[codex] add Graphify integration

[riderx]

Summary (AI generated)

• Add the project-scoped Graphify skill under .agents/skills/graphify so AI agents can build and query code knowledge graphs.
• Commit the generated Graphify code graph output under graphify-out/ so agents can query it directly from the repository.
• Add bun run graphify:* scripts, including deterministic bun run graphify:generate for code-only AST graph refreshes.
• Refresh and amend the committed Graphify graph during release version bumps so release commits/tags keep the graph current.

Motivation (AI generated)

Graphify is only useful for AI navigation when the graph output is available in the repo and kept current. This change commits the graph and wires release automation to refresh it on every release commit.

Business Impact (AI generated)

This should make repository maintenance faster by helping agents and contributors find relevant code paths, used code, likely dead code, and usage relationships more reliably, reducing review/debug time for Capgo changes.

Test plan (AI generated)

• PATH="/tmp/capgo-graphify-venv/bin:$PATH" bun run graphify:generate
• PATH="/tmp/capgo-graphify-venv/bin:$PATH" bun run graphify:query -- "Where is generate_graphify_graph used?"
• python3 -m py_compile scripts/generate_graphify_graph.py
• python3 -m json.tool graphify-out/graph.json
• python3 -m json.tool graphify-out/cost.json
• ruby -e "require 'yaml'; YAML.load_file('.github/workflows/bump_version.yml'); puts 'workflow yaml ok'"
• bun -e "JSON.parse(await Bun.file('package.json').text()); console.log('package.json ok')"
• bun run lint:backend
• bun run lint
• bun run lint:deadcode
• bun typecheck
• GitHub Actions

Screenshots (AI generated)

Not applicable; this is repository tooling and generated graph output, with no user-facing UI changes.

Checklist (AI generated)

• My code follows the code style of this project and passes bun run lint:backend && bun run lint.
• My change requires a change to the documentation.
• I have updated the documentation accordingly.
• My change has adequate E2E test coverage. Not applicable; no user-facing E2E flow changed.
• I have tested my code manually, and I have provided steps how to reproduce my tests.

Generated with AI

[coderabbitai]

📝 Walkthrough

Walkthrough

This PR adds the Graphify skill: a full SKILL.md specification, many reference docs, CI/npm integration, a deterministic generator script, and committed generated artifacts (graph report and cost), plus minor version and ignore updates.

Changes

Graphify Skill Integration

Layer / File(s)	Summary
Skill foundation and project integration .agents/skills/graphify/.graphify_version, .gitignore, AGENTS.md, package.json, .github/workflows/bump_version.yml	Sets graphify version to 0.8.31, adds graphify-out/ ignore rules, documents Graphify usage in AGENTS.md, adds graphify:* npm scripts, and updates CI to install/regenerate Graphify and refresh tags.
Core skill specification .agents/skills/graphify/SKILL.md	Full /graphify skill definition and 9-step pipeline: detection, optional transcription, AST+semantic extraction (cache, chunking, Codex agent dispatch), merging, graph construction, clustering/labeling, visualization/exports, manifest saving for --update, cost tracking, cleanup, interpreter guardrails, and "Honesty Rules."
Reference guides for workflows .agents/skills/graphify/references/*	Adds detailed references: GitHub cloning/merge, extraction subagent prompt/spec, query/path/explain examples, transcription instructions, incremental update/merge/diff, export options (wiki/Neo4j/SVG/GraphML/MCP/benchmark), add/watch ingestion, and git/CLAUDE.md hooks.
Generation script & committed outputs scripts/generate_graphify_graph.py, graphify-out/GRAPH_REPORT.md, graphify-out/cost.json	Adds a deterministic code-only graph generator, postprocesses/stabilizes graph.json, writes GRAPH_REPORT.md (large generated report) and cost.json (zeros), and cleans prior generated artifacts.

Estimated code review effort

🎯 3 (Moderate) | ⏱️ ~25 minutes

🚥 Pre-merge checks | ✅ 4 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 0.00% which is insufficient. The required threshold is 80.00%.	Write docstrings for the functions missing them to satisfy the coverage threshold.

✅ Passed checks (4 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title '[codex] add Graphify integration' directly addresses the main change: adding Graphify integration to the project. It is concise, clear, and summarizes the primary objective.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Description check	✅ Passed	The pull request description is comprehensive, covering summary, motivation, business impact, detailed test plan with checkmarks, and a completed checklist addressing code style, documentation, testing, and manual verification.

_{✏️ Tip: You can configure your own custom pre-merge checks in the settings.}

✨ Finishing Touches

📝 Generate docstrings

• Create stacked PR
• Commit on current branch

---

_{Comment @coderabbitai help to get the list of available commands and usage tips.}

[codspeed-hq]

Merging this PR will not alter performance

✅ 43 untouched benchmarks
⏩ 2 skipped benchmarks¹

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_{Comparing codex/add-graphify (da88bd2) with main (5217280)}

Footnotes

1. 2 benchmarks were skipped, so the baseline results were used instead. If they were deleted from the codebase, click here and archive them to remove them from the performance reports. ↩

[sonarqubecloud]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud