Forensic Deepdive MCP Server

forensic-deepdive

A persistent code knowledge graph + MCP server for AI coding agents. Five durable markdown artifacts as the human-readable projection. Apache-2.0.

forensic-deepdive analyzes any codebase (9 languages, polyglot) and produces:

1. A persistent embedded graph at <repo>/.deepdive/graph.lbug — File, Symbol, Module, Commit, Author, Endpoint, and DbTable nodes plus DEFINES, MEMBER_OF, IMPORTS, CALLS, EXTENDS, IMPLEMENTS, TOUCHED_BY_COMMIT, AUTHORED_BY, CO_CHANGES_WITH, and the cross-boundary HANDLES / CALLS_ENDPOINT / ROUTES_TO / INJECTS / PERSISTS_TO edges. Every edge carries a confidence tag (EXTRACTED / INFERRED / AMBIGUOUS) — no hidden heuristics. The single Endpoint join node unifies five cross-boundary protocols (HTTP, MCP tools, registry-dispatch, gRPC, messaging/AMQP), so a frontend call resolves to its backend handler across the stack as one ROUTES_TO edge.
2. An MCP server (forensic serve) exposing 9 composite tools (impact, context, archaeology, flow, query, record_insight, recall_insights, visualize, trace) consumable by Claude Code, Cursor, Codex, Continue, Cline, Windsurf — and any other MCP-aware agent.
3. Five durable markdown artifacts under <repo>/docs/codebase/, regenerated from the graph on every extract:
   • MAP.md — what's where, ranked by centrality.
   • HOTPATHS.md — the dependency hot spots, with a per-row confidence-mix column so you see exactly how cleanly each symbol resolves.
   • ARCHAEOLOGY.md — why the code looks the way it does (git history, top authors with %, bus factor, co-change clusters, defect proximity).
   • MENTAL_MODEL.md — the doc the original author would write to onboard a new hire.
   • AGENT_BRIEF.md — ≤5 KB of assertive Never/Always rules with per-rule confidence tags. Drop-in CLAUDE.md for any project.
4. Ten shims into the target repo — 4 editor rule files (CLAUDE.md, AGENTS.md, .cursor/rules/codebase.mdc, .continue/rules/codebase.md), 5 single-intent Claude skills under .claude/skills/codebase-{exploring,debugging,impact-analysis,refactoring,onboarding}/, and a .claude-plugin/plugin.json manifest. All write-if-absent — hand-edited files are never overwritten.
5. An agent-insight layer — record_insight / recall_insights MCP tools backed by <repo>/.deepdive/insights.jsonl by default (zero dependencies, human-readable, git-friendly). The optional [graphiti] extra upgrades to a temporal knowledge graph backend above a 2-of-5 repo-size threshold.

Extract also regenerates ARCHITECTURE.md — a system-level Mermaid view of the cross-boundary graph (ROUTES_TO / INJECTS / PERSISTS_TO, confidence-styled), a separate human-validation surface (not one of the five contract artifacts, exactly like forensic visualize and serve --ui). Regenerate it on its own with forensic diagram --repo <repo>. Use it to sanity-check the graph — a wrong edge there is a wrong edge everywhere.

Add --emit-vault to also write an Obsidian-friendly vault under <output>/vault/ — every artifact gets summary:/tags: frontmatter, cross-references become [[wikilinks]], and an INDEX.md MOC ties them together (with a .obsidian/ config). A local-first second brain for humans (graph view, backlinks) and agents (triage by summary: without opening files, a traversable index). Opt-in; off by default.

Status

v0.8.0 "USABLE → USEFUL + public release" — the first public PyPI release. Builds on the frozen five-protocol cross-boundary graph (HTTP/MCP/registry/gRPC/messaging on one Endpoint join node) with a precision pass (honest call-graph confidence, distinct-caller counts, low-history/solo-repo guards), a human-validation ARCHITECTURE.md diagram surface, distribution (PyPI + MCP Registry + a Claude Code plugin), and an opt-in --emit-vault Obsidian export. The 5-artifact + 9-MCP-tool contract is frozen.

What's proven, and what isn't (honest framing). v0.8 is an assisted-analysis tool: a real fresh-agent onboarding test confirmed it's usable and that an agent auto-discovers AGENT_BRIEF.md and routes to the right skill unprompted, and a grounded MCP tool review found the git-archaeology + curated briefs are the high-trust core. The autonomous end-to-end question — does deepdive-seeding make an agent resolve real issues measurably faster — is not yet proven: a model-free localization pilot is recorded (experiments/fastcontext/RESULTS.md — the static seed is a weak prior), and the end-to-end measurement is deferred to v0.9 (it needs a GPU + a frontier main-agent endpoint). No autonomous-execution claims are made. Accepted across real repos including Apache Superset, wagtail (Django), spring-petclinic, ripgrep, fastapi, and Iris-Nearby (Flutter/Dart) — see docs/findings/.

Quick start

# install from PyPI (puts `forensic` on PATH); or run ephemerally with uvx
uv tool install forensic-deepdive
forensic info            # banner + capability panel
forensic extract /path/to/repo

# …or from source for development:
git clone https://github.com/Dhevenddra/forensic-deepdive && cd forensic-deepdive
uv sync --all-extras

# what can it do? (banner + capability panel: artifacts, protocols, MCP tools, confidence legend)
uv run forensic info

# run on any repo
uv run forensic extract /path/to/repo

# graph lands at <repo>/.deepdive/graph.lbug
# 5 markdown artifacts at <repo>/docs/codebase/
# 10 shims at <repo>/.claude/, .cursor/, .continue/, root

# trace a cross-stack feature slice (frontend call -> endpoint -> handler -> tail)
uv run forensic trace <symbol> --repo /path/to/repo

# query the graph as an MCP server (point it at the analyzed repo)
uv run forensic serve --repo /path/to/repo

# inspect every repo you've analyzed
uv run forensic list

Once published (v0.8), install without cloning: uv tool install forensic-deepdive (puts forensic on PATH) or run ephemerally with uvx forensic-deepdive …. For the MCP server in Claude Code / Cursor / VS Code / Codex, the one-liner is uvx forensic-deepdive serve --repo <repo> — see docs/install.md for per-client copy-paste blocks and the Claude Code plugin.

The 9 supported languages

Python, C, Dart, Swift, TypeScript, JavaScript, Java, Go, Rust.

The 9 MCP tools

Tool descriptions are individually ≤200 tokens so the 9-tool envelope stays comfortably inside Anthropic's per-turn skill metadata budget.

The confidence taxonomy

Every edge and every emitted claim carries EXTRACTED / INFERRED / AMBIGUOUS:

• EXTRACTED — deterministic from AST or git log. Facts.
• INFERRED — a heuristic resolved cleanly (import-graph walk, receiver-type inference, single same-name candidate cross-file). High-trust but derived.
• AMBIGUOUS — multiple candidates surfaced; the resolver couldn't disambiguate. You see every candidate, not a silent guess.

HOTPATHS shows a per-row confidence-mix column so at a glance you can tell Logger (4 EXTRACTED + 1458 INFERRED — mostly clean) from ChatToolResponse (449 AMBIGUOUS — same-name cross-file collision).

Honest-mode (pure-static, zero LLM, zero network)

forensic extract works end-to-end with no ANTHROPIC_API_KEY, no OPENAI_API_KEY, no Ollama, no network. Graphiti is opt-in via the [graphiti] PyPI extra plus a 2-of-5 repo-size threshold (≥50 k LOC, ≥25 contributors, ≥18 mo old, ≥200 PRs/12 mo, ≥100 issues with discussion). The JsonlInsightStore is the always-available floor.

Why this and not [GitNexus / CodeGraphContext / DeepWiki / Sourcegraph]

GitNexus is the runaway leader — but the PolyForm Noncommercial license locks every commercial user out. That's the wedge: Apache-2.0 + honest confidence + git archaeology + persistent agent memory + the 5 markdown artifacts as a fallback for any agent that doesn't speak MCP.

Local development

git clone https://github.com/Dhevenddra/forensic-deepdive
cd forensic-deepdive
uv sync --all-extras
uv run forensic --version
uv run pytest -x          # 779 tests at v0.7.0
uv run ruff check src/ tests/
uv run forensic extract tests/fixtures/tiny_fixture

Read CLAUDE.md, DECISIONS.md (81 active DECs), and PROGRESS.md before making changes. This repo dogfoods its own pattern: every session starts with the protocol in CLAUDE.md, every architectural choice is captured as a DEC-N entry, and the artifact-name contract (MAP, HOTPATHS, ARCHAEOLOGY, MENTAL_MODEL, AGENT_BRIEF) is part of the public API.

Acknowledgments

• Aider (Paul Gauthier) for the PageRank-on-Tree-sitter repo-map pattern. Algorithm ported with attribution; we do not depend on aider as a package.
• Graphify (safishamsi) for the EXTRACTED / INFERRED / AMBIGUOUS confidence taxonomy. Productized in DEC-015 across every emitter.
• GitNexus (abhigyanpatwari) for the multi-repo registry pattern (~/.deepdive/registry.json, DEC-018), the composite-MCP-tool shape, and being the licensing wedge that makes this project's Apache-2.0 differentiation matter.
• Kuzu (now Apple-archived) for the embedded graph engine; LadybugDB for the live community fork that v0.2 ships against (DEC-013).
• Zep / getzep for Graphiti — the temporal knowledge graph that powers the above-threshold insight backend (DEC-019).
• Anthropic for the Skills format, Claude Code, and the MCP protocol that makes this whole product shape possible.
• Astral for uv and ruff.
• Repomix (yamadashy) for the original v0.1 flatten-the-repo pattern, now demoted to --legacy-repomix (DEC-017) but still available for legacy use cases.

License

Apache-2.0. See LICENSE.