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revert: undo unrelated generated skill changes #9

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Merged
andrebrait merged 1 commit into from
Sep 10, 2026
Merged

revert: undo unrelated generated skill changes #9

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71 changes: 36 additions & 35 deletions graphify/skill-agents.md
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Original file line number Diff line number Diff line change
Expand Up @@ -97,7 +97,7 @@ fi
mkdir -p graphify-out
"$PYTHON" -c "import sys; open('graphify-out/.graphify_python', 'w', encoding='utf-8').write(sys.executable)"
# Save scan root so `graphify update` (no args) knows where to look next time
echo "$(cd "INPUT_PATH" && pwd)" > graphify-out/.graphify_root
echo "$(cd INPUT_PATH && pwd)" > graphify-out/.graphify_root
```

If the import succeeds, print nothing and move straight to Step 2.
Expand All @@ -108,15 +108,15 @@ If the import succeeds, print nothing and move straight to Step 2.

```bash
$(cat graphify-out/.graphify_python) -c "
import sys, json
import json
from graphify.detect import detect
from pathlib import Path
result = detect(Path(sys.argv[1]))
result = detect(Path('INPUT_PATH'))
# Write the sidecar from Python, not a shell redirect, so the same block renders
# on PowerShell hosts without console-encoding drift (#2528).
Path('graphify-out/.graphify_detect.json').write_text(json.dumps(result, ensure_ascii=False), encoding=\"utf-8\")
print(f'Detected {result[\"total_files\"]} files')
" "INPUT_PATH"
"
```

Replace INPUT_PATH with the actual path the user provided. Do NOT cat or print the JSON - read it silently and present a clean summary instead:
Expand Down Expand Up @@ -176,20 +176,21 @@ $(cat graphify-out/.graphify_python) -c "
import sys, json
from graphify.extract import collect_files, extract
from pathlib import Path
import json

code_files = []
detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encoding=\"utf-8\"))
for f in detect.get('files', {}).get('code', []):
code_files.extend(collect_files(Path(f)) if Path(f).is_dir() else [Path(f)])

if code_files:
result = extract(code_files, cache_root=Path(sys.argv[1]))
result = extract(code_files, cache_root=Path('INPUT_PATH'))
Path('graphify-out/.graphify_ast.json').write_text(json.dumps(result, indent=2, ensure_ascii=False), encoding=\"utf-8\")
print(f'AST: {len(result[\"nodes\"])} nodes, {len(result[\"edges\"])} edges')
else:
Path('graphify-out/.graphify_ast.json').write_text(json.dumps({'nodes':[],'edges':[],'input_tokens':0,'output_tokens':0}, ensure_ascii=False), encoding=\"utf-8\")
print('No code files - skipping AST extraction')
" "INPUT_PATH"
"
```

#### Part B - Semantic extraction (parallel subagents)
Expand All @@ -204,7 +205,7 @@ Path('graphify-out/.graphify_semantic.json').write_text(json.dumps({'nodes':[],'
"
```

**MANDATORY: You MUST use the subagent tool here. Reading files yourself one-by-one is forbidden - it is 5-10x slower. If you do not use the subagent tool you are doing this wrong.**
**MANDATORY: You MUST use the Agent tool here. Reading files yourself one-by-one is forbidden - it is 5-10x slower. If you do not use the Agent tool you are doing this wrong.**

Before dispatching subagents, print a timing estimate:
- Load `total_words` and file counts from `graphify-out/.graphify_detect.json`
Expand All @@ -220,7 +221,7 @@ SPEC_PATH below is the **absolute** path of the `references/extraction-spec.md`

```bash
$(cat graphify-out/.graphify_python) -c "
import sys, json
import json
from graphify.cache import check_semantic_cache
from pathlib import Path

Expand All @@ -230,7 +231,7 @@ detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encodin
# every source file (#1392). Video is transcribed to a document in Step 2.5 first.
all_files = [f for cat in ('document', 'paper', 'image') for f in detect['files'].get(cat, [])]

cached_nodes, cached_edges, cached_hyperedges, uncached = check_semantic_cache(all_files, root=sys.argv[1], prompt_file=sys.argv[2])
cached_nodes, cached_edges, cached_hyperedges, uncached = check_semantic_cache(all_files, root='INPUT_PATH', prompt_file='SPEC_PATH')

# Always (re)write the cache file: write hits, else DELETE any leftover from a prior
# run so Part C never merges a stale .graphify_cached.json (#1392).
Expand All @@ -240,7 +241,7 @@ else:
Path('graphify-out/.graphify_cached.json').unlink(missing_ok=True)
Path('graphify-out/.graphify_uncached.txt').write_text('\n'.join(uncached), encoding=\"utf-8\")
print(f'Cache: {len(all_files)-len(uncached)} files hit, {len(uncached)} files need extraction')
" "INPUT_PATH" "SPEC_PATH"
"
```

Only dispatch subagents for files listed in `graphify-out/.graphify_uncached.txt`. If all files are cached, skip to Part C directly.
Expand Down Expand Up @@ -282,7 +283,7 @@ Wait for all subagents. For each result:

If more than half the chunks failed or are missing, stop and tell the user to re-run and ensure `subagent_type="general-purpose"` is used.

Merge all chunk files into `.graphify_semantic_new.json`. **After each subagent call completes, read the real token counts from the subagent tool result's `usage` field and write them back into the chunk JSON before merging** — the chunk JSON itself always has placeholder zeros. Then run:
Merge all chunk files into `.graphify_semantic_new.json`. **After each Agent call completes, read the real token counts from the Agent tool result's `usage` field and write them back into the chunk JSON before merging** — the chunk JSON itself always has placeholder zeros. Then run:
```bash
$(cat graphify-out/.graphify_python) -c "
import json, glob
Expand All @@ -309,15 +310,15 @@ print(f'Merged {len(chunks)} chunks: {total_in:,} in / {total_out:,} out tokens'
Save new results to cache. Pass the same SPEC_PATH as Step B0 — it stamps each entry with the prompt that produced it, and a write under a different prompt than the read lands where the next run won't look (#1939):
```bash
$(cat graphify-out/.graphify_python) -c "
import sys, json
import json
from graphify.cache import save_semantic_cache
from pathlib import Path

new = json.loads(Path('graphify-out/.graphify_semantic_new.json').read_text(encoding=\"utf-8\")) if Path('graphify-out/.graphify_semantic_new.json').exists() else {'nodes':[],'edges':[],'hyperedges':[]}
uncached = [line for line in Path('graphify-out/.graphify_uncached.txt').read_text(encoding=\"utf-8\").splitlines() if line]
saved = save_semantic_cache(new.get('nodes', []), new.get('edges', []), new.get('hyperedges', []), root=sys.argv[1], allowed_source_files=uncached, prompt_file=sys.argv[2])
saved = save_semantic_cache(new.get('nodes', []), new.get('edges', []), new.get('hyperedges', []), root='INPUT_PATH', allowed_source_files=uncached, prompt_file='SPEC_PATH')
print(f'Cached {saved} files')
" "INPUT_PATH" "SPEC_PATH"
"
```

Merge cached + new results into `graphify-out/.graphify_semantic.json`:
Expand Down Expand Up @@ -406,7 +407,7 @@ detection = json.loads(Path('graphify-out/.graphify_detect.json').read_text(enc

# root= mirrors the --update runbook (#1361): relativize source_file to the same
# base so the full build and incremental --update never drift apart on re-extract.
G = build_from_json(extraction, root=sys.argv[1], directed=IS_DIRECTED)
G = build_from_json(extraction, root='INPUT_PATH', directed=IS_DIRECTED)
# Guard BEFORE any write: an empty extraction must not clobber a good graph.json /
# GRAPH_REPORT.md / analysis sidecar. Check immediately after build (#1392).
if G.number_of_nodes() == 0:
Expand All @@ -431,7 +432,7 @@ if not wrote:
print('ERROR: refused to shrink graphify-out/graph.json (existing graph has more nodes; #479).')
print('If this shrink is intentional (you deleted files), re-run a full build with --force.')
raise SystemExit(1)
report = generate(G, communities, cohesion, labels, gods, surprises, detection, tokens, sys.argv[1], suggested_questions=questions)
report = generate(G, communities, cohesion, labels, gods, surprises, detection, tokens, 'INPUT_PATH', suggested_questions=questions)
Path('graphify-out/GRAPH_REPORT.md').write_text(report, encoding=\"utf-8\")
analysis = {
'communities': {str(k): v for k, v in communities.items()},
Expand All @@ -442,7 +443,7 @@ analysis = {
}
Path('graphify-out/.graphify_analysis.json').write_text(json.dumps(analysis, indent=2, ensure_ascii=False), encoding=\"utf-8\")
print(f'Graph: {G.number_of_nodes()} nodes, {G.number_of_edges()} edges, {len(communities)} communities')
" "INPUT_PATH"
"
```

If this step prints `ERROR: Graph is empty`, stop and tell the user what happened - do not proceed to labeling or visualization.
Expand All @@ -455,12 +456,12 @@ A non-destructive diagnostic on the extraction, before labeling. It surfaces edg

```bash
$(cat graphify-out/.graphify_python) -c "
import sys, json
import json
from pathlib import Path
from graphify.diagnostics import diagnose_extraction, format_diagnostic_report

extraction = json.loads(Path('graphify-out/.graphify_extract.json').read_text(encoding=\"utf-8\"))
summary = diagnose_extraction(extraction, directed=IS_DIRECTED, root=sys.argv[1])
summary = diagnose_extraction(extraction, directed=IS_DIRECTED, root='INPUT_PATH')
print(format_diagnostic_report(summary))
flags = [f'{summary[k]} {label}' for k, label in (
('dangling_endpoint_edges', 'dangling-endpoint edges'),
Expand All @@ -470,7 +471,7 @@ flags = [f'{summary[k]} {label}' for k, label in (
('undirected_same_endpoint_collapsed_edges', 'collapsed (undirected) edges'),
) if summary.get(k, 0)]
print('GRAPH HEALTH WARNING: ' + '; '.join(flags) + ' - graph may be incomplete/corrupt.' if flags else 'Graph health: OK (no dangling/missing/collapsed edges).')
" "INPUT_PATH"
"
```

Substitute `IS_DIRECTED` and `INPUT_PATH` as in Step 4. If a `GRAPH HEALTH WARNING` prints, surface it in the final summary (do not abort — the graph is still usable, but the integrity issue must be visible, per the Honesty Rules).
Expand All @@ -496,7 +497,7 @@ detection = json.loads(Path('graphify-out/.graphify_detect.json').read_text(enc
analysis = json.loads(Path('graphify-out/.graphify_analysis.json').read_text(encoding=\"utf-8\"))

# root= as in Step 4 / the --update runbook (#1361) — same base for node-key parity.
G = build_from_json(extraction, root=sys.argv[1], directed=IS_DIRECTED)
G = build_from_json(extraction, root='INPUT_PATH', directed=IS_DIRECTED)
communities = {int(k): v for k, v in analysis['communities'].items()}
cohesion = {int(k): v for k, v in analysis['cohesion'].items()}
tokens = {'input': extraction.get('input_tokens', 0), 'output': extraction.get('output_tokens', 0)}
Expand All @@ -507,19 +508,18 @@ labels = LABELS_DICT
# Regenerate questions with real community labels (labels affect question phrasing)
questions = suggest_questions(G, communities, labels)

report = generate(G, communities, cohesion, labels, analysis['gods'], analysis['surprises'], detection, tokens, sys.argv[1], suggested_questions=questions)
report = generate(G, communities, cohesion, labels, analysis['gods'], analysis['surprises'], detection, tokens, 'INPUT_PATH', suggested_questions=questions)
Path('graphify-out/GRAPH_REPORT.md').write_text(report, encoding=\"utf-8\")
Path('graphify-out/.graphify_labels.json').write_text(json.dumps({str(k): v for k, v in labels.items()}, ensure_ascii=False), encoding=\"utf-8\")
# Re-export so graph.json nodes carry the curated community_name (#2490).
# Same extraction as Step 4, so the #479 shrink-guard passes on node count;
# if it still refuses, surface the guard message - do not force past it.
wrote = to_json(G, communities, 'graphify-out/graph.json', community_labels=labels)
if not wrote:
print('ERROR: refused to shrink graphify-out/graph.json (existing graph has more nodes; #479).')
print('If this shrink is intentional (you deleted files), re-run a full build with --force.')
raise SystemExit(1)
Path('graphify-out/GRAPH_REPORT.md').write_text(report, encoding=\"utf-8\")
Path('graphify-out/.graphify_labels.json').write_text(json.dumps({str(k): v for k, v in labels.items()}, ensure_ascii=False), encoding=\"utf-8\")
print('Report updated with community labels')
" "INPUT_PATH"
"
```

Replace `LABELS_DICT` with the actual dict you constructed (e.g. `{0: "Attention Mechanism", 1: "Training Pipeline"}`).
Expand All @@ -534,14 +534,15 @@ If `--obsidian` was given:
- If `--obsidian-dir <path>` was also given, pass it via `--dir`. Otherwise defaults to `graphify-out/obsidian`.

```bash
$(cat graphify-out/.graphify_python) -m graphify export obsidian
# Add `--dir ~/vaults/my-project` to use a custom directory.
graphify export obsidian
# or with custom dir: graphify export obsidian --dir ~/vaults/my-project
```

Generate the HTML graph (always, unless `--no-viz`):

```bash
$(cat graphify-out/.graphify_python) -m graphify export html # auto-aggregates to community view if graph > 5000 nodes
graphify export html # auto-aggregates to community view if graph > 5000 nodes
# or: graphify export html --no-viz
```

### Steps 6b-8 - Wiki, Neo4j, FalkorDB, SVG, GraphML, MCP, benchmark (only on their flags)
Expand All @@ -554,7 +555,7 @@ These run only when their flag is present (`--wiki`, `--neo4j`/`--neo4j-push`, `

```bash
$(cat graphify-out/.graphify_python) -c "
import sys, json
import json
from pathlib import Path
from datetime import datetime, timezone
from graphify.detect import save_manifest
Expand All @@ -577,7 +578,7 @@ extract = json.loads(Path('graphify-out/.graphify_extract.json').read_text(encod
# types are gated on output.
from graphify.cli import _stamped_manifest_files
_corpus = detect.get('all_files') or detect['files']
_manifest_files = _stamped_manifest_files(_corpus, extract, Path(sys.argv[1]))
_manifest_files = _stamped_manifest_files(_corpus, extract, Path('INPUT_PATH'))
# Files dispatched this run (the changed subset) but NOT stamped above still carry
# a stale semantic_hash from a prior run; clear it so detect_incremental re-queues
# them instead of reading them as unchanged (#1948).
Expand All @@ -589,7 +590,7 @@ _cleared = _dispatched - _stamped
# files newly excluded since last run are dropped rather than masquerading as
# deletions; untouched files' prior rows are still preserved (#1908).
_scan = {f for fl in _corpus.values() for f in fl}
save_manifest(_manifest_files, root=sys.argv[1], scan_corpus=_scan, clear_semantic=_cleared or None)
save_manifest(_manifest_files, root='INPUT_PATH', scan_corpus=_scan, clear_semantic=_cleared or None)

# Update cumulative cost tracker
input_tok = extract.get('input_tokens', 0)
Expand All @@ -613,10 +614,10 @@ cost_path.write_text(json.dumps(cost, indent=2, ensure_ascii=False), encoding=\"

print(f'This run: {input_tok:,} input tokens, {output_tok:,} output tokens')
print(f'All time: {cost[\"total_input_tokens\"]:,} input, {cost[\"total_output_tokens\"]:,} output ({len(cost[\"runs\"])} runs)')
" "INPUT_PATH"
"
rm -f graphify-out/.graphify_detect.json graphify-out/.graphify_extract.json graphify-out/.graphify_ast.json graphify-out/.graphify_semantic.json graphify-out/.graphify_analysis.json
find graphify-out -maxdepth 1 -name '.graphify_chunk_*.json' -delete 2>/dev/null
rm -f graphify-out/needs_update 2>/dev/null || true
rm -f graphify-out/.needs_update 2>/dev/null || true
```

Replace INPUT_PATH with the actual path (same value used in Steps 4-5) so the manifest is relativized to the scan root.
Expand Down Expand Up @@ -681,7 +682,7 @@ Both are non-default subcommands. `--update` re-extracts only new or changed fil
When `graphify-out/graph.json` already exists and the user asks a question about the corpus, answer from the graph rather than rebuilding it:

```bash
$(cat graphify-out/.graphify_python) -m graphify query "<question>"
graphify query "<question>"
```

Before traversal, expand the question against the graph's own vocabulary so a wording mismatch does not collapse the answer to noise. If the `graphify query` CLI is unavailable, fall back to an inline NetworkX traversal of `graphify-out/graph.json`. Answer using only what the graph output contains, and quote `source_location` when citing a specific fact. For that vocab-expansion step, the BFS/DFS traversal modes, the `--budget` cap, the NetworkX fallback, `save-result` feedback, and the `/graphify path` and `/graphify explain` flows, see `references/query.md`.
Expand Down
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