fix(skills): do the temp-file cleanup in Python, not shell rm/find (#2790)

graphify/skill-agents.md

@@ -348,10 +348,11 @@ merged = {
     'output_tokens': new.get('output_tokens', 0),
 }
 Path('graphify-out/.graphify_semantic.json').write_text(json.dumps(merged, indent=2, ensure_ascii=False), encoding=\"utf-8\")
+for _tmp in ['.graphify_cached.json', '.graphify_uncached.txt', '.graphify_semantic_new.json']:
+    Path('graphify-out', _tmp).unlink(missing_ok=True)
 print(f'Extraction complete - {len(deduped)} nodes, {len(all_edges)} edges ({len(cached[\"nodes\"])} from cache, {len(new.get(\"nodes\",[]))} new)')
 "
 ```
-Clean up temp files: `rm -f graphify-out/.graphify_cached.json graphify-out/.graphify_uncached.txt graphify-out/.graphify_semantic_new.json`
 
 #### Part C - Merge AST + semantic into final extraction
 
@@ -614,10 +615,13 @@ cost_path.write_text(json.dumps(cost, indent=2, ensure_ascii=False), encoding=\"
 
 print(f'This run: {input_tok:,} input tokens, {output_tok:,} output tokens')
 print(f'All time: {cost[\"total_input_tokens\"]:,} input, {cost[\"total_output_tokens\"]:,} output ({len(cost[\"runs\"])} runs)')
+
+_out = Path('graphify-out')
+for _tmp in ['.graphify_detect.json', '.graphify_extract.json', '.graphify_ast.json', '.graphify_semantic.json', '.graphify_analysis.json', '.needs_update']:
+    (_out / _tmp).unlink(missing_ok=True)
+for _chunk in _out.glob('.graphify_chunk_*.json'):
+    _chunk.unlink(missing_ok=True)
 "
-rm -f graphify-out/.graphify_detect.json graphify-out/.graphify_extract.json graphify-out/.graphify_ast.json graphify-out/.graphify_semantic.json graphify-out/.graphify_analysis.json
-find graphify-out -maxdepth 1 -name '.graphify_chunk_*.json' -delete 2>/dev/null
-rm -f graphify-out/.needs_update 2>/dev/null || true
 ```
 
 Replace INPUT_PATH with the actual path (same value used in Steps 4-5) so the manifest is relativized to the scan root.

graphify/skill-aider.md

@@ -346,10 +346,11 @@ merged = {
     'output_tokens': new.get('output_tokens', 0),
 }
 Path('.graphify_semantic.json').write_text(json.dumps(merged, indent=2))
+for _tmp in ['.graphify_cached.json', '.graphify_uncached.txt', '.graphify_semantic_new.json']:
+    Path(_tmp).unlink(missing_ok=True)
 print(f'Extraction complete - {len(deduped)} nodes, {len(all_edges)} edges ({len(cached[\"nodes\"])} from cache, {len(new.get(\"nodes\",[]))} new)')
 "
 ```
-Clean up temp files: `rm -f .graphify_cached.json .graphify_uncached.txt .graphify_semantic_new.json`
 
 #### Part C - Merge AST + semantic into final extraction
 
@@ -718,9 +719,13 @@ cost_path.write_text(json.dumps(cost, indent=2))
 
 print(f'This run: {input_tok:,} input tokens, {output_tok:,} output tokens')
 print(f'All time: {cost[\"total_input_tokens\"]:,} input, {cost[\"total_output_tokens\"]:,} output ({len(cost[\"runs\"])} runs)')
+
+for _tmp in ['.graphify_detect.json', '.graphify_extract.json', '.graphify_ast.json', '.graphify_semantic.json', '.graphify_analysis.json', '.graphify_labels.json']:
+    Path(_tmp).unlink(missing_ok=True)
+for _chunk in Path('.').glob('.graphify_chunk_*.json'):
+    _chunk.unlink(missing_ok=True)
+Path('graphify-out/.needs_update').unlink(missing_ok=True)
 "
-rm -f .graphify_detect.json .graphify_extract.json .graphify_ast.json .graphify_semantic.json .graphify_analysis.json .graphify_labels.json; find . -maxdepth 1 -name '.graphify_chunk_*.json' -delete 2>/dev/null
-rm -f graphify-out/.needs_update 2>/dev/null || true
 ```
 
 Tell the user (omit the obsidian line unless --obsidian was given):
@@ -865,11 +870,11 @@ if old_data:
         print('New nodes:', ', '.join(n['label'] for n in diff['new_nodes'][:5]))
     if diff['new_edges']:
         print('New edges:', len(diff['new_edges']))
+Path('.graphify_old.json').unlink(missing_ok=True)
 "
 ```
 
 Before the merge step, save the old graph: `cp graphify-out/graph.json .graphify_old.json`
-Clean up after: `rm -f .graphify_old.json`
 
 ---
 

graphify/skill-amp.md

@@ -348,10 +348,11 @@ merged = {
     'output_tokens': new.get('output_tokens', 0),
 }
 Path('graphify-out/.graphify_semantic.json').write_text(json.dumps(merged, indent=2, ensure_ascii=False), encoding=\"utf-8\")
+for _tmp in ['.graphify_cached.json', '.graphify_uncached.txt', '.graphify_semantic_new.json']:
+    Path('graphify-out', _tmp).unlink(missing_ok=True)
 print(f'Extraction complete - {len(deduped)} nodes, {len(all_edges)} edges ({len(cached[\"nodes\"])} from cache, {len(new.get(\"nodes\",[]))} new)')
 "
 ```
-Clean up temp files: `rm -f graphify-out/.graphify_cached.json graphify-out/.graphify_uncached.txt graphify-out/.graphify_semantic_new.json`
 
 #### Part C - Merge AST + semantic into final extraction
 
@@ -614,10 +615,13 @@ cost_path.write_text(json.dumps(cost, indent=2, ensure_ascii=False), encoding=\"
 
 print(f'This run: {input_tok:,} input tokens, {output_tok:,} output tokens')
 print(f'All time: {cost[\"total_input_tokens\"]:,} input, {cost[\"total_output_tokens\"]:,} output ({len(cost[\"runs\"])} runs)')
+
+_out = Path('graphify-out')
+for _tmp in ['.graphify_detect.json', '.graphify_extract.json', '.graphify_ast.json', '.graphify_semantic.json', '.graphify_analysis.json', '.needs_update']:
+    (_out / _tmp).unlink(missing_ok=True)
+for _chunk in _out.glob('.graphify_chunk_*.json'):
+    _chunk.unlink(missing_ok=True)
 "
-rm -f graphify-out/.graphify_detect.json graphify-out/.graphify_extract.json graphify-out/.graphify_ast.json graphify-out/.graphify_semantic.json graphify-out/.graphify_analysis.json
-find graphify-out -maxdepth 1 -name '.graphify_chunk_*.json' -delete 2>/dev/null
-rm -f graphify-out/.needs_update 2>/dev/null || true
 ```
 
 Replace INPUT_PATH with the actual path (same value used in Steps 4-5) so the manifest is relativized to the scan root.

graphify/skill-claw.md

@@ -351,10 +351,11 @@ merged = {
     'output_tokens': new.get('output_tokens', 0),
 }
 Path('graphify-out/.graphify_semantic.json').write_text(json.dumps(merged, indent=2, ensure_ascii=False), encoding=\"utf-8\")
+for _tmp in ['.graphify_cached.json', '.graphify_uncached.txt', '.graphify_semantic_new.json']:
+    Path('graphify-out', _tmp).unlink(missing_ok=True)
 print(f'Extraction complete - {len(deduped)} nodes, {len(all_edges)} edges ({len(cached[\"nodes\"])} from cache, {len(new.get(\"nodes\",[]))} new)')
 "
 ```
-Clean up temp files: `rm -f graphify-out/.graphify_cached.json graphify-out/.graphify_uncached.txt graphify-out/.graphify_semantic_new.json`
 
 #### Part C - Merge AST + semantic into final extraction
 
@@ -617,10 +618,13 @@ cost_path.write_text(json.dumps(cost, indent=2, ensure_ascii=False), encoding=\"
 
 print(f'This run: {input_tok:,} input tokens, {output_tok:,} output tokens')
 print(f'All time: {cost[\"total_input_tokens\"]:,} input, {cost[\"total_output_tokens\"]:,} output ({len(cost[\"runs\"])} runs)')
+
+_out = Path('graphify-out')
+for _tmp in ['.graphify_detect.json', '.graphify_extract.json', '.graphify_ast.json', '.graphify_semantic.json', '.graphify_analysis.json', '.needs_update']:
+    (_out / _tmp).unlink(missing_ok=True)
+for _chunk in _out.glob('.graphify_chunk_*.json'):
+    _chunk.unlink(missing_ok=True)
 "
-rm -f graphify-out/.graphify_detect.json graphify-out/.graphify_extract.json graphify-out/.graphify_ast.json graphify-out/.graphify_semantic.json graphify-out/.graphify_analysis.json
-find graphify-out -maxdepth 1 -name '.graphify_chunk_*.json' -delete 2>/dev/null
-rm -f graphify-out/.needs_update 2>/dev/null || true
 ```
 
 Replace INPUT_PATH with the actual path (same value used in Steps 4-5) so the manifest is relativized to the scan root.

graphify/skill-codex.md

@@ -348,10 +348,11 @@ merged = {
     'output_tokens': new.get('output_tokens', 0),
 }
 Path('graphify-out/.graphify_semantic.json').write_text(json.dumps(merged, indent=2, ensure_ascii=False), encoding=\"utf-8\")
+for _tmp in ['.graphify_cached.json', '.graphify_uncached.txt', '.graphify_semantic_new.json']:
+    Path('graphify-out', _tmp).unlink(missing_ok=True)
 print(f'Extraction complete - {len(deduped)} nodes, {len(all_edges)} edges ({len(cached[\"nodes\"])} from cache, {len(new.get(\"nodes\",[]))} new)')
 "
 ```
-Clean up temp files: `rm -f graphify-out/.graphify_cached.json graphify-out/.graphify_uncached.txt graphify-out/.graphify_semantic_new.json`
 
 #### Part C - Merge AST + semantic into final extraction
 
@@ -614,10 +615,13 @@ cost_path.write_text(json.dumps(cost, indent=2, ensure_ascii=False), encoding=\"
 
 print(f'This run: {input_tok:,} input tokens, {output_tok:,} output tokens')
 print(f'All time: {cost[\"total_input_tokens\"]:,} input, {cost[\"total_output_tokens\"]:,} output ({len(cost[\"runs\"])} runs)')
+
+_out = Path('graphify-out')
+for _tmp in ['.graphify_detect.json', '.graphify_extract.json', '.graphify_ast.json', '.graphify_semantic.json', '.graphify_analysis.json', '.needs_update']:
+    (_out / _tmp).unlink(missing_ok=True)
+for _chunk in _out.glob('.graphify_chunk_*.json'):
+    _chunk.unlink(missing_ok=True)
 "
-rm -f graphify-out/.graphify_detect.json graphify-out/.graphify_extract.json graphify-out/.graphify_ast.json graphify-out/.graphify_semantic.json graphify-out/.graphify_analysis.json
-find graphify-out -maxdepth 1 -name '.graphify_chunk_*.json' -delete 2>/dev/null
-rm -f graphify-out/.needs_update 2>/dev/null || true
 ```
 
 Replace INPUT_PATH with the actual path (same value used in Steps 4-5) so the manifest is relativized to the scan root.

graphify/skill-copilot.md

@@ -351,10 +351,11 @@ merged = {
     'output_tokens': new.get('output_tokens', 0),
 }
 Path('graphify-out/.graphify_semantic.json').write_text(json.dumps(merged, indent=2, ensure_ascii=False), encoding=\"utf-8\")
+for _tmp in ['.graphify_cached.json', '.graphify_uncached.txt', '.graphify_semantic_new.json']:
+    Path('graphify-out', _tmp).unlink(missing_ok=True)
 print(f'Extraction complete - {len(deduped)} nodes, {len(all_edges)} edges ({len(cached[\"nodes\"])} from cache, {len(new.get(\"nodes\",[]))} new)')
 "
 ```
-Clean up temp files: `rm -f graphify-out/.graphify_cached.json graphify-out/.graphify_uncached.txt graphify-out/.graphify_semantic_new.json`
 
 #### Part C - Merge AST + semantic into final extraction
 
@@ -617,10 +618,13 @@ cost_path.write_text(json.dumps(cost, indent=2, ensure_ascii=False), encoding=\"
 
 print(f'This run: {input_tok:,} input tokens, {output_tok:,} output tokens')
 print(f'All time: {cost[\"total_input_tokens\"]:,} input, {cost[\"total_output_tokens\"]:,} output ({len(cost[\"runs\"])} runs)')
+
+_out = Path('graphify-out')
+for _tmp in ['.graphify_detect.json', '.graphify_extract.json', '.graphify_ast.json', '.graphify_semantic.json', '.graphify_analysis.json', '.needs_update']:
+    (_out / _tmp).unlink(missing_ok=True)
+for _chunk in _out.glob('.graphify_chunk_*.json'):
+    _chunk.unlink(missing_ok=True)
 "
-rm -f graphify-out/.graphify_detect.json graphify-out/.graphify_extract.json graphify-out/.graphify_ast.json graphify-out/.graphify_semantic.json graphify-out/.graphify_analysis.json
-find graphify-out -maxdepth 1 -name '.graphify_chunk_*.json' -delete 2>/dev/null
-rm -f graphify-out/.needs_update 2>/dev/null || true
 ```
 
 Replace INPUT_PATH with the actual path (same value used in Steps 4-5) so the manifest is relativized to the scan root.

graphify/skill-devin.md

@@ -409,10 +409,11 @@ merged = {
 }
 merged = sanitize_semantic_fragment(merged)
 Path('graphify-out/.graphify_semantic.json').write_text(json.dumps(merged, indent=2))
+for _tmp in ['.graphify_cached.json', '.graphify_uncached.txt', '.graphify_semantic_new.json']:
+    Path('graphify-out', _tmp).unlink(missing_ok=True)
 print(f'Extraction complete - {len(deduped)} nodes, {len(all_edges)} edges ({len(cached[\"nodes\"])} from cache, {len(new.get(\"nodes\",[]))} new)')
 "
 ```
-Clean up temp files: `rm -f graphify-out/.graphify_cached.json graphify-out/.graphify_uncached.txt graphify-out/.graphify_semantic_new.json`
 
 #### Part C - Merge AST + semantic into final extraction
 
@@ -836,9 +837,13 @@ cost_path.write_text(json.dumps(cost, indent=2))
 
 print(f'This run: {input_tok:,} input tokens, {output_tok:,} output tokens')
 print(f'All time: {cost[\"total_input_tokens\"]:,} input, {cost[\"total_output_tokens\"]:,} output ({len(cost[\"runs\"])} runs)')
+
+_out = Path('graphify-out')
+for _tmp in ['.graphify_detect.json', '.graphify_extract.json', '.graphify_ast.json', '.graphify_semantic.json', '.graphify_analysis.json', '.graphify_labels.json', '.graphify_incremental.json', '.graphify_transcripts.json', '.graphify_old.json', '.needs_update']:
+    (_out / _tmp).unlink(missing_ok=True)
+for _chunk in _out.glob('.graphify_chunk_*.json'):
+    _chunk.unlink(missing_ok=True)
 "
-rm -f graphify-out/.graphify_detect.json graphify-out/.graphify_extract.json graphify-out/.graphify_ast.json graphify-out/.graphify_semantic.json graphify-out/.graphify_analysis.json graphify-out/.graphify_labels.json graphify-out/.graphify_incremental.json graphify-out/.graphify_transcripts.json graphify-out/.graphify_old.json; find graphify-out -maxdepth 1 -name '.graphify_chunk_*.json' -delete 2>/dev/null
-rm -f graphify-out/.needs_update 2>/dev/null || true
 ```
 
 Tell the user (omit the obsidian line unless --obsidian was given; omit the wiki line unless --wiki was given):
@@ -1001,11 +1006,11 @@ if old_data:
         print('New nodes:', ', '.join(n['label'] for n in diff['new_nodes'][:5]))
     if diff['new_edges']:
         print('New edges:', len(diff['new_edges']))
+Path('graphify-out/.graphify_old.json').unlink(missing_ok=True)
 "
 ```
 
 Before the merge step, save the old graph: `cp graphify-out/graph.json graphify-out/.graphify_old.json`
-Clean up after: `rm -f graphify-out/.graphify_old.json`
 
 ---
 

graphify/skill-droid.md

@@ -348,10 +348,11 @@ merged = {
     'output_tokens': new.get('output_tokens', 0),
 }
 Path('graphify-out/.graphify_semantic.json').write_text(json.dumps(merged, indent=2, ensure_ascii=False), encoding=\"utf-8\")
+for _tmp in ['.graphify_cached.json', '.graphify_uncached.txt', '.graphify_semantic_new.json']:
+    Path('graphify-out', _tmp).unlink(missing_ok=True)
 print(f'Extraction complete - {len(deduped)} nodes, {len(all_edges)} edges ({len(cached[\"nodes\"])} from cache, {len(new.get(\"nodes\",[]))} new)')
 "
 ```
-Clean up temp files: `rm -f graphify-out/.graphify_cached.json graphify-out/.graphify_uncached.txt graphify-out/.graphify_semantic_new.json`
 
 #### Part C - Merge AST + semantic into final extraction
 
@@ -614,10 +615,13 @@ cost_path.write_text(json.dumps(cost, indent=2, ensure_ascii=False), encoding=\"
 
 print(f'This run: {input_tok:,} input tokens, {output_tok:,} output tokens')
 print(f'All time: {cost[\"total_input_tokens\"]:,} input, {cost[\"total_output_tokens\"]:,} output ({len(cost[\"runs\"])} runs)')
+
+_out = Path('graphify-out')
+for _tmp in ['.graphify_detect.json', '.graphify_extract.json', '.graphify_ast.json', '.graphify_semantic.json', '.graphify_analysis.json', '.needs_update']:
+    (_out / _tmp).unlink(missing_ok=True)
+for _chunk in _out.glob('.graphify_chunk_*.json'):
+    _chunk.unlink(missing_ok=True)
 "
-rm -f graphify-out/.graphify_detect.json graphify-out/.graphify_extract.json graphify-out/.graphify_ast.json graphify-out/.graphify_semantic.json graphify-out/.graphify_analysis.json
-find graphify-out -maxdepth 1 -name '.graphify_chunk_*.json' -delete 2>/dev/null
-rm -f graphify-out/.needs_update 2>/dev/null || true
 ```
 
 Replace INPUT_PATH with the actual path (same value used in Steps 4-5) so the manifest is relativized to the scan root.

graphify/skill-kilo.md

@@ -351,10 +351,11 @@ merged = {
     'output_tokens': new.get('output_tokens', 0),
 }
 Path('graphify-out/.graphify_semantic.json').write_text(json.dumps(merged, indent=2, ensure_ascii=False), encoding=\"utf-8\")
+for _tmp in ['.graphify_cached.json', '.graphify_uncached.txt', '.graphify_semantic_new.json']:
+    Path('graphify-out', _tmp).unlink(missing_ok=True)
 print(f'Extraction complete - {len(deduped)} nodes, {len(all_edges)} edges ({len(cached[\"nodes\"])} from cache, {len(new.get(\"nodes\",[]))} new)')
 "
 ```
-Clean up temp files: `rm -f graphify-out/.graphify_cached.json graphify-out/.graphify_uncached.txt graphify-out/.graphify_semantic_new.json`
 
 #### Part C - Merge AST + semantic into final extraction
 
@@ -617,10 +618,13 @@ cost_path.write_text(json.dumps(cost, indent=2, ensure_ascii=False), encoding=\"
 
 print(f'This run: {input_tok:,} input tokens, {output_tok:,} output tokens')
 print(f'All time: {cost[\"total_input_tokens\"]:,} input, {cost[\"total_output_tokens\"]:,} output ({len(cost[\"runs\"])} runs)')
+
+_out = Path('graphify-out')
+for _tmp in ['.graphify_detect.json', '.graphify_extract.json', '.graphify_ast.json', '.graphify_semantic.json', '.graphify_analysis.json', '.needs_update']:
+    (_out / _tmp).unlink(missing_ok=True)
+for _chunk in _out.glob('.graphify_chunk_*.json'):
+    _chunk.unlink(missing_ok=True)
 "
-rm -f graphify-out/.graphify_detect.json graphify-out/.graphify_extract.json graphify-out/.graphify_ast.json graphify-out/.graphify_semantic.json graphify-out/.graphify_analysis.json
-find graphify-out -maxdepth 1 -name '.graphify_chunk_*.json' -delete 2>/dev/null
-rm -f graphify-out/.needs_update 2>/dev/null || true
 ```
 
 Replace INPUT_PATH with the actual path (same value used in Steps 4-5) so the manifest is relativized to the scan root.

graphify/skill-kiro.md

@@ -351,10 +351,11 @@ merged = {
     'output_tokens': new.get('output_tokens', 0),
 }
 Path('graphify-out/.graphify_semantic.json').write_text(json.dumps(merged, indent=2, ensure_ascii=False), encoding=\"utf-8\")
+for _tmp in ['.graphify_cached.json', '.graphify_uncached.txt', '.graphify_semantic_new.json']:
+    Path('graphify-out', _tmp).unlink(missing_ok=True)
 print(f'Extraction complete - {len(deduped)} nodes, {len(all_edges)} edges ({len(cached[\"nodes\"])} from cache, {len(new.get(\"nodes\",[]))} new)')
 "
 ```
-Clean up temp files: `rm -f graphify-out/.graphify_cached.json graphify-out/.graphify_uncached.txt graphify-out/.graphify_semantic_new.json`
 
 #### Part C - Merge AST + semantic into final extraction
 
@@ -617,10 +618,13 @@ cost_path.write_text(json.dumps(cost, indent=2, ensure_ascii=False), encoding=\"
 
 print(f'This run: {input_tok:,} input tokens, {output_tok:,} output tokens')
 print(f'All time: {cost[\"total_input_tokens\"]:,} input, {cost[\"total_output_tokens\"]:,} output ({len(cost[\"runs\"])} runs)')
+
+_out = Path('graphify-out')
+for _tmp in ['.graphify_detect.json', '.graphify_extract.json', '.graphify_ast.json', '.graphify_semantic.json', '.graphify_analysis.json', '.needs_update']:
+    (_out / _tmp).unlink(missing_ok=True)
+for _chunk in _out.glob('.graphify_chunk_*.json'):
+    _chunk.unlink(missing_ok=True)
 "
-rm -f graphify-out/.graphify_detect.json graphify-out/.graphify_extract.json graphify-out/.graphify_ast.json graphify-out/.graphify_semantic.json graphify-out/.graphify_analysis.json
-find graphify-out -maxdepth 1 -name '.graphify_chunk_*.json' -delete 2>/dev/null
-rm -f graphify-out/.needs_update 2>/dev/null || true
 ```
 
 Replace INPUT_PATH with the actual path (same value used in Steps 4-5) so the manifest is relativized to the scan root.