forensic-deepdive

forensic-deepdive gives an AI coding agent forensic understanding of an unfamiliar codebase — a persistent knowledge graph, an MCP server, and five durable markdown artifacts, so your agent stops re-discovering the same architecture from scratch every session.

uv tool install forensic-deepdive && forensic extract /path/to/repo

Why this is different: every edge and every emitted claim carries a confidence tag — EXTRACTED (deterministic fact) / INFERRED (a heuristic resolved cleanly) / AMBIGUOUS (multiple candidates, shown, not guessed) — so your agent knows what to trust before it acts on it. Nothing else in this category tags confidence at all.

Why not GitNexus / CodeGraphContext / DeepWiki / Sourcegraph

GitNexus is the runaway leader in this category — but its PolyForm Noncommercial license locks every commercial user out. forensic-deepdive is the Apache-2.0 alternative: same persistent-graph-plus-MCP shape, plus honest confidence tags, git archaeology, persistent agent memory, and the 5 markdown artifacts as a fallback for any agent that doesn't speak MCP — with a license your employer's legal team will actually sign off on.

What it produces

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

v0.10.0 "The Upgrade Path" — an integrity release. v0.9 shipped correct, and then its findings run caught --refresh-shims being structurally unable to refresh half its targets, with 909 tests green over it. The cause wasn't the fix — it was that every test in the suite wrote into an empty directory, so only the first run had ever been tested. Everyone who isn't a new user lives on the untested path.

So 0.10 adds almost no surface. It makes the guarantees already made real: running Deepdive over a repo that already carries a previous release's output now provably converges (and provably leaves your hand-edited files alone), extract tells you when generated shims are stale instead of waiting for you to know the flag exists, and a stale examples/ fails CI rather than being caught by eye mid-release. New: forensic extract --timings, per-phase wall clock.

It also contains a cancelled feature, which is the more useful story. The planned performance work targeted PageRank. The profile required before touching it measured PageRank at 0.04 % of a large extract, and the already-batched store writes at 79–87 %. The optimization was disproven before it was written — see docs/findings/v0.10/PROFILE.md. Confirming a known technique had been applied had been mistaken for confirming it was fast.

The engine, the graph, the contract layer and the 5-artifact + 9-MCP-tool contract are unchanged from 0.9, and emitted content is byte-identical but for the version footer.

⚠ If you installed 0.8.0 or 0.9.0 and forensic serve stopped working — this is why. Those releases declare mcp>=1.27.1 with no upper bound. mcp 2.0.0 removed mcp.server.fastmcp, which the MCP server imports, so a fresh install of 0.8.0 or 0.9.0 today resolves to mcp 2.0.0 and fails on import. Our development lockfile pinned 1.27.1, so every local check stayed green and only the clean-environment wheel smoke in CI could see it. Fix: upgrade to 0.10.0 (which caps mcp<2), or pin mcp<2 yourself. Nothing else about those releases is affected.

What's proven, and what isn't — the honest-framing section moved to docs/findings/HONEST.md (unchanged content, DEC-119). Short version: proven usable with real agent auto-discovery; not proven to make autonomous issue resolution measurably faster end-to-end (hardware-gated). This is an assisted-analysis tool, and it is not overclaimed as more.

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

# guided setup: analyze a repo, then wire it up as an MCP server
# (--yes takes every default: scriptable, and the one mode that needs no extra)
uv run forensic onboard --repo /path/to/repo

# 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

# interactive query REPL over one held-open store (needs the [interactive] extra)
# bare text = natural-language query (no LLM) · :cypher <q> = raw Cypher · :help · Ctrl-D exits
uv run forensic repl --repo /path/to/repo

# full-screen terminal graph browser — the loopback-free sibling of serve --ui
# 1/2/3 = Symbols/Files/Endpoints · type to filter · c/e/l = confidence/edge/language · Enter = context · i/f = impact/flow
uv run forensic browse --repo /path/to/repo

# the session shell: all of the above over ONE held-open graph, with history
# in-session: extract · query · trace · impact · flow · diagram · browse · onboard · serve
uv run deepdive --repo /path/to/repo