/badge/agent_surfaces-45-purple)](https://github.com/DeusData/codebase-memory-mcp)
[![Agents](https://img.shields.io/badge/agent_surfaces-46-purple)](https://github.com/DeusData/codebase-memory-mcp)
[![Pure C](https://img.shields.io/badge/pure_C-no_language_runtime-blue)](https://github.com/DeusData/codebase-memory-mcp)
[![Platform](https://img.shields.io/badge/macOS_%7C_Linux_%7C_Windows-supported-lightgrey)](https://github.com/DeusData/codebase-memory-mcp/releases/latest)
[![OpenSSF Scorecard](https://api.scorecard.dev/projects/github.com/DeusData/codebase-memory-mcp/badge)](https://scorecard.dev/viewer/?uri=github.com/DeusData/codebase-memory-mcp)
Expand All @@ -16,7 +16,7 @@

**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 native executable with a small verified runtime-asset set for macOS, Linux, and Windows — download, run `install`, done.

High-quality parsing through [tree-sitter](https://tree-sitter.github.io/tree-sitter/) AST analysis across all 162 languages, enhanced with [**Hybrid LSP** semantic type resolution](#hybrid-lsp) for Python, TypeScript / JavaScript / JSX / TSX, PHP, C#, Go, C, C++, Java, Kotlin, Rust, and Perl — producing a persistent knowledge graph of functions, classes, call chains, HTTP routes, and cross-service links. 17 MCP tools. No language runtime, hosted service, or API key. Plug and play across 45 supported automatic/conditional client surfaces.
High-quality parsing through [tree-sitter](https://tree-sitter.github.io/tree-sitter/) AST analysis across all 162 languages, enhanced with [**Hybrid LSP** semantic type resolution](#hybrid-lsp) for Python, TypeScript / JavaScript / JSX / TSX, PHP, C#, Go, C, C++, Java, Kotlin, Rust, and Perl — producing a persistent knowledge graph of functions, classes, call chains, HTTP routes, and cross-service links. 17 MCP tools. No language runtime, hosted service, or API key. Plug and play across 46 supported automatic/conditional client surfaces.

> **Research** — The design and benchmarks behind this project are described in the preprint [*Codebase-Memory: Tree-Sitter-Based Knowledge Graphs for LLM Code Exploration via MCP*](https://arxiv.org/abs/2603.27277) (arXiv:2603.27277). Evaluated across 31 real-world repositories: 83% answer quality, 10× fewer tokens, 2.1× fewer tool calls vs. file-by-file exploration.

Expand All @@ -34,7 +34,7 @@ High-quality parsing through [tree-sitter](https://tree-sitter.github.io/tree-si
- **Plug and play** — native executable plus authenticated release-owned assets for macOS (arm64/amd64), Linux (arm64/amd64), and Windows (amd64). The native install needs no Docker, language runtime, or API keys. Download → `install` → restart agent → done.
- **162 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.
- **45 supported automatic/conditional client surfaces** — `install` configures detected clients and safely activates conditional clients only when their documented platform, marker, or explicit existing config path is present. See [Multi-Agent Support](#multi-agent-support) for the complete matrix and manual/UI-only boundaries.
- **46 supported automatic/conditional client surfaces** — `install` configures detected clients and safely activates conditional clients only when their documented platform, marker, or explicit existing config path is present. See [Multi-Agent Support](#multi-agent-support) for the complete matrix and manual/UI-only boundaries.
- **Built-in graph visualization** — 3D interactive UI at `localhost:9749`, served from the binary itself.
- **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.
- **17 MCP tools** — search, trace, architecture, impact analysis, targeted index-coverage checks, Cypher queries, dead code detection, cross-service HTTP linking, ADR management, and more.
Expand Down Expand Up @@ -477,7 +477,7 @@ Restart your agent. Verify with `/mcp` — you should see `codebase-memory-mcp`

## Multi-Agent Support

`install` configures 45 client surfaces: 39 detected automatically and 6
`install` configures 46 client surfaces: 40 detected automatically and 6
conditional or explicit. “Conditional” means the installer writes only when the
documented platform or an explicit, already-existing config path proves the
target is active. It never flips experimental feature flags, enables plugins,
Expand Down Expand Up @@ -544,6 +544,7 @@ overwrite user-modified agents.
| Pi | Detected | — | `~/.pi/agent/AGENTS.md` + skill; MCP/subagents require an explicit reviewed extension |
| IBM Bob IDE | Conditional | Existing `~/.bob/mcp.json` | Shared rule + IDE skill; no invented hook or agent |
| Oh My Pi (omp) | Detected | Effective agent directory (`OMP_PROFILE` / `PI_CODING_AGENT_DIR`; default `~/.omp/agent/mcp.json`) | Skill and three direct-MCP graph-tool subagents (Scout/Verify/Auditor); preserves user `AGENTS.md` |
| agentty | Detected | `~/.agentty/mcp.json` (overridden by `$AGENTTY_MCP_CONFIG`) | Skill in `~/.agentty/skills` (Claude-compatible SKILL.md) |
| Sourcegraph Cody | Explicit opt-in | Existing `$CBM_CODY_CONFIG_PATH` | MCP only |

For Codex, install keeps only a tiny managed activation pointer in global
Expand Down Expand Up @@ -892,7 +893,7 @@ src/
main.c Entry point (MCP stdio server + CLI + install/update/config)
daemon/ Per-account session coordination, IPC, lifecycle, shared jobs/watchers
mcp/ MCP server (17 tools, JSON-RPC 2.0, session detection, auto-index)
cli/ Install/uninstall/update/config (45 client surfaces, hooks, instructions)
cli/ Install/uninstall/update/config (46 client surfaces, 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
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10 changes: 5 additions & 5 deletions docs/index.html
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<meta charset="UTF-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>codebase-memory-mcp — Code Intelligence Knowledge Graph for AI Coding Agents</title>
<meta name="description" content="codebase-memory-mcp is an open-source MCP server that indexes any codebase into a persistent knowledge graph so AI coding agents answer structural questions with ~120x fewer tokens. 162 languages, Hybrid LSP type resolution, local semantic vector search, code-clone detection, sub-1ms queries, Linux kernel indexed in 3 minutes. Native executable with verified assets and no language runtime. One command configures 45 automatic/conditional client surfaces.">
<meta name="description" content="codebase-memory-mcp is an open-source MCP server that indexes any codebase into a persistent knowledge graph so AI coding agents answer structural questions with ~120x fewer tokens. 162 languages, Hybrid LSP type resolution, local semantic vector search, code-clone detection, sub-1ms queries, Linux kernel indexed in 3 minutes. Native executable with verified assets and no language runtime. One command configures 46 automatic/conditional client surfaces.">
<meta name="keywords" content="MCP server, code intelligence, knowledge graph, tree-sitter, Hybrid LSP, semantic code search, code embeddings, code clone detection, cross-repo analysis, data-flow analysis, Claude Code, Codex CLI, Gemini CLI, Cursor, Zed, code exploration, token reduction, call graph, dead code detection">
<meta name="author" content="DeusData">
<meta name="robots" content="index, follow, max-image-preview:large, max-snippet:-1">
Expand Down Expand Up @@ -68,7 +68,7 @@
"Infrastructure-as-code indexing for Dockerfiles, Kubernetes, and Kustomize",
"Built-in 3D graph visualization UI",
"Auto-sync background watcher for incremental re-indexing",
"One command configures 45 automatic/conditional client surfaces"
"One command configures 46 automatic/conditional client surfaces"
],
"author": {
"@type": "Organization",
Expand Down Expand Up @@ -157,7 +157,7 @@
"name": "Which AI coding agents work with codebase-memory-mcp?",
"acceptedAnswer": {
"@type": "Answer",
"text": "A single install command configures 45 automatic/conditional client surfaces. The 39 detected surfaces are Claude Code, Codex CLI, Gemini CLI, Zed, OpenCode, Antigravity, Aider, KiloCode, VS Code, Cursor, Windsurf, Augment / Auggie, OpenClaw, Kiro, Junie, Hermes, OpenHands, Cline, Warp, Qwen Code, GitHub Copilot CLI, Factory Droid, Crush, Goose, Mistral Vibe, Grok Build, Qoder CLI, Kimi Code CLI, GitLab Duo CLI, Rovo Dev CLI, Amp, Devin CLI / Local, Tabnine, Amazon Q Developer IDE, CodeBuddy Code CLI, IBM Bob Shell, Pochi, Pi, and Oh My Pi (omp). Continue / cn, Visual Studio, TRAE, Roo Code, IBM Bob IDE, and Sourcegraph Cody are conditional or explicit integrations. Qodo, Warp MCP, JetBrains AI/ACP, GitHub Copilot coding agent, Jules, CodeRabbit, Replit, BLACKBOX AI, Plandex, and SWE-agent require manual, UI, cloud, or repository-managed setup and are not counted among the 45."
"text": "A single install command configures 46 automatic/conditional client surfaces. The 40 detected surfaces are Claude Code, Codex CLI, Gemini CLI, Zed, OpenCode, Antigravity, Aider, KiloCode, VS Code, Cursor, Windsurf, Augment / Auggie, OpenClaw, Kiro, Junie, Hermes, OpenHands, Cline, Warp, Qwen Code, GitHub Copilot CLI, Factory Droid, Crush, Goose, Mistral Vibe, Grok Build, Qoder CLI, Kimi Code CLI, GitLab Duo CLI, Rovo Dev CLI, Amp, Devin CLI / Local, Tabnine, Amazon Q Developer IDE, CodeBuddy Code CLI, IBM Bob Shell, Pochi, Pi, Oh My Pi (omp), and agentty. Continue / cn, Visual Studio, TRAE, Roo Code, IBM Bob IDE, and Sourcegraph Cody are conditional or explicit integrations. Qodo, Warp MCP, JetBrains AI/ACP, GitHub Copilot coding agent, Jules, CodeRabbit, Replit, BLACKBOX AI, Plandex, and SWE-agent require manual, UI, cloud, or repository-managed setup and are not counted among the 46."
}
},
{
Expand Down Expand Up @@ -527,12 +527,12 @@ <h2>How do I install codebase-memory-mcp?</h2>
<span class="cmd">"Index this project"</span>
</div>
<p class="muted">
One command configures 45 automatic/conditional client surfaces. <strong>Detected automatically (39):</strong>
One command configures 46 automatic/conditional client surfaces. <strong>Detected automatically (40):</strong>
Claude Code, Codex CLI, Gemini CLI, Zed, OpenCode, Antigravity, Aider, KiloCode, VS Code, Cursor,
Windsurf, Augment / Auggie, OpenClaw, Kiro, Junie, Hermes, OpenHands, Cline, Warp, Qwen Code,
GitHub Copilot CLI, Factory Droid, Crush, Goose, Mistral Vibe, Grok Build, Qoder CLI, Kimi Code CLI,
GitLab Duo CLI, Rovo Dev CLI, Amp, Devin CLI / Local, Tabnine, Amazon Q Developer IDE,
CodeBuddy Code CLI, IBM Bob Shell, Pochi, Pi, and Oh My Pi (omp).
CodeBuddy Code CLI, IBM Bob Shell, Pochi, Pi, Oh My Pi (omp), and agentty.
</p>
<p class="muted">
<strong>Conditional or explicit (6):</strong> Continue / cn, Visual Studio, TRAE, Roo Code, IBM Bob IDE,
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2 changes: 1 addition & 1 deletion docs/llms.txt
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Expand Up @@ -12,7 +12,7 @@
- Semantic & similarity edges: SEMANTICALLY_RELATED (vocabulary-mismatch matches) and SIMILAR_TO (MinHash + LSH near-clone / duplicate detection).
- Cross-repo intelligence: CROSS_* edges link nodes across multiple repos indexed in one store; multi-galaxy 3D layout and cross-repo architecture summary.
- Cross-service linking: HTTP route ↔ call-site matching, plus gRPC/GraphQL/tRPC detection and pub/sub channels (EMITS/LISTENS_ON for Socket.IO, EventEmitter, generic buses).
- Supported agents: 45 automatic/conditional client surfaces (39 automatically detected + 6 conditional/explicit): Claude Code, Codex CLI, Gemini CLI, Zed, OpenCode, Antigravity, Aider, KiloCode, VS Code, Cursor, Windsurf, Augment / Auggie, OpenClaw, Kiro, Junie, Hermes, OpenHands, Cline, Warp, Qwen Code, GitHub Copilot CLI, Factory Droid, Crush, Goose, Mistral Vibe, Grok Build, Qoder CLI, Kimi Code CLI, GitLab Duo CLI, Rovo Dev CLI, Amp, Devin CLI / Local, Tabnine, Continue / cn, Visual Studio, TRAE, Roo Code, Amazon Q Developer IDE, CodeBuddy Code CLI, IBM Bob IDE, IBM Bob Shell, Pochi, Pi, Oh My Pi (omp), and Sourcegraph Cody.
- Supported agents: 46 automatic/conditional client surfaces (40 automatically detected + 6 conditional/explicit): Claude Code, Codex CLI, Gemini CLI, Zed, OpenCode, Antigravity, Aider, KiloCode, VS Code, Cursor, Windsurf, Augment / Auggie, OpenClaw, Kiro, Junie, Hermes, OpenHands, Cline, Warp, Qwen Code, GitHub Copilot CLI, Factory Droid, Crush, Goose, Mistral Vibe, Grok Build, Qoder CLI, Kimi Code CLI, GitLab Duo CLI, Rovo Dev CLI, Amp, Devin CLI / Local, Tabnine, Continue / cn, Visual Studio, TRAE, Roo Code, Amazon Q Developer IDE, CodeBuddy Code CLI, IBM Bob IDE, IBM Bob Shell, Pochi, Pi, Oh My Pi (omp), agentty, and Sourcegraph Cody.
- Agent profiles: documented custom-agent formats receive Scout (fast/provisional), Verify (default/task-directed), and Auditor (bounded/full verification) definitions. Every direct tier checks exact path/scope coverage with check_index_coverage and falls back to source for flagged gaps; unsafe child-MCP formats use explicit parent handoff. Kiro and Junie use positive-allowlist Scout/Analysis server profiles (7/11 tools); Qoder combines named-server selection with exact tier-specific MCP tool IDs, while Factory uses exact registered IDs without additive whole-server exposure. Foreign Junie aliases are preserved and force parent handoff.
- Performance: Linux kernel (28M LOC, 75K files) full index in 3 minutes → 4.81M nodes, 7.72M edges; Cypher queries in under 1ms.
- Distribution: verified runtime set (native executable plus authenticated release-owned assets); fully static Linux builds are available in the `-portable` archives. Also available through npm, PyPI, Homebrew, Scoop, Winget, Chocolatey, AUR, and `go install`.
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6 changes: 3 additions & 3 deletions pkg/npm/README.md
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Expand Up @@ -7,7 +7,7 @@

**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. This npm wrapper downloads, verifies, and caches the selected native runtime set: the executable, its authenticated integration asset, and—when requested—the content-addressed UI pack.

High-quality parsing through [tree-sitter](https://tree-sitter.github.io/tree-sitter/) AST analysis across 162 languages — producing a persistent knowledge graph of functions, classes, call chains, HTTP routes, and cross-service links. 17 MCP tools. No hosted service or API key; this package requires Node.js to manage and launch the cached native runtime set. Plug and play across 45 automatic/conditional client surfaces.
High-quality parsing through [tree-sitter](https://tree-sitter.github.io/tree-sitter/) AST analysis across 162 languages — producing a persistent knowledge graph of functions, classes, call chains, HTTP routes, and cross-service links. 17 MCP tools. No hosted service or API key; this package requires Node.js to manage and launch the cached native runtime set. Plug and play across 46 automatic/conditional client surfaces.

## Installation

Expand All @@ -31,8 +31,8 @@ Restart your agent. Say **"Index this project"** — done.
- **Plug and play** — verified native runtime sets for macOS (arm64/amd64), Linux (arm64/amd64), and Windows (arm64/amd64). No Docker or API keys; Node.js owns package download, cache repair, and launch.
- **162 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.
- **45 supported automatic/conditional client surfaces** — `install` configures the appropriate MCP, durable-context, and documented hook surfaces without widening client permissions.
- **Detected automatically (39)** — Claude Code, Codex CLI, Gemini CLI, Zed, OpenCode, Antigravity, Aider, KiloCode, VS Code, Cursor, Windsurf, Augment / Auggie, OpenClaw, Kiro, Junie, Hermes, OpenHands, Cline, Warp, Qwen Code, GitHub Copilot CLI, Factory Droid, Crush, Goose, Mistral Vibe, Grok Build, Qoder CLI, Kimi Code CLI, GitLab Duo CLI, Rovo Dev CLI, Amp, Devin CLI / Local, Tabnine, Amazon Q Developer IDE, CodeBuddy Code CLI, IBM Bob Shell, Pochi, Pi, and Oh My Pi (omp).
- **46 supported automatic/conditional client surfaces** — `install` configures the appropriate MCP, durable-context, and documented hook surfaces without widening client permissions.
- **Detected automatically (40)** — Claude Code, Codex CLI, Gemini CLI, Zed, OpenCode, Antigravity, Aider, KiloCode, VS Code, Cursor, Windsurf, Augment / Auggie, OpenClaw, Kiro, Junie, Hermes, OpenHands, Cline, Warp, Qwen Code, GitHub Copilot CLI, Factory Droid, Crush, Goose, Mistral Vibe, Grok Build, Qoder CLI, Kimi Code CLI, GitLab Duo CLI, Rovo Dev CLI, Amp, Devin CLI / Local, Tabnine, Amazon Q Developer IDE, CodeBuddy Code CLI, IBM Bob Shell, Pochi, Pi, Oh My Pi (omp), and agentty.
- **Conditional or explicit (6)** — Continue / cn, Visual Studio, TRAE, Roo Code, IBM Bob IDE, and Sourcegraph Cody. Bob IDE is touched only when `~/.bob/mcp.json` already exists.
- **New documented adapters** — CodeBuddy uses `~/.codebuddy/.mcp.json` while preserving active older files; Bob Shell uses `~/.bob/mcp_settings.json`; Pochi uses the `mcp` section in `~/.pochi/config.jsonc`; Amazon Q Developer IDE defaults to `~/.aws/amazonq/default.json` while preserving either documented alternative.
- **Lifecycle hooks stay conservative** — Kimi uses `UserPromptSubmit`; on macOS/Linux, GitLab Duo gets a fail-open user `SessionStart`, while Devin gets `UserPromptSubmit`, `PostCompaction`, and a deduplicated `SessionStart` when Claude does not already provide it. Qoder, GitLab Duo, Devin, and Factory hooks are withheld on Windows without a documented shell/executor contract. Cline's auto-activating file hooks are withheld because their context output is not reliably consumed, CodeBuddy beta hooks are not auto-installed, and Cursor context hooks remain withheld.
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