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Fix crash/data-loss bugs in the generated skill runbooks (#1392)

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Five fixes in the skillgen fragments (re-rendered): chunk paths now derive from
cwd to match where Part C globs (a non-cwd scan produced "no nodes"); the
code-only fast path writes an empty .graphify_semantic.json so Part C doesn't
FileNotFoundError; --cluster-only relies on the self-contained CLI instead of
re-running Steps 5-9 against deleted intermediate files; and Step 4 runs the
zero-node guard before any write and only writes GRAPH_REPORT.md / analysis when
to_json actually persisted the graph (honoring the #479 shrink-guard).

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
This commit is contained in:
Safi
2026-06-19 15:19:07 +01:00
co-authored by Claude Opus 4.8
parent 7d07a24708
commit 30fe8bab61
60 changed files with 704 additions and 243 deletions
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CHANGELOG.md
+2
View File
@@ -4,6 +4,8 @@ Full release notes with details on each version: [GitHub Releases](https://githu
## Unreleased
- Fix: generated Claude/agent skill — crash & data-loss bugs in the runbooks (#1392). (1) Semantic chunk files were written under the **scanned dir** (`.graphify_root`) but the merge globs **cwd** `graphify-out/`, so a non-cwd scan produced "no nodes"; chunk paths are now derived from cwd. (2) Code-only corpora skipped Part B but Part C reads `.graphify_semantic.json` unconditionally → `FileNotFoundError`; the fast path now writes an empty semantic file first. (3) `--cluster-only` told the agent to re-run Steps 5–9, which read intermediate files a prior cleanup deleted → `FileNotFoundError`; it now relies on the self-contained `graphify cluster-only` CLI. (4) Step 4's zero-node guard ran *after* `GRAPH_REPORT.md`/`graph.json`/analysis were written, and `GRAPH_REPORT.md` was written before `to_json`'s #479 shrink-guard; the guard now runs before any write and the report/analysis are written only when `to_json` actually persisted the graph.
## 0.8.43 (2026-06-19)
- Feat: package manifests are now parsed deterministically into a dependency graph. `apm.yml`, `pyproject.toml`, `go.mod`, and `pom.xml` each yield ONE canonical package node per package (keyed by name) plus `depends_on` edges, routed to the AST path so the LLM never sees them. Previously `apm.yml` was an LLM-handled document, so the same package got a different file-anchored id from its own manifest than from each dependent's dependency reference and split into duplicate nodes; a package referenced from N manifests is now a single hub node (#1377).
graphify/skill-amp.md
+25 -8
View File
@@ -190,7 +190,15 @@ else:
#### Part B - Semantic extraction (parallel subagents)
**Fast path:** If detection found zero docs, papers, and images (code-only corpus), skip Part B entirely and go straight to Part C. AST handles code - there is nothing for semantic subagents to do.
**Fast path:** If detection found zero docs, papers, and images (code-only corpus), skip Part B entirely and go straight to Part C. AST handles code - there is nothing for semantic subagents to do. **First write an empty semantic file** so Part C's merge has its input (it reads `.graphify_semantic.json` unconditionally; without this a code-only run hits `FileNotFoundError`):
```bash
$(cat graphify-out/.graphify_python) -c "
import json
from pathlib import Path
Path('graphify-out/.graphify_semantic.json').write_text(json.dumps({'nodes':[],'edges':[],'hyperedges':[],'input_tokens':0,'output_tokens':0}), encoding='utf-8')
"
```
**MANDATORY: You MUST use the Agent tool here. Reading files yourself one-by-one is forbidden - it is 5-10x slower. If you do not use the Agent tool you are doing this wrong.**
@@ -243,7 +251,7 @@ Each subagent writes its result to its own `graphify-out/.graphify_chunk_NN.json
CHUNK_PATH must be an **absolute** path — derive it before dispatching:
```bash
PROJECT_ROOT=$(cat graphify-out/.graphify_root)
PROJECT_ROOT=$(pwd) # cwd — where Part C globs graphify-out/ (NOT .graphify_root/scan dir, #1392)
# Then for chunk N: CHUNK_PATH="${PROJECT_ROOT}/graphify-out/.graphify_chunk_0N.json"
```
@@ -385,6 +393,12 @@ 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='INPUT_PATH')
# 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:
print('ERROR: Graph is empty - extraction produced no nodes.')
print('Possible causes: all files were skipped, binary-only corpus, or extraction failed.')
raise SystemExit(1)
communities = cluster(G)
cohesion = score_all(G, communities)
tokens = {'input': extraction.get('input_tokens', 0), 'output': extraction.get('output_tokens', 0)}
@@ -394,10 +408,17 @@ labels = {cid: 'Community ' + str(cid) for cid in communities}
# Placeholder questions - regenerated with real labels in Step 5
questions = suggest_questions(G, communities, labels)
# Export FIRST and honor the #479 shrink-guard: to_json returns False (writing
# nothing) when the new graph is smaller than the existing graph.json. Only write
# GRAPH_REPORT.md + the analysis sidecar when the graph was actually written, so
# they never describe a graph that graph.json doesn't contain (#1392).
wrote = to_json(G, communities, 'graphify-out/graph.json')
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, '.', suggested_questions=questions)
Path('graphify-out/GRAPH_REPORT.md').write_text(report, encoding=\"utf-8\")
to_json(G, communities, 'graphify-out/graph.json')
analysis = {
'communities': {str(k): v for k, v in communities.items()},
'cohesion': {str(k): v for k, v in cohesion.items()},
@@ -406,10 +427,6 @@ analysis = {
'questions': questions,
}
Path('graphify-out/.graphify_analysis.json').write_text(json.dumps(analysis, indent=2, ensure_ascii=False), encoding=\"utf-8\")
if G.number_of_nodes() == 0:
print('ERROR: Graph is empty - extraction produced no nodes.')
print('Possible causes: all files were skipped, binary-only corpus, or extraction failed.')
raise SystemExit(1)
print(f'Graph: {G.number_of_nodes()} nodes, {G.number_of_edges()} edges, {len(communities)} communities')
"
```
graphify/skill-claw.md
+25 -8
View File
@@ -190,7 +190,15 @@ else:
#### Part B - Semantic extraction (parallel subagents)
**Fast path:** If detection found zero docs, papers, and images (code-only corpus), skip Part B entirely and go straight to Part C. AST handles code - there is nothing for semantic subagents to do.
**Fast path:** If detection found zero docs, papers, and images (code-only corpus), skip Part B entirely and go straight to Part C. AST handles code - there is nothing for semantic subagents to do. **First write an empty semantic file** so Part C's merge has its input (it reads `.graphify_semantic.json` unconditionally; without this a code-only run hits `FileNotFoundError`):
```bash
$(cat graphify-out/.graphify_python) -c "
import json
from pathlib import Path
Path('graphify-out/.graphify_semantic.json').write_text(json.dumps({'nodes':[],'edges':[],'hyperedges':[],'input_tokens':0,'output_tokens':0}), encoding='utf-8')
"
```
**MANDATORY: You MUST use the Agent tool here. Reading files yourself one-by-one is forbidden - it is 5-10x slower. If you do not use the Agent tool you are doing this wrong.**
@@ -246,7 +254,7 @@ Each subagent receives this exact prompt (substitute FILE_LIST, CHUNK_NUM, TOTAL
CHUNK_PATH must be an **absolute** path — derive it before dispatching:
```bash
PROJECT_ROOT=$(cat graphify-out/.graphify_root)
PROJECT_ROOT=$(pwd) # cwd — where Part C globs graphify-out/ (NOT .graphify_root/scan dir, #1392)
# Then for chunk N: CHUNK_PATH="${PROJECT_ROOT}/graphify-out/.graphify_chunk_0N.json"
```
@@ -388,6 +396,12 @@ 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='INPUT_PATH')
# 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:
print('ERROR: Graph is empty - extraction produced no nodes.')
print('Possible causes: all files were skipped, binary-only corpus, or extraction failed.')
raise SystemExit(1)
communities = cluster(G)
cohesion = score_all(G, communities)
tokens = {'input': extraction.get('input_tokens', 0), 'output': extraction.get('output_tokens', 0)}
@@ -397,10 +411,17 @@ labels = {cid: 'Community ' + str(cid) for cid in communities}
# Placeholder questions - regenerated with real labels in Step 5
questions = suggest_questions(G, communities, labels)
# Export FIRST and honor the #479 shrink-guard: to_json returns False (writing
# nothing) when the new graph is smaller than the existing graph.json. Only write
# GRAPH_REPORT.md + the analysis sidecar when the graph was actually written, so
# they never describe a graph that graph.json doesn't contain (#1392).
wrote = to_json(G, communities, 'graphify-out/graph.json')
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, '.', suggested_questions=questions)
Path('graphify-out/GRAPH_REPORT.md').write_text(report, encoding=\"utf-8\")
to_json(G, communities, 'graphify-out/graph.json')
analysis = {
'communities': {str(k): v for k, v in communities.items()},
'cohesion': {str(k): v for k, v in cohesion.items()},
@@ -409,10 +430,6 @@ analysis = {
'questions': questions,
}
Path('graphify-out/.graphify_analysis.json').write_text(json.dumps(analysis, indent=2, ensure_ascii=False), encoding=\"utf-8\")
if G.number_of_nodes() == 0:
print('ERROR: Graph is empty - extraction produced no nodes.')
print('Possible causes: all files were skipped, binary-only corpus, or extraction failed.')
raise SystemExit(1)
print(f'Graph: {G.number_of_nodes()} nodes, {G.number_of_edges()} edges, {len(communities)} communities')
"
```
graphify/skill-codex.md
+24 -7
View File
@@ -190,7 +190,15 @@ else:
#### Part B - Semantic extraction (parallel subagents)
**Fast path:** If detection found zero docs, papers, and images (code-only corpus), skip Part B entirely and go straight to Part C. AST handles code - there is nothing for semantic subagents to do.
**Fast path:** If detection found zero docs, papers, and images (code-only corpus), skip Part B entirely and go straight to Part C. AST handles code - there is nothing for semantic subagents to do. **First write an empty semantic file** so Part C's merge has its input (it reads `.graphify_semantic.json` unconditionally; without this a code-only run hits `FileNotFoundError`):
```bash
$(cat graphify-out/.graphify_python) -c "
import json
from pathlib import Path
Path('graphify-out/.graphify_semantic.json').write_text(json.dumps({'nodes':[],'edges':[],'hyperedges':[],'input_tokens':0,'output_tokens':0}), encoding='utf-8')
"
```
**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.**
@@ -385,6 +393,12 @@ 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='INPUT_PATH')
# 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:
print('ERROR: Graph is empty - extraction produced no nodes.')
print('Possible causes: all files were skipped, binary-only corpus, or extraction failed.')
raise SystemExit(1)
communities = cluster(G)
cohesion = score_all(G, communities)
tokens = {'input': extraction.get('input_tokens', 0), 'output': extraction.get('output_tokens', 0)}
@@ -394,10 +408,17 @@ labels = {cid: 'Community ' + str(cid) for cid in communities}
# Placeholder questions - regenerated with real labels in Step 5
questions = suggest_questions(G, communities, labels)
# Export FIRST and honor the #479 shrink-guard: to_json returns False (writing
# nothing) when the new graph is smaller than the existing graph.json. Only write
# GRAPH_REPORT.md + the analysis sidecar when the graph was actually written, so
# they never describe a graph that graph.json doesn't contain (#1392).
wrote = to_json(G, communities, 'graphify-out/graph.json')
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, '.', suggested_questions=questions)
Path('graphify-out/GRAPH_REPORT.md').write_text(report, encoding=\"utf-8\")
to_json(G, communities, 'graphify-out/graph.json')
analysis = {
'communities': {str(k): v for k, v in communities.items()},
'cohesion': {str(k): v for k, v in cohesion.items()},
@@ -406,10 +427,6 @@ analysis = {
'questions': questions,
}
Path('graphify-out/.graphify_analysis.json').write_text(json.dumps(analysis, indent=2, ensure_ascii=False), encoding=\"utf-8\")
if G.number_of_nodes() == 0:
print('ERROR: Graph is empty - extraction produced no nodes.')
print('Possible causes: all files were skipped, binary-only corpus, or extraction failed.')
raise SystemExit(1)
print(f'Graph: {G.number_of_nodes()} nodes, {G.number_of_edges()} edges, {len(communities)} communities')
"
```
graphify/skill-copilot.md
+25 -8
View File
@@ -190,7 +190,15 @@ else:
#### Part B - Semantic extraction (parallel subagents)
**Fast path:** If detection found zero docs, papers, and images (code-only corpus), skip Part B entirely and go straight to Part C. AST handles code - there is nothing for semantic subagents to do.
**Fast path:** If detection found zero docs, papers, and images (code-only corpus), skip Part B entirely and go straight to Part C. AST handles code - there is nothing for semantic subagents to do. **First write an empty semantic file** so Part C's merge has its input (it reads `.graphify_semantic.json` unconditionally; without this a code-only run hits `FileNotFoundError`):
```bash
$(cat graphify-out/.graphify_python) -c "
import json
from pathlib import Path
Path('graphify-out/.graphify_semantic.json').write_text(json.dumps({'nodes':[],'edges':[],'hyperedges':[],'input_tokens':0,'output_tokens':0}), encoding='utf-8')
"
```
**MANDATORY: You MUST use the Agent tool here. Reading files yourself one-by-one is forbidden - it is 5-10x slower. If you do not use the Agent tool you are doing this wrong.**
@@ -246,7 +254,7 @@ Each subagent receives this exact prompt (substitute FILE_LIST, CHUNK_NUM, TOTAL
CHUNK_PATH must be an **absolute** path — derive it before dispatching:
```bash
PROJECT_ROOT=$(cat graphify-out/.graphify_root)
PROJECT_ROOT=$(pwd) # cwd — where Part C globs graphify-out/ (NOT .graphify_root/scan dir, #1392)
# Then for chunk N: CHUNK_PATH="${PROJECT_ROOT}/graphify-out/.graphify_chunk_0N.json"
```
@@ -388,6 +396,12 @@ 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='INPUT_PATH')
# 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:
print('ERROR: Graph is empty - extraction produced no nodes.')
print('Possible causes: all files were skipped, binary-only corpus, or extraction failed.')
raise SystemExit(1)
communities = cluster(G)
cohesion = score_all(G, communities)
tokens = {'input': extraction.get('input_tokens', 0), 'output': extraction.get('output_tokens', 0)}
@@ -397,10 +411,17 @@ labels = {cid: 'Community ' + str(cid) for cid in communities}
# Placeholder questions - regenerated with real labels in Step 5
questions = suggest_questions(G, communities, labels)
# Export FIRST and honor the #479 shrink-guard: to_json returns False (writing
# nothing) when the new graph is smaller than the existing graph.json. Only write
# GRAPH_REPORT.md + the analysis sidecar when the graph was actually written, so
# they never describe a graph that graph.json doesn't contain (#1392).
wrote = to_json(G, communities, 'graphify-out/graph.json')
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, '.', suggested_questions=questions)
Path('graphify-out/GRAPH_REPORT.md').write_text(report, encoding=\"utf-8\")
to_json(G, communities, 'graphify-out/graph.json')
analysis = {
'communities': {str(k): v for k, v in communities.items()},
'cohesion': {str(k): v for k, v in cohesion.items()},
@@ -409,10 +430,6 @@ analysis = {
'questions': questions,
}
Path('graphify-out/.graphify_analysis.json').write_text(json.dumps(analysis, indent=2, ensure_ascii=False), encoding=\"utf-8\")
if G.number_of_nodes() == 0:
print('ERROR: Graph is empty - extraction produced no nodes.')
print('Possible causes: all files were skipped, binary-only corpus, or extraction failed.')
raise SystemExit(1)
print(f'Graph: {G.number_of_nodes()} nodes, {G.number_of_edges()} edges, {len(communities)} communities')
"
```
graphify/skill-droid.md
+25 -8
View File
@@ -190,7 +190,15 @@ else:
#### Part B - Semantic extraction (parallel subagents)
**Fast path:** If detection found zero docs, papers, and images (code-only corpus), skip Part B entirely and go straight to Part C. AST handles code - there is nothing for semantic subagents to do.
**Fast path:** If detection found zero docs, papers, and images (code-only corpus), skip Part B entirely and go straight to Part C. AST handles code - there is nothing for semantic subagents to do. **First write an empty semantic file** so Part C's merge has its input (it reads `.graphify_semantic.json` unconditionally; without this a code-only run hits `FileNotFoundError`):
```bash
$(cat graphify-out/.graphify_python) -c "
import json
from pathlib import Path
Path('graphify-out/.graphify_semantic.json').write_text(json.dumps({'nodes':[],'edges':[],'hyperedges':[],'input_tokens':0,'output_tokens':0}), encoding='utf-8')
"
```
**MANDATORY: You MUST use the Agent tool here. Reading files yourself one-by-one is forbidden - it is 5-10x slower. If you do not use the Agent tool you are doing this wrong.**
@@ -243,7 +251,7 @@ Each subagent writes its result to its own `graphify-out/.graphify_chunk_NN.json
CHUNK_PATH must be an **absolute** path — derive it before dispatching:
```bash
PROJECT_ROOT=$(cat graphify-out/.graphify_root)
PROJECT_ROOT=$(pwd) # cwd — where Part C globs graphify-out/ (NOT .graphify_root/scan dir, #1392)
# Then for chunk N: CHUNK_PATH="${PROJECT_ROOT}/graphify-out/.graphify_chunk_0N.json"
```
@@ -385,6 +393,12 @@ 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='INPUT_PATH')
# 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:
print('ERROR: Graph is empty - extraction produced no nodes.')
print('Possible causes: all files were skipped, binary-only corpus, or extraction failed.')
raise SystemExit(1)
communities = cluster(G)
cohesion = score_all(G, communities)
tokens = {'input': extraction.get('input_tokens', 0), 'output': extraction.get('output_tokens', 0)}
@@ -394,10 +408,17 @@ labels = {cid: 'Community ' + str(cid) for cid in communities}
# Placeholder questions - regenerated with real labels in Step 5
questions = suggest_questions(G, communities, labels)
# Export FIRST and honor the #479 shrink-guard: to_json returns False (writing
# nothing) when the new graph is smaller than the existing graph.json. Only write
# GRAPH_REPORT.md + the analysis sidecar when the graph was actually written, so
# they never describe a graph that graph.json doesn't contain (#1392).
wrote = to_json(G, communities, 'graphify-out/graph.json')
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, '.', suggested_questions=questions)
Path('graphify-out/GRAPH_REPORT.md').write_text(report, encoding=\"utf-8\")
to_json(G, communities, 'graphify-out/graph.json')
analysis = {
'communities': {str(k): v for k, v in communities.items()},
'cohesion': {str(k): v for k, v in cohesion.items()},
@@ -406,10 +427,6 @@ analysis = {
'questions': questions,
}
Path('graphify-out/.graphify_analysis.json').write_text(json.dumps(analysis, indent=2, ensure_ascii=False), encoding=\"utf-8\")
if G.number_of_nodes() == 0:
print('ERROR: Graph is empty - extraction produced no nodes.')
print('Possible causes: all files were skipped, binary-only corpus, or extraction failed.')
raise SystemExit(1)
print(f'Graph: {G.number_of_nodes()} nodes, {G.number_of_edges()} edges, {len(communities)} communities')
"
```
graphify/skill-kilo.md
+25 -8
View File
@@ -190,7 +190,15 @@ else:
#### Part B - Semantic extraction (parallel subagents)
**Fast path:** If detection found zero docs, papers, and images (code-only corpus), skip Part B entirely and go straight to Part C. AST handles code - there is nothing for semantic subagents to do.
**Fast path:** If detection found zero docs, papers, and images (code-only corpus), skip Part B entirely and go straight to Part C. AST handles code - there is nothing for semantic subagents to do. **First write an empty semantic file** so Part C's merge has its input (it reads `.graphify_semantic.json` unconditionally; without this a code-only run hits `FileNotFoundError`):
```bash
$(cat graphify-out/.graphify_python) -c "
import json
from pathlib import Path
Path('graphify-out/.graphify_semantic.json').write_text(json.dumps({'nodes':[],'edges':[],'hyperedges':[],'input_tokens':0,'output_tokens':0}), encoding='utf-8')
"
```
**MANDATORY: You MUST use the Agent tool here. Reading files yourself one-by-one is forbidden - it is 5-10x slower. If you do not use the Agent tool you are doing this wrong.**
@@ -246,7 +254,7 @@ Each subagent receives this exact prompt (substitute FILE_LIST, CHUNK_NUM, TOTAL
CHUNK_PATH must be an **absolute** path — derive it before dispatching:
```bash
PROJECT_ROOT=$(cat graphify-out/.graphify_root)
PROJECT_ROOT=$(pwd) # cwd — where Part C globs graphify-out/ (NOT .graphify_root/scan dir, #1392)
# Then for chunk N: CHUNK_PATH="${PROJECT_ROOT}/graphify-out/.graphify_chunk_0N.json"
```
@@ -388,6 +396,12 @@ 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='INPUT_PATH')
# 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:
print('ERROR: Graph is empty - extraction produced no nodes.')
print('Possible causes: all files were skipped, binary-only corpus, or extraction failed.')
raise SystemExit(1)
communities = cluster(G)
cohesion = score_all(G, communities)
tokens = {'input': extraction.get('input_tokens', 0), 'output': extraction.get('output_tokens', 0)}
@@ -397,10 +411,17 @@ labels = {cid: 'Community ' + str(cid) for cid in communities}
# Placeholder questions - regenerated with real labels in Step 5
questions = suggest_questions(G, communities, labels)
# Export FIRST and honor the #479 shrink-guard: to_json returns False (writing
# nothing) when the new graph is smaller than the existing graph.json. Only write
# GRAPH_REPORT.md + the analysis sidecar when the graph was actually written, so
# they never describe a graph that graph.json doesn't contain (#1392).
wrote = to_json(G, communities, 'graphify-out/graph.json')
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, '.', suggested_questions=questions)
Path('graphify-out/GRAPH_REPORT.md').write_text(report, encoding=\"utf-8\")
to_json(G, communities, 'graphify-out/graph.json')
analysis = {
'communities': {str(k): v for k, v in communities.items()},
'cohesion': {str(k): v for k, v in cohesion.items()},
@@ -409,10 +430,6 @@ analysis = {
'questions': questions,
}
Path('graphify-out/.graphify_analysis.json').write_text(json.dumps(analysis, indent=2, ensure_ascii=False), encoding=\"utf-8\")
if G.number_of_nodes() == 0:
print('ERROR: Graph is empty - extraction produced no nodes.')
print('Possible causes: all files were skipped, binary-only corpus, or extraction failed.')
raise SystemExit(1)
print(f'Graph: {G.number_of_nodes()} nodes, {G.number_of_edges()} edges, {len(communities)} communities')
"
```
graphify/skill-kiro.md
+25 -8
View File
@@ -190,7 +190,15 @@ else:
#### Part B - Semantic extraction (parallel subagents)
**Fast path:** If detection found zero docs, papers, and images (code-only corpus), skip Part B entirely and go straight to Part C. AST handles code - there is nothing for semantic subagents to do.
**Fast path:** If detection found zero docs, papers, and images (code-only corpus), skip Part B entirely and go straight to Part C. AST handles code - there is nothing for semantic subagents to do. **First write an empty semantic file** so Part C's merge has its input (it reads `.graphify_semantic.json` unconditionally; without this a code-only run hits `FileNotFoundError`):
```bash
$(cat graphify-out/.graphify_python) -c "
import json
from pathlib import Path
Path('graphify-out/.graphify_semantic.json').write_text(json.dumps({'nodes':[],'edges':[],'hyperedges':[],'input_tokens':0,'output_tokens':0}), encoding='utf-8')
"
```
**MANDATORY: You MUST use the Agent tool here. Reading files yourself one-by-one is forbidden - it is 5-10x slower. If you do not use the Agent tool you are doing this wrong.**
@@ -246,7 +254,7 @@ Each subagent receives this exact prompt (substitute FILE_LIST, CHUNK_NUM, TOTAL
CHUNK_PATH must be an **absolute** path — derive it before dispatching:
```bash
PROJECT_ROOT=$(cat graphify-out/.graphify_root)
PROJECT_ROOT=$(pwd) # cwd — where Part C globs graphify-out/ (NOT .graphify_root/scan dir, #1392)
# Then for chunk N: CHUNK_PATH="${PROJECT_ROOT}/graphify-out/.graphify_chunk_0N.json"
```
@@ -388,6 +396,12 @@ 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='INPUT_PATH')
# 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:
print('ERROR: Graph is empty - extraction produced no nodes.')
print('Possible causes: all files were skipped, binary-only corpus, or extraction failed.')
raise SystemExit(1)
communities = cluster(G)
cohesion = score_all(G, communities)
tokens = {'input': extraction.get('input_tokens', 0), 'output': extraction.get('output_tokens', 0)}
@@ -397,10 +411,17 @@ labels = {cid: 'Community ' + str(cid) for cid in communities}
# Placeholder questions - regenerated with real labels in Step 5
questions = suggest_questions(G, communities, labels)
# Export FIRST and honor the #479 shrink-guard: to_json returns False (writing
# nothing) when the new graph is smaller than the existing graph.json. Only write
# GRAPH_REPORT.md + the analysis sidecar when the graph was actually written, so
# they never describe a graph that graph.json doesn't contain (#1392).
wrote = to_json(G, communities, 'graphify-out/graph.json')
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, '.', suggested_questions=questions)
Path('graphify-out/GRAPH_REPORT.md').write_text(report, encoding=\"utf-8\")
to_json(G, communities, 'graphify-out/graph.json')
analysis = {
'communities': {str(k): v for k, v in communities.items()},
'cohesion': {str(k): v for k, v in cohesion.items()},
@@ -409,10 +430,6 @@ analysis = {
'questions': questions,
}
Path('graphify-out/.graphify_analysis.json').write_text(json.dumps(analysis, indent=2, ensure_ascii=False), encoding=\"utf-8\")
if G.number_of_nodes() == 0:
print('ERROR: Graph is empty - extraction produced no nodes.')
print('Possible causes: all files were skipped, binary-only corpus, or extraction failed.')
raise SystemExit(1)
print(f'Graph: {G.number_of_nodes()} nodes, {G.number_of_edges()} edges, {len(communities)} communities')
"
```
graphify/skill-opencode.md
+24 -7
View File
@@ -190,7 +190,15 @@ else:
#### Part B - Semantic extraction (parallel subagents)
**Fast path:** If detection found zero docs, papers, and images (code-only corpus), skip Part B entirely and go straight to Part C. AST handles code - there is nothing for semantic subagents to do.
**Fast path:** If detection found zero docs, papers, and images (code-only corpus), skip Part B entirely and go straight to Part C. AST handles code - there is nothing for semantic subagents to do. **First write an empty semantic file** so Part C's merge has its input (it reads `.graphify_semantic.json` unconditionally; without this a code-only run hits `FileNotFoundError`):
```bash
$(cat graphify-out/.graphify_python) -c "
import json
from pathlib import Path
Path('graphify-out/.graphify_semantic.json').write_text(json.dumps({'nodes':[],'edges':[],'hyperedges':[],'input_tokens':0,'output_tokens':0}), encoding='utf-8')
"
```
**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.**
@@ -380,6 +388,12 @@ 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='INPUT_PATH')
# 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:
print('ERROR: Graph is empty - extraction produced no nodes.')
print('Possible causes: all files were skipped, binary-only corpus, or extraction failed.')
raise SystemExit(1)
communities = cluster(G)
cohesion = score_all(G, communities)
tokens = {'input': extraction.get('input_tokens', 0), 'output': extraction.get('output_tokens', 0)}
@@ -389,10 +403,17 @@ labels = {cid: 'Community ' + str(cid) for cid in communities}
# Placeholder questions - regenerated with real labels in Step 5
questions = suggest_questions(G, communities, labels)
# Export FIRST and honor the #479 shrink-guard: to_json returns False (writing
# nothing) when the new graph is smaller than the existing graph.json. Only write
# GRAPH_REPORT.md + the analysis sidecar when the graph was actually written, so
# they never describe a graph that graph.json doesn't contain (#1392).
wrote = to_json(G, communities, 'graphify-out/graph.json')
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, '.', suggested_questions=questions)
Path('graphify-out/GRAPH_REPORT.md').write_text(report, encoding=\"utf-8\")
to_json(G, communities, 'graphify-out/graph.json')
analysis = {
'communities': {str(k): v for k, v in communities.items()},
'cohesion': {str(k): v for k, v in cohesion.items()},
@@ -401,10 +422,6 @@ analysis = {
'questions': questions,
}
Path('graphify-out/.graphify_analysis.json').write_text(json.dumps(analysis, indent=2, ensure_ascii=False), encoding=\"utf-8\")
if G.number_of_nodes() == 0:
print('ERROR: Graph is empty - extraction produced no nodes.')
print('Possible causes: all files were skipped, binary-only corpus, or extraction failed.')
raise SystemExit(1)
print(f'Graph: {G.number_of_nodes()} nodes, {G.number_of_edges()} edges, {len(communities)} communities')
"
```
graphify/skill-pi.md
+25 -8
View File
@@ -190,7 +190,15 @@ else:
#### Part B - Semantic extraction (parallel subagents)
**Fast path:** If detection found zero docs, papers, and images (code-only corpus), skip Part B entirely and go straight to Part C. AST handles code - there is nothing for semantic subagents to do.
**Fast path:** If detection found zero docs, papers, and images (code-only corpus), skip Part B entirely and go straight to Part C. AST handles code - there is nothing for semantic subagents to do. **First write an empty semantic file** so Part C's merge has its input (it reads `.graphify_semantic.json` unconditionally; without this a code-only run hits `FileNotFoundError`):
```bash
$(cat graphify-out/.graphify_python) -c "
import json
from pathlib import Path
Path('graphify-out/.graphify_semantic.json').write_text(json.dumps({'nodes':[],'edges':[],'hyperedges':[],'input_tokens':0,'output_tokens':0}), encoding='utf-8')
"
```
**MANDATORY: You MUST use the Agent tool here. Reading files yourself one-by-one is forbidden - it is 5-10x slower. If you do not use the Agent tool you are doing this wrong.**
@@ -246,7 +254,7 @@ Each subagent receives this exact prompt (substitute FILE_LIST, CHUNK_NUM, TOTAL
CHUNK_PATH must be an **absolute** path — derive it before dispatching:
```bash
PROJECT_ROOT=$(cat graphify-out/.graphify_root)
PROJECT_ROOT=$(pwd) # cwd — where Part C globs graphify-out/ (NOT .graphify_root/scan dir, #1392)
# Then for chunk N: CHUNK_PATH="${PROJECT_ROOT}/graphify-out/.graphify_chunk_0N.json"
```
@@ -388,6 +396,12 @@ 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='INPUT_PATH')
# 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:
print('ERROR: Graph is empty - extraction produced no nodes.')
print('Possible causes: all files were skipped, binary-only corpus, or extraction failed.')
raise SystemExit(1)
communities = cluster(G)
cohesion = score_all(G, communities)
tokens = {'input': extraction.get('input_tokens', 0), 'output': extraction.get('output_tokens', 0)}
@@ -397,10 +411,17 @@ labels = {cid: 'Community ' + str(cid) for cid in communities}
# Placeholder questions - regenerated with real labels in Step 5
questions = suggest_questions(G, communities, labels)
# Export FIRST and honor the #479 shrink-guard: to_json returns False (writing
# nothing) when the new graph is smaller than the existing graph.json. Only write
# GRAPH_REPORT.md + the analysis sidecar when the graph was actually written, so
# they never describe a graph that graph.json doesn't contain (#1392).
wrote = to_json(G, communities, 'graphify-out/graph.json')
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, '.', suggested_questions=questions)
Path('graphify-out/GRAPH_REPORT.md').write_text(report, encoding=\"utf-8\")
to_json(G, communities, 'graphify-out/graph.json')
analysis = {
'communities': {str(k): v for k, v in communities.items()},
'cohesion': {str(k): v for k, v in cohesion.items()},
@@ -409,10 +430,6 @@ analysis = {
'questions': questions,
}
Path('graphify-out/.graphify_analysis.json').write_text(json.dumps(analysis, indent=2, ensure_ascii=False), encoding=\"utf-8\")
if G.number_of_nodes() == 0:
print('ERROR: Graph is empty - extraction produced no nodes.')
print('Possible causes: all files were skipped, binary-only corpus, or extraction failed.')
raise SystemExit(1)
print(f'Graph: {G.number_of_nodes()} nodes, {G.number_of_edges()} edges, {len(communities)} communities')
"
```
graphify/skill-trae.md
+25 -8
View File
@@ -190,7 +190,15 @@ else:
#### Part B - Semantic extraction (parallel subagents)
**Fast path:** If detection found zero docs, papers, and images (code-only corpus), skip Part B entirely and go straight to Part C. AST handles code - there is nothing for semantic subagents to do.
**Fast path:** If detection found zero docs, papers, and images (code-only corpus), skip Part B entirely and go straight to Part C. AST handles code - there is nothing for semantic subagents to do. **First write an empty semantic file** so Part C's merge has its input (it reads `.graphify_semantic.json` unconditionally; without this a code-only run hits `FileNotFoundError`):
```bash
$(cat graphify-out/.graphify_python) -c "
import json
from pathlib import Path
Path('graphify-out/.graphify_semantic.json').write_text(json.dumps({'nodes':[],'edges':[],'hyperedges':[],'input_tokens':0,'output_tokens':0}), encoding='utf-8')
"
```
**MANDATORY: You MUST use the Agent tool here. Reading files yourself one-by-one is forbidden - it is 5-10x slower. If you do not use the Agent tool you are doing this wrong.**
@@ -244,7 +252,7 @@ Each subagent writes its result to its own `graphify-out/.graphify_chunk_NN.json
CHUNK_PATH must be an **absolute** path — derive it before dispatching:
```bash
PROJECT_ROOT=$(cat graphify-out/.graphify_root)
PROJECT_ROOT=$(pwd) # cwd — where Part C globs graphify-out/ (NOT .graphify_root/scan dir, #1392)
# Then for chunk N: CHUNK_PATH="${PROJECT_ROOT}/graphify-out/.graphify_chunk_0N.json"
```
@@ -386,6 +394,12 @@ 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='INPUT_PATH')
# 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:
print('ERROR: Graph is empty - extraction produced no nodes.')
print('Possible causes: all files were skipped, binary-only corpus, or extraction failed.')
raise SystemExit(1)
communities = cluster(G)
cohesion = score_all(G, communities)
tokens = {'input': extraction.get('input_tokens', 0), 'output': extraction.get('output_tokens', 0)}
@@ -395,10 +409,17 @@ labels = {cid: 'Community ' + str(cid) for cid in communities}
# Placeholder questions - regenerated with real labels in Step 5
questions = suggest_questions(G, communities, labels)
# Export FIRST and honor the #479 shrink-guard: to_json returns False (writing
# nothing) when the new graph is smaller than the existing graph.json. Only write
# GRAPH_REPORT.md + the analysis sidecar when the graph was actually written, so
# they never describe a graph that graph.json doesn't contain (#1392).
wrote = to_json(G, communities, 'graphify-out/graph.json')
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, '.', suggested_questions=questions)
Path('graphify-out/GRAPH_REPORT.md').write_text(report, encoding=\"utf-8\")
to_json(G, communities, 'graphify-out/graph.json')
analysis = {
'communities': {str(k): v for k, v in communities.items()},
'cohesion': {str(k): v for k, v in cohesion.items()},
@@ -407,10 +428,6 @@ analysis = {
'questions': questions,
}
Path('graphify-out/.graphify_analysis.json').write_text(json.dumps(analysis, indent=2, ensure_ascii=False), encoding=\"utf-8\")
if G.number_of_nodes() == 0:
print('ERROR: Graph is empty - extraction produced no nodes.')
print('Possible causes: all files were skipped, binary-only corpus, or extraction failed.')
raise SystemExit(1)
print(f'Graph: {G.number_of_nodes()} nodes, {G.number_of_edges()} edges, {len(communities)} communities')
"
```
graphify/skill-vscode.md
+25 -8
View File
@@ -190,7 +190,15 @@ else:
#### Part B - Semantic extraction (parallel subagents)
**Fast path:** If detection found zero docs, papers, and images (code-only corpus), skip Part B entirely and go straight to Part C. AST handles code - there is nothing for semantic subagents to do.
**Fast path:** If detection found zero docs, papers, and images (code-only corpus), skip Part B entirely and go straight to Part C. AST handles code - there is nothing for semantic subagents to do. **First write an empty semantic file** so Part C's merge has its input (it reads `.graphify_semantic.json` unconditionally; without this a code-only run hits `FileNotFoundError`):
```bash
$(cat graphify-out/.graphify_python) -c "
import json
from pathlib import Path
Path('graphify-out/.graphify_semantic.json').write_text(json.dumps({'nodes':[],'edges':[],'hyperedges':[],'input_tokens':0,'output_tokens':0}), encoding='utf-8')
"
```
**MANDATORY: You MUST use the Agent tool here. Reading files yourself one-by-one is forbidden - it is 5-10x slower. If you do not use the Agent tool you are doing this wrong.**
@@ -238,7 +246,7 @@ For each chunk of uncached files (20-25 per chunk), give a subagent the extracti
```bash
# After pasting a subagent's JSON for chunk N, save it (replace N and PASTED_JSON):
PROJECT_ROOT=$(cat graphify-out/.graphify_root)
PROJECT_ROOT=$(pwd) # cwd — where Part C globs graphify-out/ (NOT .graphify_root/scan dir, #1392)
cat > "${PROJECT_ROOT}/graphify-out/.graphify_chunk_0N.json" <<'CHUNK_JSON'
PASTED_JSON
CHUNK_JSON
@@ -384,6 +392,12 @@ 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='INPUT_PATH')
# 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:
print('ERROR: Graph is empty - extraction produced no nodes.')
print('Possible causes: all files were skipped, binary-only corpus, or extraction failed.')
raise SystemExit(1)
communities = cluster(G)
cohesion = score_all(G, communities)
tokens = {'input': extraction.get('input_tokens', 0), 'output': extraction.get('output_tokens', 0)}
@@ -393,10 +407,17 @@ labels = {cid: 'Community ' + str(cid) for cid in communities}
# Placeholder questions - regenerated with real labels in Step 5
questions = suggest_questions(G, communities, labels)
# Export FIRST and honor the #479 shrink-guard: to_json returns False (writing
# nothing) when the new graph is smaller than the existing graph.json. Only write
# GRAPH_REPORT.md + the analysis sidecar when the graph was actually written, so
# they never describe a graph that graph.json doesn't contain (#1392).
wrote = to_json(G, communities, 'graphify-out/graph.json')
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, '.', suggested_questions=questions)
Path('graphify-out/GRAPH_REPORT.md').write_text(report, encoding=\"utf-8\")
to_json(G, communities, 'graphify-out/graph.json')
analysis = {
'communities': {str(k): v for k, v in communities.items()},
'cohesion': {str(k): v for k, v in cohesion.items()},
@@ -405,10 +426,6 @@ analysis = {
'questions': questions,
}
Path('graphify-out/.graphify_analysis.json').write_text(json.dumps(analysis, indent=2, ensure_ascii=False), encoding=\"utf-8\")
if G.number_of_nodes() == 0:
print('ERROR: Graph is empty - extraction produced no nodes.')
print('Possible causes: all files were skipped, binary-only corpus, or extraction failed.')
raise SystemExit(1)
print(f'Graph: {G.number_of_nodes()} nodes, {G.number_of_edges()} edges, {len(communities)} communities')
"
```
graphify/skill-windows.md
+25 -8
View File
@@ -212,7 +212,15 @@ else:
#### Part B - Semantic extraction (parallel subagents)
**Fast path:** If detection found zero docs, papers, and images (code-only corpus), skip Part B entirely and go straight to Part C. AST handles code - there is nothing for semantic subagents to do.
**Fast path:** If detection found zero docs, papers, and images (code-only corpus), skip Part B entirely and go straight to Part C. AST handles code - there is nothing for semantic subagents to do. **First write an empty semantic file** so Part C's merge has its input (it reads `.graphify_semantic.json` unconditionally; without this a code-only run hits `FileNotFoundError`):
```bash
$(cat graphify-out/.graphify_python) -c "
import json
from pathlib import Path
Path('graphify-out/.graphify_semantic.json').write_text(json.dumps({'nodes':[],'edges':[],'hyperedges':[],'input_tokens':0,'output_tokens':0}), encoding='utf-8')
"
```
**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.**
@@ -268,7 +276,7 @@ Each subagent receives this exact prompt (substitute FILE_LIST, CHUNK_NUM, TOTAL
CHUNK_PATH must be an **absolute** path — derive it before dispatching:
```powershell
$PROJECT_ROOT = Get-Content graphify-out\.graphify_root
$PROJECT_ROOT = (Get-Location).Path # cwd — where Part C globs graphify-out\ (NOT .graphify_root/scan dir, #1392)
# Then for chunk N: $CHUNK_PATH = Join-Path $PROJECT_ROOT "graphify-out\.graphify_chunk_0N.json"
```
@@ -410,6 +418,12 @@ 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='INPUT_PATH')
# 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:
print('ERROR: Graph is empty - extraction produced no nodes.')
print('Possible causes: all files were skipped, binary-only corpus, or extraction failed.')
raise SystemExit(1)
communities = cluster(G)
cohesion = score_all(G, communities)
tokens = {'input': extraction.get('input_tokens', 0), 'output': extraction.get('output_tokens', 0)}
@@ -419,10 +433,17 @@ labels = {cid: 'Community ' + str(cid) for cid in communities}
# Placeholder questions - regenerated with real labels in Step 5
questions = suggest_questions(G, communities, labels)
# Export FIRST and honor the #479 shrink-guard: to_json returns False (writing
# nothing) when the new graph is smaller than the existing graph.json. Only write
# GRAPH_REPORT.md + the analysis sidecar when the graph was actually written, so
# they never describe a graph that graph.json doesn't contain (#1392).
wrote = to_json(G, communities, 'graphify-out/graph.json')
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, '.', suggested_questions=questions)
Path('graphify-out/GRAPH_REPORT.md').write_text(report, encoding=\"utf-8\")
to_json(G, communities, 'graphify-out/graph.json')
analysis = {
'communities': {str(k): v for k, v in communities.items()},
'cohesion': {str(k): v for k, v in cohesion.items()},
@@ -431,10 +452,6 @@ analysis = {
'questions': questions,
}
Path('graphify-out/.graphify_analysis.json').write_text(json.dumps(analysis, indent=2, ensure_ascii=False), encoding=\"utf-8\")
if G.number_of_nodes() == 0:
print('ERROR: Graph is empty - extraction produced no nodes.')
print('Possible causes: all files were skipped, binary-only corpus, or extraction failed.')
raise SystemExit(1)
print(f'Graph: {G.number_of_nodes()} nodes, {G.number_of_edges()} edges, {len(communities)} communities')
"
```
graphify/skill.md
+25 -8
View File
@@ -190,7 +190,15 @@ else:
#### Part B - Semantic extraction (parallel subagents)
**Fast path:** If detection found zero docs, papers, and images (code-only corpus), skip Part B entirely and go straight to Part C. AST handles code - there is nothing for semantic subagents to do.
**Fast path:** If detection found zero docs, papers, and images (code-only corpus), skip Part B entirely and go straight to Part C. AST handles code - there is nothing for semantic subagents to do. **First write an empty semantic file** so Part C's merge has its input (it reads `.graphify_semantic.json` unconditionally; without this a code-only run hits `FileNotFoundError`):
```bash
$(cat graphify-out/.graphify_python) -c "
import json
from pathlib import Path
Path('graphify-out/.graphify_semantic.json').write_text(json.dumps({'nodes':[],'edges':[],'hyperedges':[],'input_tokens':0,'output_tokens':0}), encoding='utf-8')
"
```
**MANDATORY: You MUST use the Agent tool here. Reading files yourself one-by-one is forbidden - it is 5-10x slower. If you do not use the Agent tool you are doing this wrong.**
@@ -246,7 +254,7 @@ Each subagent receives this exact prompt (substitute FILE_LIST, CHUNK_NUM, TOTAL
CHUNK_PATH must be an **absolute** path — derive it before dispatching:
```bash
PROJECT_ROOT=$(cat graphify-out/.graphify_root)
PROJECT_ROOT=$(pwd) # cwd — where Part C globs graphify-out/ (NOT .graphify_root/scan dir, #1392)
# Then for chunk N: CHUNK_PATH="${PROJECT_ROOT}/graphify-out/.graphify_chunk_0N.json"
```
@@ -388,6 +396,12 @@ 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='INPUT_PATH')
# 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:
print('ERROR: Graph is empty - extraction produced no nodes.')
print('Possible causes: all files were skipped, binary-only corpus, or extraction failed.')
raise SystemExit(1)
communities = cluster(G)
cohesion = score_all(G, communities)
tokens = {'input': extraction.get('input_tokens', 0), 'output': extraction.get('output_tokens', 0)}
@@ -397,10 +411,17 @@ labels = {cid: 'Community ' + str(cid) for cid in communities}
# Placeholder questions - regenerated with real labels in Step 5
questions = suggest_questions(G, communities, labels)
# Export FIRST and honor the #479 shrink-guard: to_json returns False (writing
# nothing) when the new graph is smaller than the existing graph.json. Only write
# GRAPH_REPORT.md + the analysis sidecar when the graph was actually written, so
# they never describe a graph that graph.json doesn't contain (#1392).
wrote = to_json(G, communities, 'graphify-out/graph.json')
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, '.', suggested_questions=questions)
Path('graphify-out/GRAPH_REPORT.md').write_text(report, encoding=\"utf-8\")
to_json(G, communities, 'graphify-out/graph.json')
analysis = {
'communities': {str(k): v for k, v in communities.items()},
'cohesion': {str(k): v for k, v in cohesion.items()},
@@ -409,10 +430,6 @@ analysis = {
'questions': questions,
}
Path('graphify-out/.graphify_analysis.json').write_text(json.dumps(analysis, indent=2, ensure_ascii=False), encoding=\"utf-8\")
if G.number_of_nodes() == 0:
print('ERROR: Graph is empty - extraction produced no nodes.')
print('Possible causes: all files were skipped, binary-only corpus, or extraction failed.')
raise SystemExit(1)
print(f'Graph: {G.number_of_nodes()} nodes, {G.number_of_edges()} edges, {len(communities)} communities')
"
```
graphify/skills/amp/references/update.md
+1 -1
View File
@@ -182,4 +182,4 @@ 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).
`graphify cluster-only .` is **self-contained**: it re-clusters, names communities, and regenerates `GRAPH_REPORT.md`, `graph.json`, and `graph.html` from the existing graph. **Do not re-run Steps 5–9** — they read intermediate files (`.graphify_extract.json`, `.graphify_detect.json`, `.graphify_analysis.json`) that a prior build's cleanup (Step 9) already deleted, so they raise `FileNotFoundError` (#1392). When it finishes, present the refreshed `GRAPH_REPORT.md` summary as usual.
graphify/skills/claude/references/update.md
+1 -1
View File
@@ -182,4 +182,4 @@ 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).
`graphify cluster-only .` is **self-contained**: it re-clusters, names communities, and regenerates `GRAPH_REPORT.md`, `graph.json`, and `graph.html` from the existing graph. **Do not re-run Steps 5–9** — they read intermediate files (`.graphify_extract.json`, `.graphify_detect.json`, `.graphify_analysis.json`) that a prior build's cleanup (Step 9) already deleted, so they raise `FileNotFoundError` (#1392). When it finishes, present the refreshed `GRAPH_REPORT.md` summary as usual.
graphify/skills/claw/references/update.md
+1 -1
View File
@@ -182,4 +182,4 @@ 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).
`graphify cluster-only .` is **self-contained**: it re-clusters, names communities, and regenerates `GRAPH_REPORT.md`, `graph.json`, and `graph.html` from the existing graph. **Do not re-run Steps 5–9** — they read intermediate files (`.graphify_extract.json`, `.graphify_detect.json`, `.graphify_analysis.json`) that a prior build's cleanup (Step 9) already deleted, so they raise `FileNotFoundError` (#1392). When it finishes, present the refreshed `GRAPH_REPORT.md` summary as usual.
graphify/skills/codex/references/update.md
+1 -1
View File
@@ -182,4 +182,4 @@ 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).
`graphify cluster-only .` is **self-contained**: it re-clusters, names communities, and regenerates `GRAPH_REPORT.md`, `graph.json`, and `graph.html` from the existing graph. **Do not re-run Steps 5–9** — they read intermediate files (`.graphify_extract.json`, `.graphify_detect.json`, `.graphify_analysis.json`) that a prior build's cleanup (Step 9) already deleted, so they raise `FileNotFoundError` (#1392). When it finishes, present the refreshed `GRAPH_REPORT.md` summary as usual.
graphify/skills/copilot/references/update.md
+1 -1
View File
@@ -182,4 +182,4 @@ 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).
`graphify cluster-only .` is **self-contained**: it re-clusters, names communities, and regenerates `GRAPH_REPORT.md`, `graph.json`, and `graph.html` from the existing graph. **Do not re-run Steps 5–9** — they read intermediate files (`.graphify_extract.json`, `.graphify_detect.json`, `.graphify_analysis.json`) that a prior build's cleanup (Step 9) already deleted, so they raise `FileNotFoundError` (#1392). When it finishes, present the refreshed `GRAPH_REPORT.md` summary as usual.
graphify/skills/droid/references/update.md
+1 -1
View File
@@ -182,4 +182,4 @@ 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).
`graphify cluster-only .` is **self-contained**: it re-clusters, names communities, and regenerates `GRAPH_REPORT.md`, `graph.json`, and `graph.html` from the existing graph. **Do not re-run Steps 5–9** — they read intermediate files (`.graphify_extract.json`, `.graphify_detect.json`, `.graphify_analysis.json`) that a prior build's cleanup (Step 9) already deleted, so they raise `FileNotFoundError` (#1392). When it finishes, present the refreshed `GRAPH_REPORT.md` summary as usual.
graphify/skills/kilo/references/update.md
+1 -1
View File
@@ -182,4 +182,4 @@ 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).
`graphify cluster-only .` is **self-contained**: it re-clusters, names communities, and regenerates `GRAPH_REPORT.md`, `graph.json`, and `graph.html` from the existing graph. **Do not re-run Steps 5–9** — they read intermediate files (`.graphify_extract.json`, `.graphify_detect.json`, `.graphify_analysis.json`) that a prior build's cleanup (Step 9) already deleted, so they raise `FileNotFoundError` (#1392). When it finishes, present the refreshed `GRAPH_REPORT.md` summary as usual.
graphify/skills/kiro/references/update.md
+1 -1
View File
@@ -182,4 +182,4 @@ 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).
`graphify cluster-only .` is **self-contained**: it re-clusters, names communities, and regenerates `GRAPH_REPORT.md`, `graph.json`, and `graph.html` from the existing graph. **Do not re-run Steps 5–9** — they read intermediate files (`.graphify_extract.json`, `.graphify_detect.json`, `.graphify_analysis.json`) that a prior build's cleanup (Step 9) already deleted, so they raise `FileNotFoundError` (#1392). When it finishes, present the refreshed `GRAPH_REPORT.md` summary as usual.
graphify/skills/opencode/references/update.md
+1 -1
View File
@@ -182,4 +182,4 @@ 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).
`graphify cluster-only .` is **self-contained**: it re-clusters, names communities, and regenerates `GRAPH_REPORT.md`, `graph.json`, and `graph.html` from the existing graph. **Do not re-run Steps 5–9** — they read intermediate files (`.graphify_extract.json`, `.graphify_detect.json`, `.graphify_analysis.json`) that a prior build's cleanup (Step 9) already deleted, so they raise `FileNotFoundError` (#1392). When it finishes, present the refreshed `GRAPH_REPORT.md` summary as usual.
graphify/skills/pi/references/update.md
+1 -1
View File
@@ -182,4 +182,4 @@ 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).
`graphify cluster-only .` is **self-contained**: it re-clusters, names communities, and regenerates `GRAPH_REPORT.md`, `graph.json`, and `graph.html` from the existing graph. **Do not re-run Steps 5–9** — they read intermediate files (`.graphify_extract.json`, `.graphify_detect.json`, `.graphify_analysis.json`) that a prior build's cleanup (Step 9) already deleted, so they raise `FileNotFoundError` (#1392). When it finishes, present the refreshed `GRAPH_REPORT.md` summary as usual.
graphify/skills/trae/references/update.md
+1 -1
View File
@@ -182,4 +182,4 @@ 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).
`graphify cluster-only .` is **self-contained**: it re-clusters, names communities, and regenerates `GRAPH_REPORT.md`, `graph.json`, and `graph.html` from the existing graph. **Do not re-run Steps 5–9** — they read intermediate files (`.graphify_extract.json`, `.graphify_detect.json`, `.graphify_analysis.json`) that a prior build's cleanup (Step 9) already deleted, so they raise `FileNotFoundError` (#1392). When it finishes, present the refreshed `GRAPH_REPORT.md` summary as usual.
graphify/skills/vscode/references/update.md
+1 -1
View File
@@ -182,4 +182,4 @@ 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).
`graphify cluster-only .` is **self-contained**: it re-clusters, names communities, and regenerates `GRAPH_REPORT.md`, `graph.json`, and `graph.html` from the existing graph. **Do not re-run Steps 5–9** — they read intermediate files (`.graphify_extract.json`, `.graphify_detect.json`, `.graphify_analysis.json`) that a prior build's cleanup (Step 9) already deleted, so they raise `FileNotFoundError` (#1392). When it finishes, present the refreshed `GRAPH_REPORT.md` summary as usual.
graphify/skills/windows/references/update.md
+1 -1
View File
@@ -182,4 +182,4 @@ 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).
`graphify cluster-only .` is **self-contained**: it re-clusters, names communities, and regenerates `GRAPH_REPORT.md`, `graph.json`, and `graph.html` from the existing graph. **Do not re-run Steps 5–9** — they read intermediate files (`.graphify_extract.json`, `.graphify_detect.json`, `.graphify_analysis.json`) that a prior build's cleanup (Step 9) already deleted, so they raise `FileNotFoundError` (#1392). When it finishes, present the refreshed `GRAPH_REPORT.md` summary as usual.
tools/skillgen/expected/graphify__skill-amp.md
+25 -8
View File
@@ -190,7 +190,15 @@ else:
#### Part B - Semantic extraction (parallel subagents)
**Fast path:** If detection found zero docs, papers, and images (code-only corpus), skip Part B entirely and go straight to Part C. AST handles code - there is nothing for semantic subagents to do.
**Fast path:** If detection found zero docs, papers, and images (code-only corpus), skip Part B entirely and go straight to Part C. AST handles code - there is nothing for semantic subagents to do. **First write an empty semantic file** so Part C's merge has its input (it reads `.graphify_semantic.json` unconditionally; without this a code-only run hits `FileNotFoundError`):
```bash
$(cat graphify-out/.graphify_python) -c "
import json
from pathlib import Path
Path('graphify-out/.graphify_semantic.json').write_text(json.dumps({'nodes':[],'edges':[],'hyperedges':[],'input_tokens':0,'output_tokens':0}), encoding='utf-8')
"
```
**MANDATORY: You MUST use the Agent tool here. Reading files yourself one-by-one is forbidden - it is 5-10x slower. If you do not use the Agent tool you are doing this wrong.**
@@ -243,7 +251,7 @@ Each subagent writes its result to its own `graphify-out/.graphify_chunk_NN.json
CHUNK_PATH must be an **absolute** path — derive it before dispatching:
```bash
PROJECT_ROOT=$(cat graphify-out/.graphify_root)
PROJECT_ROOT=$(pwd) # cwd — where Part C globs graphify-out/ (NOT .graphify_root/scan dir, #1392)
# Then for chunk N: CHUNK_PATH="${PROJECT_ROOT}/graphify-out/.graphify_chunk_0N.json"
```
@@ -385,6 +393,12 @@ 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='INPUT_PATH')
# 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:
print('ERROR: Graph is empty - extraction produced no nodes.')
print('Possible causes: all files were skipped, binary-only corpus, or extraction failed.')
raise SystemExit(1)
communities = cluster(G)
cohesion = score_all(G, communities)
tokens = {'input': extraction.get('input_tokens', 0), 'output': extraction.get('output_tokens', 0)}
@@ -394,10 +408,17 @@ labels = {cid: 'Community ' + str(cid) for cid in communities}
# Placeholder questions - regenerated with real labels in Step 5
questions = suggest_questions(G, communities, labels)
# Export FIRST and honor the #479 shrink-guard: to_json returns False (writing
# nothing) when the new graph is smaller than the existing graph.json. Only write
# GRAPH_REPORT.md + the analysis sidecar when the graph was actually written, so
# they never describe a graph that graph.json doesn't contain (#1392).
wrote = to_json(G, communities, 'graphify-out/graph.json')
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, '.', suggested_questions=questions)
Path('graphify-out/GRAPH_REPORT.md').write_text(report, encoding=\"utf-8\")
to_json(G, communities, 'graphify-out/graph.json')
analysis = {
'communities': {str(k): v for k, v in communities.items()},
'cohesion': {str(k): v for k, v in cohesion.items()},
@@ -406,10 +427,6 @@ analysis = {
'questions': questions,
}
Path('graphify-out/.graphify_analysis.json').write_text(json.dumps(analysis, indent=2, ensure_ascii=False), encoding=\"utf-8\")
if G.number_of_nodes() == 0:
print('ERROR: Graph is empty - extraction produced no nodes.')
print('Possible causes: all files were skipped, binary-only corpus, or extraction failed.')
raise SystemExit(1)
print(f'Graph: {G.number_of_nodes()} nodes, {G.number_of_edges()} edges, {len(communities)} communities')
"
```
tools/skillgen/expected/graphify__skill-claw.md
+25 -8
View File
@@ -190,7 +190,15 @@ else:
#### Part B - Semantic extraction (parallel subagents)
**Fast path:** If detection found zero docs, papers, and images (code-only corpus), skip Part B entirely and go straight to Part C. AST handles code - there is nothing for semantic subagents to do.
**Fast path:** If detection found zero docs, papers, and images (code-only corpus), skip Part B entirely and go straight to Part C. AST handles code - there is nothing for semantic subagents to do. **First write an empty semantic file** so Part C's merge has its input (it reads `.graphify_semantic.json` unconditionally; without this a code-only run hits `FileNotFoundError`):
```bash
$(cat graphify-out/.graphify_python) -c "
import json
from pathlib import Path
Path('graphify-out/.graphify_semantic.json').write_text(json.dumps({'nodes':[],'edges':[],'hyperedges':[],'input_tokens':0,'output_tokens':0}), encoding='utf-8')
"
```
**MANDATORY: You MUST use the Agent tool here. Reading files yourself one-by-one is forbidden - it is 5-10x slower. If you do not use the Agent tool you are doing this wrong.**
@@ -246,7 +254,7 @@ Each subagent receives this exact prompt (substitute FILE_LIST, CHUNK_NUM, TOTAL
CHUNK_PATH must be an **absolute** path — derive it before dispatching:
```bash
PROJECT_ROOT=$(cat graphify-out/.graphify_root)
PROJECT_ROOT=$(pwd) # cwd — where Part C globs graphify-out/ (NOT .graphify_root/scan dir, #1392)
# Then for chunk N: CHUNK_PATH="${PROJECT_ROOT}/graphify-out/.graphify_chunk_0N.json"
```
@@ -388,6 +396,12 @@ 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='INPUT_PATH')
# 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:
print('ERROR: Graph is empty - extraction produced no nodes.')
print('Possible causes: all files were skipped, binary-only corpus, or extraction failed.')
raise SystemExit(1)
communities = cluster(G)
cohesion = score_all(G, communities)
tokens = {'input': extraction.get('input_tokens', 0), 'output': extraction.get('output_tokens', 0)}
@@ -397,10 +411,17 @@ labels = {cid: 'Community ' + str(cid) for cid in communities}
# Placeholder questions - regenerated with real labels in Step 5
questions = suggest_questions(G, communities, labels)
# Export FIRST and honor the #479 shrink-guard: to_json returns False (writing
# nothing) when the new graph is smaller than the existing graph.json. Only write
# GRAPH_REPORT.md + the analysis sidecar when the graph was actually written, so
# they never describe a graph that graph.json doesn't contain (#1392).
wrote = to_json(G, communities, 'graphify-out/graph.json')
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, '.', suggested_questions=questions)
Path('graphify-out/GRAPH_REPORT.md').write_text(report, encoding=\"utf-8\")
to_json(G, communities, 'graphify-out/graph.json')
analysis = {
'communities': {str(k): v for k, v in communities.items()},
'cohesion': {str(k): v for k, v in cohesion.items()},
@@ -409,10 +430,6 @@ analysis = {
'questions': questions,
}
Path('graphify-out/.graphify_analysis.json').write_text(json.dumps(analysis, indent=2, ensure_ascii=False), encoding=\"utf-8\")
if G.number_of_nodes() == 0:
print('ERROR: Graph is empty - extraction produced no nodes.')
print('Possible causes: all files were skipped, binary-only corpus, or extraction failed.')
raise SystemExit(1)
print(f'Graph: {G.number_of_nodes()} nodes, {G.number_of_edges()} edges, {len(communities)} communities')
"
```
tools/skillgen/expected/graphify__skill-codex.md
+24 -7
View File
@@ -190,7 +190,15 @@ else:
#### Part B - Semantic extraction (parallel subagents)
**Fast path:** If detection found zero docs, papers, and images (code-only corpus), skip Part B entirely and go straight to Part C. AST handles code - there is nothing for semantic subagents to do.
**Fast path:** If detection found zero docs, papers, and images (code-only corpus), skip Part B entirely and go straight to Part C. AST handles code - there is nothing for semantic subagents to do. **First write an empty semantic file** so Part C's merge has its input (it reads `.graphify_semantic.json` unconditionally; without this a code-only run hits `FileNotFoundError`):
```bash
$(cat graphify-out/.graphify_python) -c "
import json
from pathlib import Path
Path('graphify-out/.graphify_semantic.json').write_text(json.dumps({'nodes':[],'edges':[],'hyperedges':[],'input_tokens':0,'output_tokens':0}), encoding='utf-8')
"
```
**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.**
@@ -385,6 +393,12 @@ 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='INPUT_PATH')
# 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:
print('ERROR: Graph is empty - extraction produced no nodes.')
print('Possible causes: all files were skipped, binary-only corpus, or extraction failed.')
raise SystemExit(1)
communities = cluster(G)
cohesion = score_all(G, communities)
tokens = {'input': extraction.get('input_tokens', 0), 'output': extraction.get('output_tokens', 0)}
@@ -394,10 +408,17 @@ labels = {cid: 'Community ' + str(cid) for cid in communities}
# Placeholder questions - regenerated with real labels in Step 5
questions = suggest_questions(G, communities, labels)
# Export FIRST and honor the #479 shrink-guard: to_json returns False (writing
# nothing) when the new graph is smaller than the existing graph.json. Only write
# GRAPH_REPORT.md + the analysis sidecar when the graph was actually written, so
# they never describe a graph that graph.json doesn't contain (#1392).
wrote = to_json(G, communities, 'graphify-out/graph.json')
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, '.', suggested_questions=questions)
Path('graphify-out/GRAPH_REPORT.md').write_text(report, encoding=\"utf-8\")
to_json(G, communities, 'graphify-out/graph.json')
analysis = {
'communities': {str(k): v for k, v in communities.items()},
'cohesion': {str(k): v for k, v in cohesion.items()},
@@ -406,10 +427,6 @@ analysis = {
'questions': questions,
}
Path('graphify-out/.graphify_analysis.json').write_text(json.dumps(analysis, indent=2, ensure_ascii=False), encoding=\"utf-8\")
if G.number_of_nodes() == 0:
print('ERROR: Graph is empty - extraction produced no nodes.')
print('Possible causes: all files were skipped, binary-only corpus, or extraction failed.')
raise SystemExit(1)
print(f'Graph: {G.number_of_nodes()} nodes, {G.number_of_edges()} edges, {len(communities)} communities')
"
```
tools/skillgen/expected/graphify__skill-copilot.md
+25 -8
View File
@@ -190,7 +190,15 @@ else:
#### Part B - Semantic extraction (parallel subagents)
**Fast path:** If detection found zero docs, papers, and images (code-only corpus), skip Part B entirely and go straight to Part C. AST handles code - there is nothing for semantic subagents to do.
**Fast path:** If detection found zero docs, papers, and images (code-only corpus), skip Part B entirely and go straight to Part C. AST handles code - there is nothing for semantic subagents to do. **First write an empty semantic file** so Part C's merge has its input (it reads `.graphify_semantic.json` unconditionally; without this a code-only run hits `FileNotFoundError`):
```bash
$(cat graphify-out/.graphify_python) -c "
import json
from pathlib import Path
Path('graphify-out/.graphify_semantic.json').write_text(json.dumps({'nodes':[],'edges':[],'hyperedges':[],'input_tokens':0,'output_tokens':0}), encoding='utf-8')
"
```
**MANDATORY: You MUST use the Agent tool here. Reading files yourself one-by-one is forbidden - it is 5-10x slower. If you do not use the Agent tool you are doing this wrong.**
@@ -246,7 +254,7 @@ Each subagent receives this exact prompt (substitute FILE_LIST, CHUNK_NUM, TOTAL
CHUNK_PATH must be an **absolute** path — derive it before dispatching:
```bash
PROJECT_ROOT=$(cat graphify-out/.graphify_root)
PROJECT_ROOT=$(pwd) # cwd — where Part C globs graphify-out/ (NOT .graphify_root/scan dir, #1392)
# Then for chunk N: CHUNK_PATH="${PROJECT_ROOT}/graphify-out/.graphify_chunk_0N.json"
```
@@ -388,6 +396,12 @@ 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='INPUT_PATH')
# 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:
print('ERROR: Graph is empty - extraction produced no nodes.')
print('Possible causes: all files were skipped, binary-only corpus, or extraction failed.')
raise SystemExit(1)
communities = cluster(G)
cohesion = score_all(G, communities)
tokens = {'input': extraction.get('input_tokens', 0), 'output': extraction.get('output_tokens', 0)}
@@ -397,10 +411,17 @@ labels = {cid: 'Community ' + str(cid) for cid in communities}
# Placeholder questions - regenerated with real labels in Step 5
questions = suggest_questions(G, communities, labels)
# Export FIRST and honor the #479 shrink-guard: to_json returns False (writing
# nothing) when the new graph is smaller than the existing graph.json. Only write
# GRAPH_REPORT.md + the analysis sidecar when the graph was actually written, so
# they never describe a graph that graph.json doesn't contain (#1392).
wrote = to_json(G, communities, 'graphify-out/graph.json')
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, '.', suggested_questions=questions)
Path('graphify-out/GRAPH_REPORT.md').write_text(report, encoding=\"utf-8\")
to_json(G, communities, 'graphify-out/graph.json')
analysis = {
'communities': {str(k): v for k, v in communities.items()},
'cohesion': {str(k): v for k, v in cohesion.items()},
@@ -409,10 +430,6 @@ analysis = {
'questions': questions,
}
Path('graphify-out/.graphify_analysis.json').write_text(json.dumps(analysis, indent=2, ensure_ascii=False), encoding=\"utf-8\")
if G.number_of_nodes() == 0:
print('ERROR: Graph is empty - extraction produced no nodes.')
print('Possible causes: all files were skipped, binary-only corpus, or extraction failed.')
raise SystemExit(1)
print(f'Graph: {G.number_of_nodes()} nodes, {G.number_of_edges()} edges, {len(communities)} communities')
"
```
tools/skillgen/expected/graphify__skill-droid.md
+25 -8
View File
@@ -190,7 +190,15 @@ else:
#### Part B - Semantic extraction (parallel subagents)
**Fast path:** If detection found zero docs, papers, and images (code-only corpus), skip Part B entirely and go straight to Part C. AST handles code - there is nothing for semantic subagents to do.
**Fast path:** If detection found zero docs, papers, and images (code-only corpus), skip Part B entirely and go straight to Part C. AST handles code - there is nothing for semantic subagents to do. **First write an empty semantic file** so Part C's merge has its input (it reads `.graphify_semantic.json` unconditionally; without this a code-only run hits `FileNotFoundError`):
```bash
$(cat graphify-out/.graphify_python) -c "
import json
from pathlib import Path
Path('graphify-out/.graphify_semantic.json').write_text(json.dumps({'nodes':[],'edges':[],'hyperedges':[],'input_tokens':0,'output_tokens':0}), encoding='utf-8')
"
```
**MANDATORY: You MUST use the Agent tool here. Reading files yourself one-by-one is forbidden - it is 5-10x slower. If you do not use the Agent tool you are doing this wrong.**
@@ -243,7 +251,7 @@ Each subagent writes its result to its own `graphify-out/.graphify_chunk_NN.json
CHUNK_PATH must be an **absolute** path — derive it before dispatching:
```bash
PROJECT_ROOT=$(cat graphify-out/.graphify_root)
PROJECT_ROOT=$(pwd) # cwd — where Part C globs graphify-out/ (NOT .graphify_root/scan dir, #1392)
# Then for chunk N: CHUNK_PATH="${PROJECT_ROOT}/graphify-out/.graphify_chunk_0N.json"
```
@@ -385,6 +393,12 @@ 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='INPUT_PATH')
# 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:
print('ERROR: Graph is empty - extraction produced no nodes.')
print('Possible causes: all files were skipped, binary-only corpus, or extraction failed.')
raise SystemExit(1)
communities = cluster(G)
cohesion = score_all(G, communities)
tokens = {'input': extraction.get('input_tokens', 0), 'output': extraction.get('output_tokens', 0)}
@@ -394,10 +408,17 @@ labels = {cid: 'Community ' + str(cid) for cid in communities}
# Placeholder questions - regenerated with real labels in Step 5
questions = suggest_questions(G, communities, labels)
# Export FIRST and honor the #479 shrink-guard: to_json returns False (writing
# nothing) when the new graph is smaller than the existing graph.json. Only write
# GRAPH_REPORT.md + the analysis sidecar when the graph was actually written, so
# they never describe a graph that graph.json doesn't contain (#1392).
wrote = to_json(G, communities, 'graphify-out/graph.json')
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, '.', suggested_questions=questions)
Path('graphify-out/GRAPH_REPORT.md').write_text(report, encoding=\"utf-8\")
to_json(G, communities, 'graphify-out/graph.json')
analysis = {
'communities': {str(k): v for k, v in communities.items()},
'cohesion': {str(k): v for k, v in cohesion.items()},
@@ -406,10 +427,6 @@ analysis = {
'questions': questions,
}
Path('graphify-out/.graphify_analysis.json').write_text(json.dumps(analysis, indent=2, ensure_ascii=False), encoding=\"utf-8\")
if G.number_of_nodes() == 0:
print('ERROR: Graph is empty - extraction produced no nodes.')
print('Possible causes: all files were skipped, binary-only corpus, or extraction failed.')
raise SystemExit(1)
print(f'Graph: {G.number_of_nodes()} nodes, {G.number_of_edges()} edges, {len(communities)} communities')
"
```
tools/skillgen/expected/graphify__skill-kilo.md
+25 -8
View File
@@ -190,7 +190,15 @@ else:
#### Part B - Semantic extraction (parallel subagents)
**Fast path:** If detection found zero docs, papers, and images (code-only corpus), skip Part B entirely and go straight to Part C. AST handles code - there is nothing for semantic subagents to do.
**Fast path:** If detection found zero docs, papers, and images (code-only corpus), skip Part B entirely and go straight to Part C. AST handles code - there is nothing for semantic subagents to do. **First write an empty semantic file** so Part C's merge has its input (it reads `.graphify_semantic.json` unconditionally; without this a code-only run hits `FileNotFoundError`):
```bash
$(cat graphify-out/.graphify_python) -c "
import json
from pathlib import Path
Path('graphify-out/.graphify_semantic.json').write_text(json.dumps({'nodes':[],'edges':[],'hyperedges':[],'input_tokens':0,'output_tokens':0}), encoding='utf-8')
"
```
**MANDATORY: You MUST use the Agent tool here. Reading files yourself one-by-one is forbidden - it is 5-10x slower. If you do not use the Agent tool you are doing this wrong.**
@@ -246,7 +254,7 @@ Each subagent receives this exact prompt (substitute FILE_LIST, CHUNK_NUM, TOTAL
CHUNK_PATH must be an **absolute** path — derive it before dispatching:
```bash
PROJECT_ROOT=$(cat graphify-out/.graphify_root)
PROJECT_ROOT=$(pwd) # cwd — where Part C globs graphify-out/ (NOT .graphify_root/scan dir, #1392)
# Then for chunk N: CHUNK_PATH="${PROJECT_ROOT}/graphify-out/.graphify_chunk_0N.json"
```
@@ -388,6 +396,12 @@ 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='INPUT_PATH')
# 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:
print('ERROR: Graph is empty - extraction produced no nodes.')
print('Possible causes: all files were skipped, binary-only corpus, or extraction failed.')
raise SystemExit(1)
communities = cluster(G)
cohesion = score_all(G, communities)
tokens = {'input': extraction.get('input_tokens', 0), 'output': extraction.get('output_tokens', 0)}
@@ -397,10 +411,17 @@ labels = {cid: 'Community ' + str(cid) for cid in communities}
# Placeholder questions - regenerated with real labels in Step 5
questions = suggest_questions(G, communities, labels)
# Export FIRST and honor the #479 shrink-guard: to_json returns False (writing
# nothing) when the new graph is smaller than the existing graph.json. Only write
# GRAPH_REPORT.md + the analysis sidecar when the graph was actually written, so
# they never describe a graph that graph.json doesn't contain (#1392).
wrote = to_json(G, communities, 'graphify-out/graph.json')
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, '.', suggested_questions=questions)
Path('graphify-out/GRAPH_REPORT.md').write_text(report, encoding=\"utf-8\")
to_json(G, communities, 'graphify-out/graph.json')
analysis = {
'communities': {str(k): v for k, v in communities.items()},
'cohesion': {str(k): v for k, v in cohesion.items()},
@@ -409,10 +430,6 @@ analysis = {
'questions': questions,
}
Path('graphify-out/.graphify_analysis.json').write_text(json.dumps(analysis, indent=2, ensure_ascii=False), encoding=\"utf-8\")
if G.number_of_nodes() == 0:
print('ERROR: Graph is empty - extraction produced no nodes.')
print('Possible causes: all files were skipped, binary-only corpus, or extraction failed.')
raise SystemExit(1)
print(f'Graph: {G.number_of_nodes()} nodes, {G.number_of_edges()} edges, {len(communities)} communities')
"
```
tools/skillgen/expected/graphify__skill-kiro.md
+25 -8
View File
@@ -190,7 +190,15 @@ else:
#### Part B - Semantic extraction (parallel subagents)
**Fast path:** If detection found zero docs, papers, and images (code-only corpus), skip Part B entirely and go straight to Part C. AST handles code - there is nothing for semantic subagents to do.
**Fast path:** If detection found zero docs, papers, and images (code-only corpus), skip Part B entirely and go straight to Part C. AST handles code - there is nothing for semantic subagents to do. **First write an empty semantic file** so Part C's merge has its input (it reads `.graphify_semantic.json` unconditionally; without this a code-only run hits `FileNotFoundError`):
```bash
$(cat graphify-out/.graphify_python) -c "
import json
from pathlib import Path
Path('graphify-out/.graphify_semantic.json').write_text(json.dumps({'nodes':[],'edges':[],'hyperedges':[],'input_tokens':0,'output_tokens':0}), encoding='utf-8')
"
```
**MANDATORY: You MUST use the Agent tool here. Reading files yourself one-by-one is forbidden - it is 5-10x slower. If you do not use the Agent tool you are doing this wrong.**
@@ -246,7 +254,7 @@ Each subagent receives this exact prompt (substitute FILE_LIST, CHUNK_NUM, TOTAL
CHUNK_PATH must be an **absolute** path — derive it before dispatching:
```bash
PROJECT_ROOT=$(cat graphify-out/.graphify_root)
PROJECT_ROOT=$(pwd) # cwd — where Part C globs graphify-out/ (NOT .graphify_root/scan dir, #1392)
# Then for chunk N: CHUNK_PATH="${PROJECT_ROOT}/graphify-out/.graphify_chunk_0N.json"
```
@@ -388,6 +396,12 @@ 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='INPUT_PATH')
# 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:
print('ERROR: Graph is empty - extraction produced no nodes.')
print('Possible causes: all files were skipped, binary-only corpus, or extraction failed.')
raise SystemExit(1)
communities = cluster(G)
cohesion = score_all(G, communities)
tokens = {'input': extraction.get('input_tokens', 0), 'output': extraction.get('output_tokens', 0)}
@@ -397,10 +411,17 @@ labels = {cid: 'Community ' + str(cid) for cid in communities}
# Placeholder questions - regenerated with real labels in Step 5
questions = suggest_questions(G, communities, labels)
# Export FIRST and honor the #479 shrink-guard: to_json returns False (writing
# nothing) when the new graph is smaller than the existing graph.json. Only write
# GRAPH_REPORT.md + the analysis sidecar when the graph was actually written, so
# they never describe a graph that graph.json doesn't contain (#1392).
wrote = to_json(G, communities, 'graphify-out/graph.json')
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, '.', suggested_questions=questions)
Path('graphify-out/GRAPH_REPORT.md').write_text(report, encoding=\"utf-8\")
to_json(G, communities, 'graphify-out/graph.json')
analysis = {
'communities': {str(k): v for k, v in communities.items()},
'cohesion': {str(k): v for k, v in cohesion.items()},
@@ -409,10 +430,6 @@ analysis = {
'questions': questions,
}
Path('graphify-out/.graphify_analysis.json').write_text(json.dumps(analysis, indent=2, ensure_ascii=False), encoding=\"utf-8\")
if G.number_of_nodes() == 0:
print('ERROR: Graph is empty - extraction produced no nodes.')
print('Possible causes: all files were skipped, binary-only corpus, or extraction failed.')
raise SystemExit(1)
print(f'Graph: {G.number_of_nodes()} nodes, {G.number_of_edges()} edges, {len(communities)} communities')
"
```
tools/skillgen/expected/graphify__skill-opencode.md
+24 -7
View File
@@ -190,7 +190,15 @@ else:
#### Part B - Semantic extraction (parallel subagents)
**Fast path:** If detection found zero docs, papers, and images (code-only corpus), skip Part B entirely and go straight to Part C. AST handles code - there is nothing for semantic subagents to do.
**Fast path:** If detection found zero docs, papers, and images (code-only corpus), skip Part B entirely and go straight to Part C. AST handles code - there is nothing for semantic subagents to do. **First write an empty semantic file** so Part C's merge has its input (it reads `.graphify_semantic.json` unconditionally; without this a code-only run hits `FileNotFoundError`):
```bash
$(cat graphify-out/.graphify_python) -c "
import json
from pathlib import Path
Path('graphify-out/.graphify_semantic.json').write_text(json.dumps({'nodes':[],'edges':[],'hyperedges':[],'input_tokens':0,'output_tokens':0}), encoding='utf-8')
"
```
**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.**
@@ -380,6 +388,12 @@ 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='INPUT_PATH')
# 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:
print('ERROR: Graph is empty - extraction produced no nodes.')
print('Possible causes: all files were skipped, binary-only corpus, or extraction failed.')
raise SystemExit(1)
communities = cluster(G)
cohesion = score_all(G, communities)
tokens = {'input': extraction.get('input_tokens', 0), 'output': extraction.get('output_tokens', 0)}
@@ -389,10 +403,17 @@ labels = {cid: 'Community ' + str(cid) for cid in communities}
# Placeholder questions - regenerated with real labels in Step 5
questions = suggest_questions(G, communities, labels)
# Export FIRST and honor the #479 shrink-guard: to_json returns False (writing
# nothing) when the new graph is smaller than the existing graph.json. Only write
# GRAPH_REPORT.md + the analysis sidecar when the graph was actually written, so
# they never describe a graph that graph.json doesn't contain (#1392).
wrote = to_json(G, communities, 'graphify-out/graph.json')
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, '.', suggested_questions=questions)
Path('graphify-out/GRAPH_REPORT.md').write_text(report, encoding=\"utf-8\")
to_json(G, communities, 'graphify-out/graph.json')
analysis = {
'communities': {str(k): v for k, v in communities.items()},
'cohesion': {str(k): v for k, v in cohesion.items()},
@@ -401,10 +422,6 @@ analysis = {
'questions': questions,
}
Path('graphify-out/.graphify_analysis.json').write_text(json.dumps(analysis, indent=2, ensure_ascii=False), encoding=\"utf-8\")
if G.number_of_nodes() == 0:
print('ERROR: Graph is empty - extraction produced no nodes.')
print('Possible causes: all files were skipped, binary-only corpus, or extraction failed.')
raise SystemExit(1)
print(f'Graph: {G.number_of_nodes()} nodes, {G.number_of_edges()} edges, {len(communities)} communities')
"
```
tools/skillgen/expected/graphify__skill-pi.md
+25 -8
View File
@@ -190,7 +190,15 @@ else:
#### Part B - Semantic extraction (parallel subagents)
**Fast path:** If detection found zero docs, papers, and images (code-only corpus), skip Part B entirely and go straight to Part C. AST handles code - there is nothing for semantic subagents to do.
**Fast path:** If detection found zero docs, papers, and images (code-only corpus), skip Part B entirely and go straight to Part C. AST handles code - there is nothing for semantic subagents to do. **First write an empty semantic file** so Part C's merge has its input (it reads `.graphify_semantic.json` unconditionally; without this a code-only run hits `FileNotFoundError`):
```bash
$(cat graphify-out/.graphify_python) -c "
import json
from pathlib import Path
Path('graphify-out/.graphify_semantic.json').write_text(json.dumps({'nodes':[],'edges':[],'hyperedges':[],'input_tokens':0,'output_tokens':0}), encoding='utf-8')
"
```
**MANDATORY: You MUST use the Agent tool here. Reading files yourself one-by-one is forbidden - it is 5-10x slower. If you do not use the Agent tool you are doing this wrong.**
@@ -246,7 +254,7 @@ Each subagent receives this exact prompt (substitute FILE_LIST, CHUNK_NUM, TOTAL
CHUNK_PATH must be an **absolute** path — derive it before dispatching:
```bash
PROJECT_ROOT=$(cat graphify-out/.graphify_root)
PROJECT_ROOT=$(pwd) # cwd — where Part C globs graphify-out/ (NOT .graphify_root/scan dir, #1392)
# Then for chunk N: CHUNK_PATH="${PROJECT_ROOT}/graphify-out/.graphify_chunk_0N.json"
```
@@ -388,6 +396,12 @@ 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='INPUT_PATH')
# 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:
print('ERROR: Graph is empty - extraction produced no nodes.')
print('Possible causes: all files were skipped, binary-only corpus, or extraction failed.')
raise SystemExit(1)
communities = cluster(G)
cohesion = score_all(G, communities)
tokens = {'input': extraction.get('input_tokens', 0), 'output': extraction.get('output_tokens', 0)}
@@ -397,10 +411,17 @@ labels = {cid: 'Community ' + str(cid) for cid in communities}
# Placeholder questions - regenerated with real labels in Step 5
questions = suggest_questions(G, communities, labels)
# Export FIRST and honor the #479 shrink-guard: to_json returns False (writing
# nothing) when the new graph is smaller than the existing graph.json. Only write
# GRAPH_REPORT.md + the analysis sidecar when the graph was actually written, so
# they never describe a graph that graph.json doesn't contain (#1392).
wrote = to_json(G, communities, 'graphify-out/graph.json')
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, '.', suggested_questions=questions)
Path('graphify-out/GRAPH_REPORT.md').write_text(report, encoding=\"utf-8\")
to_json(G, communities, 'graphify-out/graph.json')
analysis = {
'communities': {str(k): v for k, v in communities.items()},
'cohesion': {str(k): v for k, v in cohesion.items()},
@@ -409,10 +430,6 @@ analysis = {
'questions': questions,
}
Path('graphify-out/.graphify_analysis.json').write_text(json.dumps(analysis, indent=2, ensure_ascii=False), encoding=\"utf-8\")
if G.number_of_nodes() == 0:
print('ERROR: Graph is empty - extraction produced no nodes.')
print('Possible causes: all files were skipped, binary-only corpus, or extraction failed.')
raise SystemExit(1)
print(f'Graph: {G.number_of_nodes()} nodes, {G.number_of_edges()} edges, {len(communities)} communities')
"
```
tools/skillgen/expected/graphify__skill-trae.md
+25 -8
View File
@@ -190,7 +190,15 @@ else:
#### Part B - Semantic extraction (parallel subagents)
**Fast path:** If detection found zero docs, papers, and images (code-only corpus), skip Part B entirely and go straight to Part C. AST handles code - there is nothing for semantic subagents to do.
**Fast path:** If detection found zero docs, papers, and images (code-only corpus), skip Part B entirely and go straight to Part C. AST handles code - there is nothing for semantic subagents to do. **First write an empty semantic file** so Part C's merge has its input (it reads `.graphify_semantic.json` unconditionally; without this a code-only run hits `FileNotFoundError`):
```bash
$(cat graphify-out/.graphify_python) -c "
import json
from pathlib import Path
Path('graphify-out/.graphify_semantic.json').write_text(json.dumps({'nodes':[],'edges':[],'hyperedges':[],'input_tokens':0,'output_tokens':0}), encoding='utf-8')
"
```
**MANDATORY: You MUST use the Agent tool here. Reading files yourself one-by-one is forbidden - it is 5-10x slower. If you do not use the Agent tool you are doing this wrong.**
@@ -244,7 +252,7 @@ Each subagent writes its result to its own `graphify-out/.graphify_chunk_NN.json
CHUNK_PATH must be an **absolute** path — derive it before dispatching:
```bash
PROJECT_ROOT=$(cat graphify-out/.graphify_root)
PROJECT_ROOT=$(pwd) # cwd — where Part C globs graphify-out/ (NOT .graphify_root/scan dir, #1392)
# Then for chunk N: CHUNK_PATH="${PROJECT_ROOT}/graphify-out/.graphify_chunk_0N.json"
```
@@ -386,6 +394,12 @@ 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='INPUT_PATH')
# 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:
print('ERROR: Graph is empty - extraction produced no nodes.')
print('Possible causes: all files were skipped, binary-only corpus, or extraction failed.')
raise SystemExit(1)
communities = cluster(G)
cohesion = score_all(G, communities)
tokens = {'input': extraction.get('input_tokens', 0), 'output': extraction.get('output_tokens', 0)}
@@ -395,10 +409,17 @@ labels = {cid: 'Community ' + str(cid) for cid in communities}
# Placeholder questions - regenerated with real labels in Step 5
questions = suggest_questions(G, communities, labels)
# Export FIRST and honor the #479 shrink-guard: to_json returns False (writing
# nothing) when the new graph is smaller than the existing graph.json. Only write
# GRAPH_REPORT.md + the analysis sidecar when the graph was actually written, so
# they never describe a graph that graph.json doesn't contain (#1392).
wrote = to_json(G, communities, 'graphify-out/graph.json')
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, '.', suggested_questions=questions)
Path('graphify-out/GRAPH_REPORT.md').write_text(report, encoding=\"utf-8\")
to_json(G, communities, 'graphify-out/graph.json')
analysis = {
'communities': {str(k): v for k, v in communities.items()},
'cohesion': {str(k): v for k, v in cohesion.items()},
@@ -407,10 +428,6 @@ analysis = {
'questions': questions,
}
Path('graphify-out/.graphify_analysis.json').write_text(json.dumps(analysis, indent=2, ensure_ascii=False), encoding=\"utf-8\")
if G.number_of_nodes() == 0:
print('ERROR: Graph is empty - extraction produced no nodes.')
print('Possible causes: all files were skipped, binary-only corpus, or extraction failed.')
raise SystemExit(1)
print(f'Graph: {G.number_of_nodes()} nodes, {G.number_of_edges()} edges, {len(communities)} communities')
"
```
tools/skillgen/expected/graphify__skill-vscode.md
+25 -8
View File
@@ -190,7 +190,15 @@ else:
#### Part B - Semantic extraction (parallel subagents)
**Fast path:** If detection found zero docs, papers, and images (code-only corpus), skip Part B entirely and go straight to Part C. AST handles code - there is nothing for semantic subagents to do.
**Fast path:** If detection found zero docs, papers, and images (code-only corpus), skip Part B entirely and go straight to Part C. AST handles code - there is nothing for semantic subagents to do. **First write an empty semantic file** so Part C's merge has its input (it reads `.graphify_semantic.json` unconditionally; without this a code-only run hits `FileNotFoundError`):
```bash
$(cat graphify-out/.graphify_python) -c "
import json
from pathlib import Path
Path('graphify-out/.graphify_semantic.json').write_text(json.dumps({'nodes':[],'edges':[],'hyperedges':[],'input_tokens':0,'output_tokens':0}), encoding='utf-8')
"
```
**MANDATORY: You MUST use the Agent tool here. Reading files yourself one-by-one is forbidden - it is 5-10x slower. If you do not use the Agent tool you are doing this wrong.**
@@ -238,7 +246,7 @@ For each chunk of uncached files (20-25 per chunk), give a subagent the extracti
```bash
# After pasting a subagent's JSON for chunk N, save it (replace N and PASTED_JSON):
PROJECT_ROOT=$(cat graphify-out/.graphify_root)
PROJECT_ROOT=$(pwd) # cwd — where Part C globs graphify-out/ (NOT .graphify_root/scan dir, #1392)
cat > "${PROJECT_ROOT}/graphify-out/.graphify_chunk_0N.json" <<'CHUNK_JSON'
PASTED_JSON
CHUNK_JSON
@@ -384,6 +392,12 @@ 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='INPUT_PATH')
# 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:
print('ERROR: Graph is empty - extraction produced no nodes.')
print('Possible causes: all files were skipped, binary-only corpus, or extraction failed.')
raise SystemExit(1)
communities = cluster(G)
cohesion = score_all(G, communities)
tokens = {'input': extraction.get('input_tokens', 0), 'output': extraction.get('output_tokens', 0)}
@@ -393,10 +407,17 @@ labels = {cid: 'Community ' + str(cid) for cid in communities}
# Placeholder questions - regenerated with real labels in Step 5
questions = suggest_questions(G, communities, labels)
# Export FIRST and honor the #479 shrink-guard: to_json returns False (writing
# nothing) when the new graph is smaller than the existing graph.json. Only write
# GRAPH_REPORT.md + the analysis sidecar when the graph was actually written, so
# they never describe a graph that graph.json doesn't contain (#1392).
wrote = to_json(G, communities, 'graphify-out/graph.json')
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, '.', suggested_questions=questions)
Path('graphify-out/GRAPH_REPORT.md').write_text(report, encoding=\"utf-8\")
to_json(G, communities, 'graphify-out/graph.json')
analysis = {
'communities': {str(k): v for k, v in communities.items()},
'cohesion': {str(k): v for k, v in cohesion.items()},
@@ -405,10 +426,6 @@ analysis = {
'questions': questions,
}
Path('graphify-out/.graphify_analysis.json').write_text(json.dumps(analysis, indent=2, ensure_ascii=False), encoding=\"utf-8\")
if G.number_of_nodes() == 0:
print('ERROR: Graph is empty - extraction produced no nodes.')
print('Possible causes: all files were skipped, binary-only corpus, or extraction failed.')
raise SystemExit(1)
print(f'Graph: {G.number_of_nodes()} nodes, {G.number_of_edges()} edges, {len(communities)} communities')
"
```
tools/skillgen/expected/graphify__skill-windows.md
+25 -8
View File
@@ -212,7 +212,15 @@ else:
#### Part B - Semantic extraction (parallel subagents)
**Fast path:** If detection found zero docs, papers, and images (code-only corpus), skip Part B entirely and go straight to Part C. AST handles code - there is nothing for semantic subagents to do.
**Fast path:** If detection found zero docs, papers, and images (code-only corpus), skip Part B entirely and go straight to Part C. AST handles code - there is nothing for semantic subagents to do. **First write an empty semantic file** so Part C's merge has its input (it reads `.graphify_semantic.json` unconditionally; without this a code-only run hits `FileNotFoundError`):
```bash
$(cat graphify-out/.graphify_python) -c "
import json
from pathlib import Path
Path('graphify-out/.graphify_semantic.json').write_text(json.dumps({'nodes':[],'edges':[],'hyperedges':[],'input_tokens':0,'output_tokens':0}), encoding='utf-8')
"
```
**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.**
@@ -268,7 +276,7 @@ Each subagent receives this exact prompt (substitute FILE_LIST, CHUNK_NUM, TOTAL
CHUNK_PATH must be an **absolute** path — derive it before dispatching:
```powershell
$PROJECT_ROOT = Get-Content graphify-out\.graphify_root
$PROJECT_ROOT = (Get-Location).Path # cwd — where Part C globs graphify-out\ (NOT .graphify_root/scan dir, #1392)
# Then for chunk N: $CHUNK_PATH = Join-Path $PROJECT_ROOT "graphify-out\.graphify_chunk_0N.json"
```
@@ -410,6 +418,12 @@ 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='INPUT_PATH')
# 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:
print('ERROR: Graph is empty - extraction produced no nodes.')
print('Possible causes: all files were skipped, binary-only corpus, or extraction failed.')
raise SystemExit(1)
communities = cluster(G)
cohesion = score_all(G, communities)
tokens = {'input': extraction.get('input_tokens', 0), 'output': extraction.get('output_tokens', 0)}
@@ -419,10 +433,17 @@ labels = {cid: 'Community ' + str(cid) for cid in communities}
# Placeholder questions - regenerated with real labels in Step 5
questions = suggest_questions(G, communities, labels)
# Export FIRST and honor the #479 shrink-guard: to_json returns False (writing
# nothing) when the new graph is smaller than the existing graph.json. Only write
# GRAPH_REPORT.md + the analysis sidecar when the graph was actually written, so
# they never describe a graph that graph.json doesn't contain (#1392).
wrote = to_json(G, communities, 'graphify-out/graph.json')
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, '.', suggested_questions=questions)
Path('graphify-out/GRAPH_REPORT.md').write_text(report, encoding=\"utf-8\")
to_json(G, communities, 'graphify-out/graph.json')
analysis = {
'communities': {str(k): v for k, v in communities.items()},
'cohesion': {str(k): v for k, v in cohesion.items()},
@@ -431,10 +452,6 @@ analysis = {
'questions': questions,
}
Path('graphify-out/.graphify_analysis.json').write_text(json.dumps(analysis, indent=2, ensure_ascii=False), encoding=\"utf-8\")
if G.number_of_nodes() == 0:
print('ERROR: Graph is empty - extraction produced no nodes.')
print('Possible causes: all files were skipped, binary-only corpus, or extraction failed.')
raise SystemExit(1)
print(f'Graph: {G.number_of_nodes()} nodes, {G.number_of_edges()} edges, {len(communities)} communities')
"
```
tools/skillgen/expected/graphify__skill.md
+25 -8
View File
@@ -190,7 +190,15 @@ else:
#### Part B - Semantic extraction (parallel subagents)
**Fast path:** If detection found zero docs, papers, and images (code-only corpus), skip Part B entirely and go straight to Part C. AST handles code - there is nothing for semantic subagents to do.
**Fast path:** If detection found zero docs, papers, and images (code-only corpus), skip Part B entirely and go straight to Part C. AST handles code - there is nothing for semantic subagents to do. **First write an empty semantic file** so Part C's merge has its input (it reads `.graphify_semantic.json` unconditionally; without this a code-only run hits `FileNotFoundError`):
```bash
$(cat graphify-out/.graphify_python) -c "
import json
from pathlib import Path
Path('graphify-out/.graphify_semantic.json').write_text(json.dumps({'nodes':[],'edges':[],'hyperedges':[],'input_tokens':0,'output_tokens':0}), encoding='utf-8')
"
```
**MANDATORY: You MUST use the Agent tool here. Reading files yourself one-by-one is forbidden - it is 5-10x slower. If you do not use the Agent tool you are doing this wrong.**
@@ -246,7 +254,7 @@ Each subagent receives this exact prompt (substitute FILE_LIST, CHUNK_NUM, TOTAL
CHUNK_PATH must be an **absolute** path — derive it before dispatching:
```bash
PROJECT_ROOT=$(cat graphify-out/.graphify_root)
PROJECT_ROOT=$(pwd) # cwd — where Part C globs graphify-out/ (NOT .graphify_root/scan dir, #1392)
# Then for chunk N: CHUNK_PATH="${PROJECT_ROOT}/graphify-out/.graphify_chunk_0N.json"
```
@@ -388,6 +396,12 @@ 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='INPUT_PATH')
# 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:
print('ERROR: Graph is empty - extraction produced no nodes.')
print('Possible causes: all files were skipped, binary-only corpus, or extraction failed.')
raise SystemExit(1)
communities = cluster(G)
cohesion = score_all(G, communities)
tokens = {'input': extraction.get('input_tokens', 0), 'output': extraction.get('output_tokens', 0)}
@@ -397,10 +411,17 @@ labels = {cid: 'Community ' + str(cid) for cid in communities}
# Placeholder questions - regenerated with real labels in Step 5
questions = suggest_questions(G, communities, labels)
# Export FIRST and honor the #479 shrink-guard: to_json returns False (writing
# nothing) when the new graph is smaller than the existing graph.json. Only write
# GRAPH_REPORT.md + the analysis sidecar when the graph was actually written, so
# they never describe a graph that graph.json doesn't contain (#1392).
wrote = to_json(G, communities, 'graphify-out/graph.json')
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, '.', suggested_questions=questions)
Path('graphify-out/GRAPH_REPORT.md').write_text(report, encoding=\"utf-8\")
to_json(G, communities, 'graphify-out/graph.json')
analysis = {
'communities': {str(k): v for k, v in communities.items()},
'cohesion': {str(k): v for k, v in cohesion.items()},
@@ -409,10 +430,6 @@ analysis = {
'questions': questions,
}
Path('graphify-out/.graphify_analysis.json').write_text(json.dumps(analysis, indent=2, ensure_ascii=False), encoding=\"utf-8\")
if G.number_of_nodes() == 0:
print('ERROR: Graph is empty - extraction produced no nodes.')
print('Possible causes: all files were skipped, binary-only corpus, or extraction failed.')
raise SystemExit(1)
print(f'Graph: {G.number_of_nodes()} nodes, {G.number_of_edges()} edges, {len(communities)} communities')
"
```
tools/skillgen/expected/graphify__skills__amp__references__update.md
+1 -1
View File
@@ -182,4 +182,4 @@ 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).
`graphify cluster-only .` is **self-contained**: it re-clusters, names communities, and regenerates `GRAPH_REPORT.md`, `graph.json`, and `graph.html` from the existing graph. **Do not re-run Steps 5–9** — they read intermediate files (`.graphify_extract.json`, `.graphify_detect.json`, `.graphify_analysis.json`) that a prior build's cleanup (Step 9) already deleted, so they raise `FileNotFoundError` (#1392). When it finishes, present the refreshed `GRAPH_REPORT.md` summary as usual.
tools/skillgen/expected/graphify__skills__claude__references__update.md
+1 -1
View File
@@ -182,4 +182,4 @@ 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).
`graphify cluster-only .` is **self-contained**: it re-clusters, names communities, and regenerates `GRAPH_REPORT.md`, `graph.json`, and `graph.html` from the existing graph. **Do not re-run Steps 5–9** — they read intermediate files (`.graphify_extract.json`, `.graphify_detect.json`, `.graphify_analysis.json`) that a prior build's cleanup (Step 9) already deleted, so they raise `FileNotFoundError` (#1392). When it finishes, present the refreshed `GRAPH_REPORT.md` summary as usual.
tools/skillgen/expected/graphify__skills__claw__references__update.md
+1 -1
View File
@@ -182,4 +182,4 @@ 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).
`graphify cluster-only .` is **self-contained**: it re-clusters, names communities, and regenerates `GRAPH_REPORT.md`, `graph.json`, and `graph.html` from the existing graph. **Do not re-run Steps 5–9** — they read intermediate files (`.graphify_extract.json`, `.graphify_detect.json`, `.graphify_analysis.json`) that a prior build's cleanup (Step 9) already deleted, so they raise `FileNotFoundError` (#1392). When it finishes, present the refreshed `GRAPH_REPORT.md` summary as usual.
tools/skillgen/expected/graphify__skills__codex__references__update.md
+1 -1
View File
@@ -182,4 +182,4 @@ 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).
`graphify cluster-only .` is **self-contained**: it re-clusters, names communities, and regenerates `GRAPH_REPORT.md`, `graph.json`, and `graph.html` from the existing graph. **Do not re-run Steps 5–9** — they read intermediate files (`.graphify_extract.json`, `.graphify_detect.json`, `.graphify_analysis.json`) that a prior build's cleanup (Step 9) already deleted, so they raise `FileNotFoundError` (#1392). When it finishes, present the refreshed `GRAPH_REPORT.md` summary as usual.
tools/skillgen/expected/graphify__skills__copilot__references__update.md
+1 -1
View File
@@ -182,4 +182,4 @@ 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).
`graphify cluster-only .` is **self-contained**: it re-clusters, names communities, and regenerates `GRAPH_REPORT.md`, `graph.json`, and `graph.html` from the existing graph. **Do not re-run Steps 5–9** — they read intermediate files (`.graphify_extract.json`, `.graphify_detect.json`, `.graphify_analysis.json`) that a prior build's cleanup (Step 9) already deleted, so they raise `FileNotFoundError` (#1392). When it finishes, present the refreshed `GRAPH_REPORT.md` summary as usual.
tools/skillgen/expected/graphify__skills__droid__references__update.md
+1 -1
View File
@@ -182,4 +182,4 @@ 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).
`graphify cluster-only .` is **self-contained**: it re-clusters, names communities, and regenerates `GRAPH_REPORT.md`, `graph.json`, and `graph.html` from the existing graph. **Do not re-run Steps 5–9** — they read intermediate files (`.graphify_extract.json`, `.graphify_detect.json`, `.graphify_analysis.json`) that a prior build's cleanup (Step 9) already deleted, so they raise `FileNotFoundError` (#1392). When it finishes, present the refreshed `GRAPH_REPORT.md` summary as usual.
tools/skillgen/expected/graphify__skills__kilo__references__update.md
+1 -1
View File
@@ -182,4 +182,4 @@ 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).
`graphify cluster-only .` is **self-contained**: it re-clusters, names communities, and regenerates `GRAPH_REPORT.md`, `graph.json`, and `graph.html` from the existing graph. **Do not re-run Steps 5–9** — they read intermediate files (`.graphify_extract.json`, `.graphify_detect.json`, `.graphify_analysis.json`) that a prior build's cleanup (Step 9) already deleted, so they raise `FileNotFoundError` (#1392). When it finishes, present the refreshed `GRAPH_REPORT.md` summary as usual.
tools/skillgen/expected/graphify__skills__kiro__references__update.md
+1 -1
View File
@@ -182,4 +182,4 @@ 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).
`graphify cluster-only .` is **self-contained**: it re-clusters, names communities, and regenerates `GRAPH_REPORT.md`, `graph.json`, and `graph.html` from the existing graph. **Do not re-run Steps 5–9** — they read intermediate files (`.graphify_extract.json`, `.graphify_detect.json`, `.graphify_analysis.json`) that a prior build's cleanup (Step 9) already deleted, so they raise `FileNotFoundError` (#1392). When it finishes, present the refreshed `GRAPH_REPORT.md` summary as usual.
tools/skillgen/expected/graphify__skills__opencode__references__update.md
+1 -1
View File
@@ -182,4 +182,4 @@ 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).
`graphify cluster-only .` is **self-contained**: it re-clusters, names communities, and regenerates `GRAPH_REPORT.md`, `graph.json`, and `graph.html` from the existing graph. **Do not re-run Steps 5–9** — they read intermediate files (`.graphify_extract.json`, `.graphify_detect.json`, `.graphify_analysis.json`) that a prior build's cleanup (Step 9) already deleted, so they raise `FileNotFoundError` (#1392). When it finishes, present the refreshed `GRAPH_REPORT.md` summary as usual.
tools/skillgen/expected/graphify__skills__pi__references__update.md
+1 -1
View File
@@ -182,4 +182,4 @@ 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).
`graphify cluster-only .` is **self-contained**: it re-clusters, names communities, and regenerates `GRAPH_REPORT.md`, `graph.json`, and `graph.html` from the existing graph. **Do not re-run Steps 5–9** — they read intermediate files (`.graphify_extract.json`, `.graphify_detect.json`, `.graphify_analysis.json`) that a prior build's cleanup (Step 9) already deleted, so they raise `FileNotFoundError` (#1392). When it finishes, present the refreshed `GRAPH_REPORT.md` summary as usual.
tools/skillgen/expected/graphify__skills__trae__references__update.md
+1 -1
View File
@@ -182,4 +182,4 @@ 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).
`graphify cluster-only .` is **self-contained**: it re-clusters, names communities, and regenerates `GRAPH_REPORT.md`, `graph.json`, and `graph.html` from the existing graph. **Do not re-run Steps 5–9** — they read intermediate files (`.graphify_extract.json`, `.graphify_detect.json`, `.graphify_analysis.json`) that a prior build's cleanup (Step 9) already deleted, so they raise `FileNotFoundError` (#1392). When it finishes, present the refreshed `GRAPH_REPORT.md` summary as usual.
tools/skillgen/expected/graphify__skills__vscode__references__update.md
+1 -1
View File
@@ -182,4 +182,4 @@ 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).
`graphify cluster-only .` is **self-contained**: it re-clusters, names communities, and regenerates `GRAPH_REPORT.md`, `graph.json`, and `graph.html` from the existing graph. **Do not re-run Steps 5–9** — they read intermediate files (`.graphify_extract.json`, `.graphify_detect.json`, `.graphify_analysis.json`) that a prior build's cleanup (Step 9) already deleted, so they raise `FileNotFoundError` (#1392). When it finishes, present the refreshed `GRAPH_REPORT.md` summary as usual.
tools/skillgen/expected/graphify__skills__windows__references__update.md
+1 -1
View File
@@ -182,4 +182,4 @@ 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).
`graphify cluster-only .` is **self-contained**: it re-clusters, names communities, and regenerates `GRAPH_REPORT.md`, `graph.json`, and `graph.html` from the existing graph. **Do not re-run Steps 5–9** — they read intermediate files (`.graphify_extract.json`, `.graphify_detect.json`, `.graphify_analysis.json`) that a prior build's cleanup (Step 9) already deleted, so they raise `FileNotFoundError` (#1392). When it finishes, present the refreshed `GRAPH_REPORT.md` summary as usual.
tools/skillgen/fragments/core/core.md
+24 -7
View File
@@ -149,7 +149,15 @@ else:
#### Part B - Semantic extraction (parallel subagents)
**Fast path:** If detection found zero docs, papers, and images (code-only corpus), skip Part B entirely and go straight to Part C. AST handles code - there is nothing for semantic subagents to do.
**Fast path:** If detection found zero docs, papers, and images (code-only corpus), skip Part B entirely and go straight to Part C. AST handles code - there is nothing for semantic subagents to do. **First write an empty semantic file** so Part C's merge has its input (it reads `.graphify_semantic.json` unconditionally; without this a code-only run hits `FileNotFoundError`):
```bash
$(cat graphify-out/.graphify_python) -c "
import json
from pathlib import Path
Path('graphify-out/.graphify_semantic.json').write_text(json.dumps({'nodes':[],'edges':[],'hyperedges':[],'input_tokens':0,'output_tokens':0}), encoding='utf-8')
"
```
**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.**
@@ -323,6 +331,12 @@ 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='INPUT_PATH')
# 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:
print('ERROR: Graph is empty - extraction produced no nodes.')
print('Possible causes: all files were skipped, binary-only corpus, or extraction failed.')
raise SystemExit(1)
communities = cluster(G)
cohesion = score_all(G, communities)
tokens = {'input': extraction.get('input_tokens', 0), 'output': extraction.get('output_tokens', 0)}
@@ -332,10 +346,17 @@ labels = {cid: 'Community ' + str(cid) for cid in communities}
# Placeholder questions - regenerated with real labels in Step 5
questions = suggest_questions(G, communities, labels)
# Export FIRST and honor the #479 shrink-guard: to_json returns False (writing
# nothing) when the new graph is smaller than the existing graph.json. Only write
# GRAPH_REPORT.md + the analysis sidecar when the graph was actually written, so
# they never describe a graph that graph.json doesn't contain (#1392).
wrote = to_json(G, communities, 'graphify-out/graph.json')
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, '.', suggested_questions=questions)
Path('graphify-out/GRAPH_REPORT.md').write_text(report, encoding=\"utf-8\")
to_json(G, communities, 'graphify-out/graph.json')
analysis = {
'communities': {str(k): v for k, v in communities.items()},
'cohesion': {str(k): v for k, v in cohesion.items()},
@@ -344,10 +365,6 @@ analysis = {
'questions': questions,
}
Path('graphify-out/.graphify_analysis.json').write_text(json.dumps(analysis, indent=2, ensure_ascii=False), encoding=\"utf-8\")
if G.number_of_nodes() == 0:
print('ERROR: Graph is empty - extraction produced no nodes.')
print('Possible causes: all files were skipped, binary-only corpus, or extraction failed.')
raise SystemExit(1)
print(f'Graph: {G.number_of_nodes()} nodes, {G.number_of_edges()} edges, {len(communities)} communities')
"
```
tools/skillgen/fragments/dispatch/agent-tool-disk-powershell.md
+1 -1
View File
@@ -16,7 +16,7 @@ Each subagent receives this exact prompt (substitute FILE_LIST, CHUNK_NUM, TOTAL
CHUNK_PATH must be an **absolute** path — derive it before dispatching:
```powershell
$PROJECT_ROOT = Get-Content graphify-out\.graphify_root
$PROJECT_ROOT = (Get-Location).Path # cwd — where Part C globs graphify-out\ (NOT .graphify_root/scan dir, #1392)
# Then for chunk N: $CHUNK_PATH = Join-Path $PROJECT_ROOT "graphify-out\.graphify_chunk_0N.json"
```
tools/skillgen/fragments/dispatch/agent-tool-disk.md
+1 -1
View File
@@ -16,7 +16,7 @@ Each subagent receives this exact prompt (substitute FILE_LIST, CHUNK_NUM, TOTAL
CHUNK_PATH must be an **absolute** path — derive it before dispatching:
```bash
PROJECT_ROOT=$(cat graphify-out/.graphify_root)
PROJECT_ROOT=$(pwd) # cwd — where Part C globs graphify-out/ (NOT .graphify_root/scan dir, #1392)
# Then for chunk N: CHUNK_PATH="${PROJECT_ROOT}/graphify-out/.graphify_chunk_0N.json"
```
tools/skillgen/fragments/dispatch/manual-paste.md
+1 -1
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@@ -8,7 +8,7 @@ For each chunk of uncached files (20-25 per chunk), give a subagent the extracti
```bash
# After pasting a subagent's JSON for chunk N, save it (replace N and PASTED_JSON):
PROJECT_ROOT=$(cat graphify-out/.graphify_root)
PROJECT_ROOT=$(pwd) # cwd — where Part C globs graphify-out/ (NOT .graphify_root/scan dir, #1392)
cat > "${PROJECT_ROOT}/graphify-out/.graphify_chunk_0N.json" <<'CHUNK_JSON'
PASTED_JSON
CHUNK_JSON
tools/skillgen/fragments/dispatch/task-tool-disk-trae.md
+1 -1
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@@ -14,7 +14,7 @@ Each subagent writes its result to its own `graphify-out/.graphify_chunk_NN.json
CHUNK_PATH must be an **absolute** path — derive it before dispatching:
```bash
PROJECT_ROOT=$(cat graphify-out/.graphify_root)
PROJECT_ROOT=$(pwd) # cwd — where Part C globs graphify-out/ (NOT .graphify_root/scan dir, #1392)
# Then for chunk N: CHUNK_PATH="${PROJECT_ROOT}/graphify-out/.graphify_chunk_0N.json"
```
tools/skillgen/fragments/dispatch/task-tool-disk.md
+1 -1
View File
@@ -13,7 +13,7 @@ Each subagent writes its result to its own `graphify-out/.graphify_chunk_NN.json
CHUNK_PATH must be an **absolute** path — derive it before dispatching:
```bash
PROJECT_ROOT=$(cat graphify-out/.graphify_root)
PROJECT_ROOT=$(pwd) # cwd — where Part C globs graphify-out/ (NOT .graphify_root/scan dir, #1392)
# Then for chunk N: CHUNK_PATH="${PROJECT_ROOT}/graphify-out/.graphify_chunk_0N.json"
```
tools/skillgen/fragments/references/shared/update.md
+1 -1
View File
@@ -182,4 +182,4 @@ 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).
`graphify cluster-only .` is **self-contained**: it re-clusters, names communities, and regenerates `GRAPH_REPORT.md`, `graph.json`, and `graph.html` from the existing graph. **Do not re-run Steps 5–9** — they read intermediate files (`.graphify_extract.json`, `.graphify_detect.json`, `.graphify_analysis.json`) that a prior build's cleanup (Step 9) already deleted, so they raise `FileNotFoundError` (#1392). When it finishes, present the refreshed `GRAPH_REPORT.md` summary as usual.