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iomgaa 6bdb802f01 chore: track claude skills, tools, templates, reference code and research-wiki

- 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

2026-07-06 20:59:03 -04:00

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graphify reference: extra exports and benchmark

Load this when the user passed one of the export flags (--wiki, --neo4j, --neo4j-push, --svg, --graphml, --mcp), or when the corpus is large enough for the token-reduction benchmark. Each step runs only for its own flag.

Step 6b - Wiki (only if --wiki flag)

Only run this step if --wiki was explicitly given in the original command.

Run this before Step 9 (cleanup) so .graphify_labels.json is still available.

graphify export wiki

Step 7 - Neo4j export (only if --neo4j or --neo4j-push flag)

If --neo4j - generate a Cypher file for manual import:

graphify export neo4j

If --neo4j-push <uri> - push directly to a running Neo4j instance. Ask the user for credentials if not provided:

graphify export neo4j --push bolt://localhost:7687 --user neo4j --password PASSWORD

Default URI is bolt://localhost:7687, default user is neo4j. Uses MERGE - safe to re-run without creating duplicates.

Step 7b - SVG export (only if --svg flag)

graphify export svg

Step 7c - GraphML export (only if --graphml flag)

graphify export graphml

Step 7d - MCP server (only if --mcp flag)

python3 -m graphify.serve graphify-out/graph.json

This starts a stdio MCP server that exposes tools: query_graph, get_node, get_neighbors, get_community, god_nodes, graph_stats, shortest_path. Add to Claude Desktop or any MCP-compatible agent orchestrator so other agents can query the graph live.

To configure in Claude Desktop, add to claude_desktop_config.json:

{
  "mcpServers": {
    "graphify": {
      "command": "python3",
      "args": ["-m", "graphify.serve", "/absolute/path/to/graphify-out/graph.json"]
    }
  }
}

Step 8 - Token reduction benchmark (only if total_words > 5000)

If total_words from graphify-out/.graphify_detect.json is greater than 5,000, run:

graphify benchmark

Print the output directly in chat. If total_words <= 5000, skip silently - the graph value is structural clarity, not token compression, for small corpora.

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