Add Graphify integration#197
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Pull request overview
This PR introduces a Graphify-based “knowledge graph” artifact set and companion workflow/docs so contributors can query cross-file relationships and keep the graph updated over time.
Changes:
- Adds committed Graphify outputs (
graphify-out/GRAPH_REPORT.md,graphify-out/manifest.json) plus ignore rules to avoid committing other generated artifacts. - Adds a Graphify usage section to
CLAUDE.mdand a new.claude/skills/graphify/skill with reference docs. - Updates local tooling configuration (pre-commit + detect-secrets) to accommodate Graphify output files.
Reviewed changes
Copilot reviewed 19 out of 21 changed files in this pull request and generated 3 comments.
Show a summary per file
| File | Description |
|---|---|
| graphify-out/manifest.json | Adds a generated manifest of scanned files + hashes. |
| graphify-out/GRAPH_REPORT.md | Adds a generated high-level architecture/community report. |
| CLAUDE.md | Documents how to use Graphify for codebase questions and refreshing the graph. |
| .secrets.baseline | Excludes graphify-out/ from detect-secrets scanning. |
| .pre-commit-config.yaml | Reformats config and excludes graphify-out/graph.json from large-file hook. |
| .graphifyignore | Excludes vendor/, storage/, and docs/ from graph generation. |
| .gitignore | Ignores some Graphify-generated artifacts (cache, html, dotfiles, etc.). |
| .claudeignore | Prevents Claude tooling from reading graphify-out/ and graph.json. |
| .claude/skills/graphify/SKILL.md | Adds an in-repo skill/runbook for building/querying Graphify graphs. |
| .claude/skills/graphify/references/update.md | Adds incremental update / cluster-only guidance. |
| .claude/skills/graphify/references/transcribe.md | Adds audio/video transcription guidance for ingestion. |
| .claude/skills/graphify/references/query.md | Adds query/path/explain guidance + fallback traversal steps. |
| .claude/skills/graphify/references/hooks.md | Adds post-commit hook + CLAUDE integration guidance. |
| .claude/skills/graphify/references/github-and-merge.md | Adds GitHub clone + cross-repo merge guidance. |
| .claude/skills/graphify/references/extraction-spec.md | Defines the semantic extraction subagent JSON schema + rules. |
| .claude/skills/graphify/references/exports.md | Adds optional export/benchmark/MCP server guidance. |
| .claude/skills/graphify/references/add-watch.md | Adds add and --watch guidance. |
| .claude/skills/graphify/.graphify_version | Records the intended Graphify skill version. |
| .claude/settings.json | Adds Claude hooks intended to guard reads/searches via Graphify. |
| .claude/CLAUDE.md | Adds a short note telling Claude sessions how to use the Graphify skill. |
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| - If graphify-out/wiki/index.md exists, use it for broad navigation instead of raw source browsing. | ||
| - Read graphify-out/GRAPH_REPORT.md only for broad architecture review or when query/path/explain do not surface enough context. | ||
| - After modifying code, run `graphify update .` to keep the graph current (AST-only, no API cost). |
The raw post-commit hook rebuilt the graph in a detached background process after the commit landed, so graphify-out/* drifted from what was actually committed (and diverged again on any CI rebuild). Moving the rebuild into .pre-commit-config.yaml runs it synchronously before the commit, in an isolated venv pinned to graphifyy==0.9.12 (no more fragile system-Python interpreter probing), so the graph is always in sync with what gets committed. Uninstalled the old post-commit/post-checkout git hooks via `graphify hook uninstall`. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
.claude/settings.json's PreToolUse hooks hardcoded
/home/aquarion/.local/bin/graphify, which only exists on this machine
- would break for any other contributor and in CI. graphify is on
PATH after a normal install, so drop the absolute path.
Left the "AST-only, no API cost" CLAUDE.md note as-is after checking
graphify/cli.py: `graphify update .` calls _rebuild_code exclusively
and explicitly defers doc/image changes to a separate /graphify
--update step, so the claim is accurate as scoped ("after modifying
code").
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Bare "graphify" resolves via $PATH, but vendor/bin (composer-writable) sits ahead of ~/.local/bin on this system's PATH. Since this hook fires automatically on every Bash/Read/Glob tool call with no confirmation prompt, a malicious graphify binary dropped into vendor/bin (e.g. via a compromised composer package) would silently execute instead of the real one. $HOME/.local/bin/graphify is a fixed path - immune to PATH-order shadowing - while still resolving correctly per contributor, so it keeps the portability fix without reopening the hijack risk. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Rebasing onto main's squashed react-doctor merge (18 deleted files, pnpm hardening, pre-commit fixes) changed the codebase composition, so the graph needed a rebuild to reflect current state. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
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Integrate Graphify into the codebase, enabling knowledge graph capabilities and enhancing project documentation and analysis features. This addition includes necessary configurations, scripts, and documentation for effective usage.