# System map — Graphify-Labs/graphify

> Canonical page: https://codevetter.com/unpack/graphify/system-map

# System map — Graphify-Labs/graphify

Scanned commit 20a20d30d8e7eef77675651f0199d87f913bd3e7 (2026-09-20). Generated by codevetter codevetter 1.12.0 on 2026-09-22.

A single-package Python CLI (`graphifyy`) structured as a staged pipeline: detect -> extract -> build -> cluster -> analyze -> report -> export, with each stage in its own module communicating through plain dicts and NetworkX graphs. The same library is driven two ways: headless via `graphify extract` subcommands in cli.py, or by an AI assistant following the packaged skill.md runbook that shells out to the library. Persistence is entirely file-based under graphify-out/ (graph.json, manifest.json, cache/, sidecars). Deployment surfaces are the PyPI wheel, per-platform skill files, and a Docker image that runs the MCP HTTP server.
- The canonical pipeline is detect() -> extract() -> build() -> cluster() -> analyze helpers -> report.generate() -> export.to_*(); each stage is a separate module exchanging plain dicts/NetworkX graphs with no shared state outside graphify-out/. — [ARCHITECTURE.md#L8-11](https://github.com/Graphify-Labs/graphify/blob/20a20d30d8e7eef77675651f0199d87f913bd3e7/ARCHITECTURE.md#L8-L11)
- Two console entry points ship in the wheel: `graphify` -> graphify.__main__:main and `graphify-mcp` -> graphify.serve:_main. — [pyproject.toml#L110-112](https://github.com/Graphify-Labs/graphify/blob/20a20d30d8e7eef77675651f0199d87f913bd3e7/pyproject.toml#L110-L112)
- graphify/__main__.py is a thin dispatcher: it re-exports the install subsystem from graphify/install.py (~90 names) and dispatch_command from graphify/cli.py, then main() wraps _run_cli() with broken-pipe handling. — [graphify/__main__.py#L29-131](https://github.com/Graphify-Labs/graphify/blob/20a20d30d8e7eef77675651f0199d87f913bd3e7/graphify/__main__.py#L29-L131) [graphify/__main__.py#L486-527](https://github.com/Graphify-Labs/graphify/blob/20a20d30d8e7eef77675651f0199d87f913bd3e7/graphify/__main__.py#L486-L527)
- dispatch_command(cmd) in graphify/cli.py is the single command table for all non-install subcommands: provider, prs, hook, query, affected, god-nodes, save-result, reflect, path, explain, diagnose, add, watch, cluster-only/label, update, hook-check, hook-guard, check-update, tree, merge-driver, merge-graphs, clone, export, benchmark, global, extract, cache-check, merge-chunks, merge-semantic. — [graphify/cli.py#L1064-4832](https://github.com/Graphify-Labs/graphify/blob/20a20d30d8e7eef77675651f0199d87f913bd3e7/graphify/cli.py#L1064-L4832)
- All persistent state lives under the output directory `graphify-out`, overridable via the GRAPHIFY_OUT env var, centralized in graphify/paths.py (GRAPHIFY_OUT, out_path, default_graph_json) so security/path guards honor the same override. — [graphify/paths.py#L26](https://github.com/Graphify-Labs/graphify/blob/20a20d30d8e7eef77675651f0199d87f913bd3e7/graphify/paths.py#L26) [graphify/paths.py#L359-375](https://github.com/Graphify-Labs/graphify/blob/20a20d30d8e7eef77675651f0199d87f913bd3e7/graphify/paths.py#L359-L375)
- graph.json is a NetworkX node-link JSON file; serve.py _load_graph rehydrates it with json_graph.node_link_graph, forces directed=True for rendering, and attaches a work-memory overlay sidecar. — [graphify/serve.py#L44-85](https://github.com/Graphify-Labs/graphify/blob/20a20d30d8e7eef77675651f0199d87f913bd3e7/graphify/serve.py#L44-L85)
- AST extraction scales via concurrent.futures.ProcessPoolExecutor (_extract_parallel -> _extract_single_file worker, module-level for pickling), capped by cpu_count or GRAPHIFY_MAX_WORKERS, clamped to 61 on Windows, with sequential fallback on BrokenProcessPool/OSError. — [graphify/extract.py#L6558-6745](https://github.com/Graphify-Labs/graphify/blob/20a20d30d8e7eef77675651f0199d87f913bd3e7/graphify/extract.py#L6558-L6745)
- The MCP server is built once by serve.py::_build_server and served over stdio (serve()) or Streamable HTTP via starlette/uvicorn (serve_http), with optional X-API-Key/Bearer auth and a warning when binding 0.0.0.0 unauthenticated. — [graphify/serve.py#L1795-1860](https://github.com/Graphify-Labs/graphify/blob/20a20d30d8e7eef77675651f0199d87f913bd3e7/graphify/serve.py#L1795-L1860) [graphify/serve.py#L2561-2615](https://github.com/Graphify-Labs/graphify/blob/20a20d30d8e7eef77675651f0199d87f913bd3e7/graphify/serve.py#L2561-L2615)
- The Dockerfile builds a python:3.12-slim image installing the [mcp] extra, runs as non-root uid 10001, and launches `python -m graphify.serve` with an HTTP transport default; graph.json is mounted at runtime, never baked in. — [Dockerfile#L10-25](https://github.com/Graphify-Labs/graphify/blob/20a20d30d8e7eef77675651f0199d87f913bd3e7/Dockerfile#L10-L25)
- Core dependencies are networkx, numpy, rapidfuzz, tree-sitter plus ~26 tree-sitter grammar packages; optional extras (pdf, office, video, mcp, neo4j, falkordb, sql, postgres, terraform, pascal, ocaml, commonlisp, robot, llm backends, all) gate niche extractors and integrations. — [pyproject.toml#L14-45](https://github.com/Graphify-Labs/graphify/blob/20a20d30d8e7eef77675651f0199d87f913bd3e7/pyproject.toml#L14-L45) [pyproject.toml#L52-108](https://github.com/Graphify-Labs/graphify/blob/20a20d30d8e7eef77675651f0199d87f913bd3e7/pyproject.toml#L52-L108)
- Per-assistant skill bundles are generated artifacts: tools/skillgen/gen.py renders graphify/skill*.md, graphify/skills/<host>/references/, and graphify/always_on/*.md from tools/skillgen/fragments/, with CI drift guards (--check, --audit-coverage, --monolith-roundtrip). — [tools/skillgen/gen.py#L1-25](https://github.com/Graphify-Labs/graphify/blob/20a20d30d8e7eef77675651f0199d87f913bd3e7/tools/skillgen/gen.py#L1-L25) [.github/workflows/ci.yml#L11-47](https://github.com/Graphify-Labs/graphify/blob/20a20d30d8e7eef77675651f0199d87f913bd3e7/.github/workflows/ci.yml#L11-L47)
- Publishing is trusted-publishing OIDC to PyPI on GitHub release (publish.yml), with a version==tag guard; release-graph.yml dogfoods the tool by building a graph of graphify itself and uploading graphify-self-graph.tar.gz as a release asset. — [.github/workflows/publish.yml#L1-45](https://github.com/Graphify-Labs/graphify/blob/20a20d30d8e7eef77675651f0199d87f913bd3e7/.github/workflows/publish.yml#L1-L45) [.github/workflows/release-graph.yml#L1-60](https://github.com/Graphify-Labs/graphify/blob/20a20d30d8e7eef77675651f0199d87f913bd3e7/.github/workflows/release-graph.yml#L1-L60)
- The repo's own AGENTS.md instructs agents to read graphify-out/GRAPH_REPORT.md and run `graphify update .` after code changes — the project dogfoods its own graph. — [AGENTS.md](https://github.com/Graphify-Labs/graphify/blob/20a20d30d8e7eef77675651f0199d87f913bd3e7/AGENTS.md)

Every claim links to its cited files at the pinned commit. Citations identify source evidence; they do not establish runtime correctness. Independent CodeVetter scan — not reviewed by upstream maintainers.

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