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
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# graphify reference: incremental update and cluster-only
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Load this only when the user passed `--update` or `--cluster-only`. A first-time full build never reads this file.
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## For --update (incremental re-extraction)
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Use when you've added or modified files since the last run. Only re-extracts changed files - saves tokens and time.
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```bash
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$(cat graphify-out/.graphify_python) -c "
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import sys, json
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from graphify.detect import detect_incremental, save_manifest
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from pathlib import Path
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result = detect_incremental(Path('INPUT_PATH'))
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new_total = result.get('new_total', 0)
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print(json.dumps(result, indent=2, ensure_ascii=False))
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Path('graphify-out/.graphify_incremental.json').write_text(json.dumps(result, ensure_ascii=False), encoding=\"utf-8\")
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deleted = list(result.get('deleted_files', []))
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if new_total == 0 and not deleted:
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print('No files changed since last run. Nothing to update.')
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raise SystemExit(0)
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if deleted:
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print(f'{len(deleted)} deleted file(s) to prune.')
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if new_total > 0:
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print(f'{new_total} new/changed file(s) to re-extract.')
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"
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```
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Then populate `.graphify_detect.json` so Steps 3A–6 (which read it unconditionally) see the right state for an incremental run. `files` carries the changed subset (drives Step 3A AST + Step 3B0 cache check on only what changed); `all_files` carries the full corpus for any step that needs corpus-wide context:
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```bash
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$(cat graphify-out/.graphify_python) -c "
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import json
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from pathlib import Path
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r = json.loads(Path('graphify-out/.graphify_incremental.json').read_text(encoding=\"utf-8\"))
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Path('graphify-out/.graphify_detect.json').write_text(json.dumps({
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'files': r.get('new_files', {}),
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'all_files': r.get('files', {}),
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'total_files': r.get('new_total', 0),
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'total_words': r.get('total_words', 0),
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'skipped_sensitive': r.get('skipped_sensitive', []),
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'needs_graph': True,
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}, ensure_ascii=False), encoding=\"utf-8\")
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"
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```
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If new files exist, first check whether all changed files are code files:
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```bash
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$(cat graphify-out/.graphify_python) -c "
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import json
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from pathlib import Path
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result = json.loads(open('graphify-out/.graphify_incremental.json', encoding='utf-8').read()) if Path('graphify-out/.graphify_incremental.json').exists() else {}
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code_exts = {'.py','.ts','.js','.go','.rs','.java','.cpp','.c','.rb','.swift','.kt','.cs','.scala','.php','.cc','.cxx','.hpp','.h','.kts','.lua','.toc','.f','.F','.f90','.F90','.f95','.F95','.f03','.F03','.f08','.F08'}
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new_files = result.get('new_files', {})
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all_changed = [f for files in new_files.values() for f in files]
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code_only = all(Path(f).suffix.lower() in code_exts for f in all_changed)
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print('code_only:', code_only)
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"
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```
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If `code_only` is True: print `[graphify update] Code-only changes detected - skipping semantic extraction (no LLM needed)`, run only Step 3A (AST) on the changed files, skip Step 3B entirely (no subagents), then go straight to merge and Steps 4–8.
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If `code_only` is False (any changed file is a doc/paper/image): run the full Steps 3A–3C pipeline as normal.
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If no new files exist (only deletions), create an empty extraction so the merge step can prune:
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```bash
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if [ ! -f graphify-out/.graphify_extract.json ]; then
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echo '[graphify update] Only deletions -- creating empty extraction for merge.'
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$(cat graphify-out/.graphify_python) -c "
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import json
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from pathlib import Path
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Path('graphify-out/.graphify_extract.json').write_text(json.dumps({'nodes':[],'edges':[],'hyperedges':[],'input_tokens':0,'output_tokens':0}), encoding='utf-8')
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"
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fi
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```
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Then:
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```bash
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$(cat graphify-out/.graphify_python) -c "
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import json
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from pathlib import Path
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from graphify.build import build_merge
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from graphify.detect import save_manifest
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# Load new extraction and incremental state
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new_extraction = json.loads(Path('graphify-out/.graphify_extract.json').read_text(encoding=\"utf-8\"))
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incremental = json.loads(Path('graphify-out/.graphify_incremental.json').read_text(encoding=\"utf-8\"))
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deleted = list(incremental.get('deleted_files', []))
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# Also prune old nodes for re-extracted (changed) files before inserting fresh AST.
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# Without this, build_merge's dedup pass tries to reconcile old and new versions of
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# the same file's nodes and can collapse same-named symbols across files (#1178).
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changed = [f for files in incremental.get('new_files', {}).values() for f in files]
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prune = list(dict.fromkeys(deleted + changed)) or None
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# Use build_merge() — reads graph.json directly without NetworkX round-trip
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# so edge direction (calls, implements, imports) is always preserved (#801).
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G = build_merge(
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[new_extraction],
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graph_path='graphify-out/graph.json',
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prune_sources=prune,
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)
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print(f'[graphify update] Merged: {G.number_of_nodes()} nodes, {G.number_of_edges()} edges')
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# Write merged result back to .graphify_extract.json so Step 4 sees the full graph
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merged_out = {
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'nodes': [{'id': n, **d} for n, d in G.nodes(data=True)],
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'edges': [
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# Explicit source/target last so they win over any stale attrs in d.
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{**{k: val for k, val in d.items() if k not in ('_src', '_tgt', 'source', 'target')},
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'source': d.get('_src', u), 'target': d.get('_tgt', v)}
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for u, v, d in G.edges(data=True)
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],
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# G.graph["hyperedges"] holds hyperedges from both existing graph.json
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# and new_extraction (build_merge combines them). Falling back to
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# new_extraction only would silently drop prior-run hyperedges (#801).
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'hyperedges': list(G.graph.get('hyperedges', [])),
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'input_tokens': new_extraction.get('input_tokens', 0),
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'output_tokens': new_extraction.get('output_tokens', 0),
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}
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Path('graphify-out/.graphify_extract.json').write_text(json.dumps(merged_out, ensure_ascii=False), encoding=\"utf-8\")
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print(f'[graphify update] Merged extraction written ({len(merged_out[\"nodes\"])} nodes, {len(merged_out[\"edges\"])} edges)')
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# Save manifest so next --update diffs against today's state, not the
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# prior run's baseline (prevents ghost-node reports on subsequent updates).
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save_manifest(incremental['files'])
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print('[graphify update] Manifest saved.')
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"
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```
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Then run Steps 4–8 on the merged graph as normal.
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After Step 4, show the graph diff:
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```bash
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$(cat graphify-out/.graphify_python) -c "
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import json
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from graphify.analyze import graph_diff
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from graphify.build import build_from_json
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from networkx.readwrite import json_graph
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import networkx as nx
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from pathlib import Path
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# Load old graph (before update) from backup written before merge
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old_data = json.loads(Path('graphify-out/.graphify_old.json').read_text(encoding=\"utf-8\")) if Path('graphify-out/.graphify_old.json').exists() else None
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new_extract = json.loads(Path('graphify-out/.graphify_extract.json').read_text(encoding=\"utf-8\"))
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G_new = build_from_json(new_extract)
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if old_data:
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G_old = json_graph.node_link_graph(old_data, edges='links')
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diff = graph_diff(G_old, G_new)
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print(diff['summary'])
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if diff['new_nodes']:
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print('New nodes:', ', '.join(n['label'] for n in diff['new_nodes'][:5]))
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if diff['new_edges']:
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print('New edges:', len(diff['new_edges']))
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"
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```
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Before the merge step, save the old graph: `cp graphify-out/graph.json graphify-out/.graphify_old.json`
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Clean up after: `rm -f graphify-out/.graphify_old.json`
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---
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## For --cluster-only
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Skip Steps 1–3. Re-run clustering on the existing graph:
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```bash
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graphify cluster-only .
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```
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Then run Steps 5–9 as normal (label communities, generate viz, benchmark, clean up, report).
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