- Add all claude skills (brainstorming, commit, debugging, TDD, etc.) - Add claude hooks (pre-commit-guard, post-edit-quality) - Add research templates (experiment plan, research brief, etc.) - Add claude tools (arxiv/semantic_scholar/openalex fetch, wiki, exa) - Add TRM4 reference implementation as algorithm fidelity baseline - Add research-wiki content (plans, index, graph, query_pack) - Update .gitignore to exclude .graphify_version runtime state
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graphify reference: GitHub clone and cross-repo merge
Load this when the user passed one or more https://github.com/... URLs, or named several local subfolders to merge into one graph.
Step 0 - Clone GitHub repo(s) (only if a GitHub URL was given)
Single repo:
LOCAL_PATH=$(graphify clone <github-url> [--branch <branch>])
# Use LOCAL_PATH as the target for all subsequent steps
Multiple repos (cross-repo graph):
# Clone each repo, run the full pipeline on each, then merge
graphify clone <url1> # → ~/.graphify/repos/<owner1>/<repo1>
graphify clone <url2> # → ~/.graphify/repos/<owner2>/<repo2>
# Run /graphify on each local path to produce their graph.json files
# Then merge:
graphify merge-graphs \
~/.graphify/repos/<owner1>/<repo1>/graphify-out/graph.json \
~/.graphify/repos/<owner2>/<repo2>/graphify-out/graph.json \
--out graphify-out/cross-repo-graph.json
Graphify clones into ~/.graphify/repos/<owner>/<repo> and reuses existing clones on repeat runs. Each node in the merged graph carries a repo attribute so you can filter by origin.
Multiple local subfolders (monorepo or multi-service layout):
The skill pipeline writes all intermediate and final outputs to graphify-out/ in the current working directory. Running the skill on each subfolder separately will clobber the same output dir. Instead, use the CLI directly for each subfolder — it places graphify-out/ inside the scanned path:
graphify extract ./core/ # → ./core/graphify-out/graph.json
graphify extract ./service/ # → ./service/graphify-out/graph.json
graphify extract ./platform/ # → ./platform/graphify-out/graph.json
# Add --backend gemini|kimi|openai|deepseek|claude-cli depending on which API key you have set
# Then merge at the project root:
graphify merge-graphs \
./core/graphify-out/graph.json \
./service/graphify-out/graph.json \
./platform/graphify-out/graph.json \
--out graphify-out/graph.json
Once graphify-out/graph.json exists, the fast path above takes over: any codebase question runs graphify query directly on the merged graph — no re-extraction, no size gate.