graphify/tools/skillgen/expected/graphify__skills__opencode__references__update.md

graphify reference: incremental update and cluster-only

Load this only when the user passed --update or --cluster-only. A first-time full build never reads this file.

For --update (incremental re-extraction)

Use when you've added or modified files since the last run. Only re-extracts changed files - saves tokens and time.

$(cat graphify-out/.graphify_python) -c "
import sys, json
from graphify.detect import detect_incremental, save_manifest
from pathlib import Path

result = detect_incremental(Path('INPUT_PATH'))
new_total = result.get('new_total', 0)
print(json.dumps(result, indent=2, ensure_ascii=False))
Path('graphify-out/.graphify_incremental.json').write_text(json.dumps(result, ensure_ascii=False), encoding=\"utf-8\")
deleted = list(result.get('deleted_files', []))
if new_total == 0 and not deleted:
    print('No files changed since last run. Nothing to update.')
    raise SystemExit(0)
if deleted:
    print(f'{len(deleted)} deleted file(s) to prune.')
if new_total > 0:
    print(f'{new_total} new/changed file(s) to re-extract.')
"

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:

$(cat graphify-out/.graphify_python) -c "
import json
from pathlib import Path
r = json.loads(Path('graphify-out/.graphify_incremental.json').read_text(encoding=\"utf-8\"))
Path('graphify-out/.graphify_detect.json').write_text(json.dumps({
    'files': r.get('new_files', {}),
    'all_files': r.get('files', {}),
    'total_files': r.get('new_total', 0),
    'total_words': r.get('total_words', 0),
    'skipped_sensitive': r.get('skipped_sensitive', []),
    'needs_graph': True,
}, ensure_ascii=False), encoding=\"utf-8\")
"

If new files exist, first check whether all changed files are code files:

$(cat graphify-out/.graphify_python) -c "
import json
from pathlib import Path

result = json.loads(open('graphify-out/.graphify_incremental.json', encoding='utf-8').read()) if Path('graphify-out/.graphify_incremental.json').exists() else {}
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'}
new_files = result.get('new_files', {})
all_changed = [f for files in new_files.values() for f in files]
code_only = all(Path(f).suffix.lower() in code_exts for f in all_changed)
print('code_only:', code_only)
"

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.

If code_only is False (any changed file is a doc/paper/image): run the full Steps 3A–3C pipeline as normal.

If no new files exist (only deletions), create an empty extraction so the merge step can prune:

if [ ! -f graphify-out/.graphify_extract.json ]; then
    echo '[graphify update] Only deletions -- creating empty extraction for merge.'
    $(cat graphify-out/.graphify_python) -c "
import json
from pathlib import Path
Path('graphify-out/.graphify_extract.json').write_text(json.dumps({'nodes':[],'edges':[],'hyperedges':[],'input_tokens':0,'output_tokens':0}), encoding='utf-8')
"
fi

Then:

$(cat graphify-out/.graphify_python) -c "
import json
from pathlib import Path
from graphify.build import build_merge
from graphify.detect import save_manifest

# Load new extraction and incremental state
new_extraction = json.loads(Path('graphify-out/.graphify_extract.json').read_text(encoding=\"utf-8\"))
incremental = json.loads(Path('graphify-out/.graphify_incremental.json').read_text(encoding=\"utf-8\"))
deleted = list(incremental.get('deleted_files', []))
# Also prune old nodes for re-extracted (changed) files before inserting fresh AST.
# Without this, build_merge's dedup pass tries to reconcile old and new versions of
# the same file's nodes and can collapse same-named symbols across files (#1178).
changed = [f for files in incremental.get('new_files', {}).values() for f in files]
prune = list(dict.fromkeys(deleted + changed)) or None

# Use build_merge() — reads graph.json directly without NetworkX round-trip
# so edge direction (calls, implements, imports) is always preserved (#801).
G = build_merge(
    [new_extraction],
    graph_path='graphify-out/graph.json',
    prune_sources=prune,
)
print(f'[graphify update] Merged: {G.number_of_nodes()} nodes, {G.number_of_edges()} edges')

# Write merged result back to .graphify_extract.json so Step 4 sees the full graph
merged_out = {
    'nodes': [{'id': n, **d} for n, d in G.nodes(data=True)],
    'edges': [
        # Explicit source/target last so they win over any stale attrs in d.
        {**{k: val for k, val in d.items() if k not in ('_src', '_tgt', 'source', 'target')},
         'source': d.get('_src', u), 'target': d.get('_tgt', v)}
        for u, v, d in G.edges(data=True)
    ],
    # G.graph["hyperedges"] holds hyperedges from both existing graph.json
    # and new_extraction (build_merge combines them). Falling back to
    # new_extraction only would silently drop prior-run hyperedges (#801).
    'hyperedges': list(G.graph.get('hyperedges', [])),
    'input_tokens': new_extraction.get('input_tokens', 0),
    'output_tokens': new_extraction.get('output_tokens', 0),
}
Path('graphify-out/.graphify_extract.json').write_text(json.dumps(merged_out, ensure_ascii=False), encoding=\"utf-8\")
print(f'[graphify update] Merged extraction written ({len(merged_out[\"nodes\"])} nodes, {len(merged_out[\"edges\"])} edges)')

# Save manifest so next --update diffs against today's state, not the
# prior run's baseline (prevents ghost-node reports on subsequent updates).
save_manifest(incremental['files'])
print('[graphify update] Manifest saved.')
"

Then run Steps 4–8 on the merged graph as normal.

After Step 4, show the graph diff:

$(cat graphify-out/.graphify_python) -c "
import json
from graphify.analyze import graph_diff
from graphify.build import build_from_json
from networkx.readwrite import json_graph
import networkx as nx
from pathlib import Path

# Load old graph (before update) from backup written before merge
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
new_extract = json.loads(Path('graphify-out/.graphify_extract.json').read_text(encoding=\"utf-8\"))
G_new = build_from_json(new_extract)

if old_data:
    G_old = json_graph.node_link_graph(old_data, edges='links')
    diff = graph_diff(G_old, G_new)
    print(diff['summary'])
    if diff['new_nodes']:
        print('New nodes:', ', '.join(n['label'] for n in diff['new_nodes'][:5]))
    if diff['new_edges']:
        print('New edges:', len(diff['new_edges']))
"

Before the merge step, save the old graph: cp graphify-out/graph.json graphify-out/.graphify_old.json Clean up after: rm -f graphify-out/.graphify_old.json

---

For --cluster-only

Skip Steps 1–3. Re-run clustering on the existing graph:

graphify cluster-only .

Then run Steps 5–9 as normal (label communities, generate viz, benchmark, clean up, report).