# Graph > Build and query a persistent, confidence-tagged knowledge graph of a repository (files, classes, functions, imports, calls, inheritance, docs) instead of rediscovering its structure from scratch every time you need codebase context. Use whenever a task needs you to understand how a codebase is put together to do the work well — a code review, "what does this PR touch and depend on", architecture questions ("how does auth connect to the database", "what depends on this service", "what would break if I changed this"), prep before a large refactor, or unfamiliar-codebase exploration — or whenever the user asks to "graph", "map", or "graphify" the repo. If a graph already exists (check .graph/graph.json), query it first and read only the exact files it points to instead of grepping broadly — that saves tokens versus rediscovering structure on every multi-file task. Skip this for a small repo, a single-file task, or a question about what one line of code does — read the file directly instead. - Skill: `microxro/graph` (Agent Skill, multi-file: 7 files) - Install (CLI): `npx skillmds@latest add microxro/graph` - Raw SKILL.md: https://api.skillmd.com/api/skills/microxro/graph/raw - Safety review: pending - Works with: Claude Code, Claude.ai, OpenAI Codex - Category: Productivity - Author: microxro (https://skillmd.com/u/microxro) - Updated: 2026-09-22 - Page: https://skillmd.com/skills/microxro/graph --- # /graph — a persistent map of the repo, so you stop rediscovering it ## What this actually is (read this before promising anything to the user) This is a scoped-down implementation of the same idea as the public Graphify project — but a Claude Code skill can't spin up a standalone server, bundle tree-sitter grammars for thirty languages, or run a real Leiden clustering library, so don't describe this skill in those terms. Here's what's real and what's simplified, honestly: - **Python gets a real AST parse** (`ast`, stdlib, always available) — imports, classes, functions, methods, inheritance, and calls are structural facts, not guesses. - **Every other language gets regex-based heuristic extraction** — good enough to find imports, top-level classes/functions, and file-level "this file calls something named X somewhere," but it is not a real parse and every edge it produces is tagged `"method": "regex"` so nothing downstream pretends otherwise. - **God nodes are real** — plain degree centrality (how many edges touch a node), computed directly, no approximation. - **Communities are real but simpler than Graphify's** — label propagation (Raghavan et al.), a legitimate community-detection algorithm implementable in pure Python, standing in for Graphify's Leiden clustering. It finds genuinely similar structural groupings; it's just a lighter algorithm. - **No MCP server, no HTTP transport, no PR triage, no git hooks, no multimodal (PDF/image/video) extraction.** If the user wants the graph updated automatically on every commit, that's a manual `--update` re-run you'd need to wire into their own git hook — don't claim it happens on its own. If you're ever unsure whether to describe something as automatic or as something you'd need to set up, say the honest, more modest version. That's the whole point of a confidence-tagged graph — don't undermine it by being vague about the tool that built it. ## The idea ``` Without a graph: With a graph: question question -> grep across the repo -> query graph.json for the region that matters -> open a dozen files -> open the handful of files it points to -> infer how they connect -> read them with the connections already known -> repeat next question -> next question starts from structure, not zero ``` The graph doesn't replace reading source — it tells you which source is worth reading first. Map, then terrain, every time: query before you grep broadly, then always verify anything load-bearing against the real file, especially before editing it. ## When to build/use one Worth it any time doing the task well requires actually understanding how the codebase fits together, not just reading the one file in front of you: a **code review** (what does this change actually touch, what depends on the code being reviewed, does it fit the surrounding module's conventions), an **architecture question** ("what actually calls this", "how does X reach Y", "what would a change to this file ripple into"), or prep before a **refactor** that touches several files. Anywhere you'd otherwise burn tokens grepping across a dozen-plus files just to build a mental model before you can even start the real task, the graph is meant to replace that step. Not worth it for a small repo you can hold in your head, a single-file change, or "what does this specific function return" — that's faster to just read. There's a global SessionStart hook (see `scripts/session_start_hook.py`, wired up in `~/.claude/settings.json`) that already does the "does a graph exist / is it fresh / should I build one" check automatically at the start of any session in a git repo with enough source files to be worth it — if it ran, you'll see a context note saying so. If you don't see that note (a smaller repo, or the hook isn't installed in this environment), decide for yourself using the criteria above rather than assuming no graph is wanted. ## Build or update the graph ``` python3 scripts/build_graph.py --out-dir .graph ``` Writes `.graph/graph.json` (the persistent graph), `.graph/GRAPH_REPORT.md` (human-readable summary — god nodes, communities, ambiguous edges worth a look, extraction errors), and `.graph/graph.html` (a self-contained, offline-capable visualization — open it in a browser, drag nodes, click one to highlight its neighborhood). Once a graph already exists, refresh it incrementally rather than rebuilding from scratch — it only re-extracts files whose content actually changed: ``` python3 scripts/build_graph.py --out-dir .graph --update ``` Respects `.gitignore` and an optional `.graphignore` (same syntax) in the repo root automatically. ## Query it ``` python3 scripts/query.py stats python3 scripts/query.py search "auth" python3 scripts/query.py neighbors "AuthService" python3 scripts/query.py explain "AuthService" python3 scripts/query.py path "LoginController" "DatabasePool" ``` `neighbors`/`explain`/`path` accept a search string, not just an exact node id — if it matches more than one node, you'll get a candidate list back instead of a guess, so be more specific rather than assuming which one was meant. `stats` is the fastest way to get oriented in an unfamiliar repo: the god-node list alone usually tells you where the real architecture lives. **The actual workflow that makes this worth doing:** before grepping broadly for a structural question, a code review, or any task that needs you to understand how a change relates to the rest of the codebase, check whether `/.graph/graph.json` exists. If it does (and isn't obviously stale — check whether recent commits touched a lot of ground since it was last built), query it first. Use what it returns to go straight to the handful of files that matter, instead of casting a wide net. If no graph exists and the repo is large enough to justify one, offer to build it before diving in — it pays for itself the moment there's a second question, and a review is usually not the last question you'll be asked about that code. ## Reading the confidence tags Every edge is one of three things, and they mean different things depending on which extraction path produced them — read `references/MODEL.md` for the full resolution rules, but the short version: - **EXTRACTED** — a literal structural fact: an import statement exists, a function/class is defined here. Trust it. - **INFERRED** (0.75–0.95) — a call or inheritance relationship that got resolved by matching a name against the repo's real symbol table. Higher score means less naming ambiguity going into the match. Treat it as probably right, not certain — verify before it drives a consequential decision. - **AMBIGUOUS** — kept, not dropped, specifically so nothing silently disappears: either the name matched zero definitions (probably an external library call) or matched more than one (a real naming collision in the repo worth knowing about). Don't treat these as facts. One asymmetry worth internalizing: **Python's call/inherit edges resolve at function granularity** (a real AST knows exactly which function a call sits inside), while **every other language's call-style edges resolve at file granularity** (regex extraction can't reliably track function boundaries, so "this file uses X somewhere" is as precise as it gets). Don't present a JS/Go/Ruby/etc. "uses" edge as if it pinpoints the calling function — it doesn't, and the report/query output labels it `uses` rather than `calls` for exactly this reason. ## Adding the semantic layer (optional, and it's your job, not a script's) Structural extraction can't know that `AuthService` is coupled to a decision documented in `AUTH_ARCHITECTURE.md`, or that a diagram explains a concept also implemented in three files. That's for you to find by actually reading docs/READMEs/comments and proposing graph fragments in the same node/edge shape the extractor uses — nodes for concepts, edges tagged `"method": "semantic"` with your own honest `INFERRED` score or `AMBIGUOUS` if you're genuinely unsure. Save them as JSON (see `references/MODEL.md` for the exact shape) and merge them in: ``` python3 scripts/build_graph.py --out-dir .graph --semantic fragments.json ``` For a large corpus, splitting this across a handful of parallel subagents (one per doc or module) keeps it fast — same principle as any other decompose-and-parallelize task, just applied to reading docs instead of writing code. ## God nodes and communities God nodes (top of `GRAPH_REPORT.md`, also `query.py stats`) are the highest-degree nodes in the graph — the files/symbols a large share of everything else touches. They're where architecture actually concentrates, and where a change is most likely to ripple. Treat a high-degree node as a signal to slow down before editing it, not just a trivia fact. Communities are structural clusters — nodes more connected to each other than to the rest of the graph. They usually correspond to real subsystems even though nothing told the algorithm what a "subsystem" is; if a community's membership looks like an obvious single concern (all the shop-related functions, all the auth-related functions), that's the graph doing its job. If a community looks arbitrary, don't force meaning onto it — label propagation is a decent heuristic, not a guarantee. ## Keeping it fresh The graph goes stale the moment source changes and nobody re-runs it — there is no hook doing this automatically. After a meaningful batch of edits (not every single save), re-run with `--update`. If you're about to answer an architecture question and the graph's `meta.generated_at` looks old relative to recent commit activity, say so and offer to refresh it rather than answering from a graph you know might be wrong. For the exact node/edge schema, the full confidence-resolution rules, and how import-target resolution works per language, see `references/MODEL.md`.