fix(skill): preserve persisted scan options across skill runs

Read existing CLI build-config options in fresh and incremental skill
scan fragments, keeping corpus boundaries consistent without changing
standalone detection API defaults. Regenerate all host artifacts and
snapshots. Add rendered-snippet regressions and explicit-override tests.

Fixes #4240.
AI-Assisted-By: AI coding assistant

(cherry picked from commit 3f68952d80)

graphify/skill-agents.md

@@ -117,7 +117,9 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.detect import detect
 from pathlib import Path
-result = detect(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 # Write the sidecar from Python, not a shell redirect, so the same block renders
 # on PowerShell hosts without console-encoding drift (#2528).
 Path('graphify-out/.graphify_detect.json').write_text(json.dumps(result, ensure_ascii=False), encoding=\"utf-8\")

graphify/skill-aider.md

@@ -111,7 +111,9 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.detect import detect
 from pathlib import Path
-result = detect(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 print(json.dumps(result))
 " > .graphify_detect.json
 ```
@@ -772,7 +774,9 @@ import sys, json
 from graphify.detect import detect_incremental, save_manifest
 from pathlib import Path
 
-result = detect_incremental(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect_incremental(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 new_total = result.get('new_total', 0)
 print(json.dumps(result, indent=2))
 Path('.graphify_incremental.json').write_text(json.dumps(result))

graphify/skill-amp.md

@@ -117,7 +117,9 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.detect import detect
 from pathlib import Path
-result = detect(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 # Write the sidecar from Python, not a shell redirect, so the same block renders
 # on PowerShell hosts without console-encoding drift (#2528).
 Path('graphify-out/.graphify_detect.json').write_text(json.dumps(result, ensure_ascii=False), encoding=\"utf-8\")

graphify/skill-claw.md

@@ -117,7 +117,9 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.detect import detect
 from pathlib import Path
-result = detect(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 # Write the sidecar from Python, not a shell redirect, so the same block renders
 # on PowerShell hosts without console-encoding drift (#2528).
 Path('graphify-out/.graphify_detect.json').write_text(json.dumps(result, ensure_ascii=False), encoding=\"utf-8\")

graphify/skill-codex.md

@@ -117,7 +117,9 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.detect import detect
 from pathlib import Path
-result = detect(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 # Write the sidecar from Python, not a shell redirect, so the same block renders
 # on PowerShell hosts without console-encoding drift (#2528).
 Path('graphify-out/.graphify_detect.json').write_text(json.dumps(result, ensure_ascii=False), encoding=\"utf-8\")

graphify/skill-copilot.md

@@ -117,7 +117,9 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.detect import detect
 from pathlib import Path
-result = detect(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 # Write the sidecar from Python, not a shell redirect, so the same block renders
 # on PowerShell hosts without console-encoding drift (#2528).
 Path('graphify-out/.graphify_detect.json').write_text(json.dumps(result, ensure_ascii=False), encoding=\"utf-8\")

graphify/skill-devin.md

@@ -124,7 +124,9 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.detect import detect
 from pathlib import Path
-result = detect(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 print(json.dumps(result))
 " > graphify-out/.graphify_detect.json
 ```
@@ -911,7 +913,9 @@ import sys, json
 from graphify.detect import detect_incremental, save_manifest
 from pathlib import Path
 
-result = detect_incremental(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect_incremental(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 new_total = result.get('new_total', 0)
 print(json.dumps(result, indent=2))
 Path('graphify-out/.graphify_incremental.json').write_text(json.dumps(result))

graphify/skill-droid.md

@@ -117,7 +117,9 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.detect import detect
 from pathlib import Path
-result = detect(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 # Write the sidecar from Python, not a shell redirect, so the same block renders
 # on PowerShell hosts without console-encoding drift (#2528).
 Path('graphify-out/.graphify_detect.json').write_text(json.dumps(result, ensure_ascii=False), encoding=\"utf-8\")

graphify/skill-kilo.md

@@ -117,7 +117,9 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.detect import detect
 from pathlib import Path
-result = detect(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 # Write the sidecar from Python, not a shell redirect, so the same block renders
 # on PowerShell hosts without console-encoding drift (#2528).
 Path('graphify-out/.graphify_detect.json').write_text(json.dumps(result, ensure_ascii=False), encoding=\"utf-8\")

graphify/skill-kiro.md

@@ -117,7 +117,9 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.detect import detect
 from pathlib import Path
-result = detect(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 # Write the sidecar from Python, not a shell redirect, so the same block renders
 # on PowerShell hosts without console-encoding drift (#2528).
 Path('graphify-out/.graphify_detect.json').write_text(json.dumps(result, ensure_ascii=False), encoding=\"utf-8\")

graphify/skill-opencode.md

@@ -117,7 +117,9 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.detect import detect
 from pathlib import Path
-result = detect(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 # Write the sidecar from Python, not a shell redirect, so the same block renders
 # on PowerShell hosts without console-encoding drift (#2528).
 Path('graphify-out/.graphify_detect.json').write_text(json.dumps(result, ensure_ascii=False), encoding=\"utf-8\")

graphify/skill-pi.md

@@ -117,7 +117,9 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.detect import detect
 from pathlib import Path
-result = detect(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 # Write the sidecar from Python, not a shell redirect, so the same block renders
 # on PowerShell hosts without console-encoding drift (#2528).
 Path('graphify-out/.graphify_detect.json').write_text(json.dumps(result, ensure_ascii=False), encoding=\"utf-8\")

graphify/skill-trae.md

@@ -117,7 +117,9 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.detect import detect
 from pathlib import Path
-result = detect(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 # Write the sidecar from Python, not a shell redirect, so the same block renders
 # on PowerShell hosts without console-encoding drift (#2528).
 Path('graphify-out/.graphify_detect.json').write_text(json.dumps(result, ensure_ascii=False), encoding=\"utf-8\")

graphify/skill-vscode.md

@@ -117,7 +117,9 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.detect import detect
 from pathlib import Path
-result = detect(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 # Write the sidecar from Python, not a shell redirect, so the same block renders
 # on PowerShell hosts without console-encoding drift (#2528).
 Path('graphify-out/.graphify_detect.json').write_text(json.dumps(result, ensure_ascii=False), encoding=\"utf-8\")

graphify/skill-windows.md

@@ -145,7 +145,9 @@ If the import succeeds, print nothing and move straight to Step 2.
 import json
 from graphify.detect import detect
 from pathlib import Path
-result = detect(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 # Write the sidecar from Python, not a shell redirect, so the same block renders
 # on PowerShell hosts without console-encoding drift (#2528).
 Path('graphify-out/.graphify_detect.json').write_text(json.dumps(result, ensure_ascii=False), encoding="utf-8")

graphify/skill.md

@@ -117,7 +117,9 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.detect import detect
 from pathlib import Path
-result = detect(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 # Write the sidecar from Python, not a shell redirect, so the same block renders
 # on PowerShell hosts without console-encoding drift (#2528).
 Path('graphify-out/.graphify_detect.json').write_text(json.dumps(result, ensure_ascii=False), encoding=\"utf-8\")

graphify/skills/agents/references/update.md

@@ -12,7 +12,9 @@ import sys, json
 from graphify.detect import detect_incremental, save_manifest
 from pathlib import Path
 
-result = detect_incremental(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect_incremental(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 new_total = result.get('new_total', 0)
 print(json.dumps(result, indent=2, ensure_ascii=False))
 Path('graphify-out/.graphify_incremental.json').write_text(json.dumps(result, ensure_ascii=False), encoding=\"utf-8\")

graphify/skills/amp/references/update.md

@@ -12,7 +12,9 @@ import sys, json
 from graphify.detect import detect_incremental, save_manifest
 from pathlib import Path
 
-result = detect_incremental(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect_incremental(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 new_total = result.get('new_total', 0)
 print(json.dumps(result, indent=2, ensure_ascii=False))
 Path('graphify-out/.graphify_incremental.json').write_text(json.dumps(result, ensure_ascii=False), encoding=\"utf-8\")

graphify/skills/claude/references/update.md

@@ -12,7 +12,9 @@ import sys, json
 from graphify.detect import detect_incremental, save_manifest
 from pathlib import Path
 
-result = detect_incremental(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect_incremental(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 new_total = result.get('new_total', 0)
 print(json.dumps(result, indent=2, ensure_ascii=False))
 Path('graphify-out/.graphify_incremental.json').write_text(json.dumps(result, ensure_ascii=False), encoding=\"utf-8\")

graphify/skills/claw/references/update.md

@@ -12,7 +12,9 @@ import sys, json
 from graphify.detect import detect_incremental, save_manifest
 from pathlib import Path
 
-result = detect_incremental(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect_incremental(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 new_total = result.get('new_total', 0)
 print(json.dumps(result, indent=2, ensure_ascii=False))
 Path('graphify-out/.graphify_incremental.json').write_text(json.dumps(result, ensure_ascii=False), encoding=\"utf-8\")

graphify/skills/codex/references/update.md

@@ -12,7 +12,9 @@ import sys, json
 from graphify.detect import detect_incremental, save_manifest
 from pathlib import Path
 
-result = detect_incremental(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect_incremental(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 new_total = result.get('new_total', 0)
 print(json.dumps(result, indent=2, ensure_ascii=False))
 Path('graphify-out/.graphify_incremental.json').write_text(json.dumps(result, ensure_ascii=False), encoding=\"utf-8\")

graphify/skills/copilot/references/update.md

@@ -12,7 +12,9 @@ import sys, json
 from graphify.detect import detect_incremental, save_manifest
 from pathlib import Path
 
-result = detect_incremental(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect_incremental(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 new_total = result.get('new_total', 0)
 print(json.dumps(result, indent=2, ensure_ascii=False))
 Path('graphify-out/.graphify_incremental.json').write_text(json.dumps(result, ensure_ascii=False), encoding=\"utf-8\")

graphify/skills/droid/references/update.md

@@ -12,7 +12,9 @@ import sys, json
 from graphify.detect import detect_incremental, save_manifest
 from pathlib import Path
 
-result = detect_incremental(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect_incremental(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 new_total = result.get('new_total', 0)
 print(json.dumps(result, indent=2, ensure_ascii=False))
 Path('graphify-out/.graphify_incremental.json').write_text(json.dumps(result, ensure_ascii=False), encoding=\"utf-8\")

graphify/skills/kilo/references/update.md

@@ -12,7 +12,9 @@ import sys, json
 from graphify.detect import detect_incremental, save_manifest
 from pathlib import Path
 
-result = detect_incremental(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect_incremental(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 new_total = result.get('new_total', 0)
 print(json.dumps(result, indent=2, ensure_ascii=False))
 Path('graphify-out/.graphify_incremental.json').write_text(json.dumps(result, ensure_ascii=False), encoding=\"utf-8\")

graphify/skills/kiro/references/update.md

@@ -12,7 +12,9 @@ import sys, json
 from graphify.detect import detect_incremental, save_manifest
 from pathlib import Path
 
-result = detect_incremental(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect_incremental(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 new_total = result.get('new_total', 0)
 print(json.dumps(result, indent=2, ensure_ascii=False))
 Path('graphify-out/.graphify_incremental.json').write_text(json.dumps(result, ensure_ascii=False), encoding=\"utf-8\")

graphify/skills/opencode/references/update.md

@@ -12,7 +12,9 @@ import sys, json
 from graphify.detect import detect_incremental, save_manifest
 from pathlib import Path
 
-result = detect_incremental(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect_incremental(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 new_total = result.get('new_total', 0)
 print(json.dumps(result, indent=2, ensure_ascii=False))
 Path('graphify-out/.graphify_incremental.json').write_text(json.dumps(result, ensure_ascii=False), encoding=\"utf-8\")

graphify/skills/pi/references/update.md

@@ -12,7 +12,9 @@ import sys, json
 from graphify.detect import detect_incremental, save_manifest
 from pathlib import Path
 
-result = detect_incremental(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect_incremental(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 new_total = result.get('new_total', 0)
 print(json.dumps(result, indent=2, ensure_ascii=False))
 Path('graphify-out/.graphify_incremental.json').write_text(json.dumps(result, ensure_ascii=False), encoding=\"utf-8\")

graphify/skills/trae/references/update.md

@@ -12,7 +12,9 @@ import sys, json
 from graphify.detect import detect_incremental, save_manifest
 from pathlib import Path
 
-result = detect_incremental(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect_incremental(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 new_total = result.get('new_total', 0)
 print(json.dumps(result, indent=2, ensure_ascii=False))
 Path('graphify-out/.graphify_incremental.json').write_text(json.dumps(result, ensure_ascii=False), encoding=\"utf-8\")

graphify/skills/vscode/references/update.md

@@ -12,7 +12,9 @@ import sys, json
 from graphify.detect import detect_incremental, save_manifest
 from pathlib import Path
 
-result = detect_incremental(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect_incremental(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 new_total = result.get('new_total', 0)
 print(json.dumps(result, indent=2, ensure_ascii=False))
 Path('graphify-out/.graphify_incremental.json').write_text(json.dumps(result, ensure_ascii=False), encoding=\"utf-8\")

graphify/skills/windows/references/update.md

@@ -12,7 +12,9 @@ import sys, json
 from graphify.detect import detect_incremental, save_manifest
 from pathlib import Path
 
-result = detect_incremental(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect_incremental(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 new_total = result.get('new_total', 0)
 print(json.dumps(result, indent=2, ensure_ascii=False))
 Path('graphify-out/.graphify_incremental.json').write_text(json.dumps(result, ensure_ascii=False), encoding=\"utf-8\")

tests/test_skill_persisted_scan_options.py

@@ -0,0 +1,76 @@
+"""Skill scans must preserve the CLI's persisted corpus boundaries (#4240)."""
+from __future__ import annotations
+import json
+import re
+import subprocess
+import sys
+from pathlib import Path
+import pytest
+from graphify import paths
+from tools.skillgen import gen
+from graphify.detect import detect, save_manifest
+from graphify.watch import _write_build_config, _read_build_excludes, _read_build_gitignore
+
+
+def _scan_blocks():
+    found = []
+    for art in gen.render_all(gen.load_platforms()):
+        for block in re.findall(r'```bash\n(.*?)```', art.content, re.S):
+            if "result = detect(Path('INPUT_PATH')" not in block and "result = detect_incremental(Path('INPUT_PATH')" not in block:
+                continue
+            m = re.search(r' -c "\n(.*)\n"', block, re.S)
+            if m:
+                found.append((art.path, m.group(1).replace('\\"', '"')))
+    assert len(found) == 31
+    return found
+
+
+@pytest.mark.parametrize('art,source', _scan_blocks(), ids=lambda value: value.split('\n', 1)[0])
+def test_skill_scan_honors_persisted_options(tmp_path, monkeypatch, art, source):
+    monkeypatch.delenv('GRAPHIFY_OUT', raising=False)
+    monkeypatch.setattr(paths, 'GRAPHIFY_OUT', 'graphify-out')
+    corpus = tmp_path / 'corpus'
+    corpus.mkdir()
+    subprocess.run(['git', 'init', '-q', str(corpus)], check=True)
+    (corpus / '.gitignore').write_text('notes/\n', encoding='utf-8')
+    (corpus / 'notes').mkdir()
+    (corpus / 'docs').mkdir()
+    for name in ('notes/a.md', 'docs/b.md', 'docs/skip.md'):
+        (corpus / name).write_text('# sample\n', encoding='utf-8')
+    out = tmp_path / 'graphify-out'
+    _write_build_config(out, excludes=['docs/skip.md'], gitignore=False)
+    # Match the skill's documented CWD-relative output/manifest layout, with
+    # INPUT_PATH pointing to a distinct corpus rather than the output parent.
+    if 'detect_incremental' in source:
+        files = detect(corpus, gitignore=False, extra_excludes=['docs/skip.md'])['files']
+        save_manifest(files, str(out / 'manifest.json'), root=corpus)
+    # Only exercise the scan contract, not subsequent sidecar/report steps.
+    src = source.split('result = ', 1)[0] + 'result = ' + source.split('result = ', 1)[1].split('\n', 1)[0]
+    src += '\nprint(json.dumps(result))\n'
+    src = src.replace('INPUT_PATH', corpus.as_posix())
+    result = subprocess.run([sys.executable, '-c', src], cwd=tmp_path, check=True, capture_output=True, text=True)
+    data = json.loads(result.stdout)
+    actual = {Path(f).relative_to(corpus).as_posix() for files in data['files'].values() for f in files}
+    assert actual == {'notes/a.md', 'docs/b.md'}, art
+    if 'detect_incremental' in source:
+        assert data['excluded_files'] == [], art
+
+
+@pytest.mark.parametrize('contents', [None, '{', '[]', '{"gitignore": "false", "excludes": 12}'])
+def test_absent_or_malformed_build_options_use_defaults(tmp_path, contents):
+    if contents is not None:
+        (tmp_path / '.graphify_build.json').write_text(contents, encoding='utf-8')
+    assert _read_build_gitignore(tmp_path) is True
+    assert _read_build_excludes(tmp_path) == []
+
+
+def test_detection_api_explicit_options_are_not_overridden(tmp_path):
+    subprocess.run(['git', 'init', '-q', str(tmp_path)], check=True)
+    (tmp_path / '.gitignore').write_text('notes/\n', encoding='utf-8')
+    (tmp_path / 'notes').mkdir()
+    for name in ('notes/a.md', 'keep.md'):
+        (tmp_path / name).write_text('# sample\n', encoding='utf-8')
+    _write_build_config(tmp_path / 'graphify-out', excludes=['keep.md'], gitignore=False)
+    data = detect(tmp_path, gitignore=True, extra_excludes=[])
+    actual = {Path(f).name for files in data['files'].values() for f in files}
+    assert actual == {'keep.md'}

tools/skillgen/expected/graphify__skill-agents.md

@@ -117,7 +117,9 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.detect import detect
 from pathlib import Path
-result = detect(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 # Write the sidecar from Python, not a shell redirect, so the same block renders
 # on PowerShell hosts without console-encoding drift (#2528).
 Path('graphify-out/.graphify_detect.json').write_text(json.dumps(result, ensure_ascii=False), encoding=\"utf-8\")

tools/skillgen/expected/graphify__skill-aider.md

@@ -111,7 +111,9 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.detect import detect
 from pathlib import Path
-result = detect(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 print(json.dumps(result))
 " > .graphify_detect.json
 ```
@@ -772,7 +774,9 @@ import sys, json
 from graphify.detect import detect_incremental, save_manifest
 from pathlib import Path
 
-result = detect_incremental(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect_incremental(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 new_total = result.get('new_total', 0)
 print(json.dumps(result, indent=2))
 Path('.graphify_incremental.json').write_text(json.dumps(result))

tools/skillgen/expected/graphify__skill-amp.md

@@ -117,7 +117,9 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.detect import detect
 from pathlib import Path
-result = detect(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 # Write the sidecar from Python, not a shell redirect, so the same block renders
 # on PowerShell hosts without console-encoding drift (#2528).
 Path('graphify-out/.graphify_detect.json').write_text(json.dumps(result, ensure_ascii=False), encoding=\"utf-8\")

tools/skillgen/expected/graphify__skill-claw.md

@@ -117,7 +117,9 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.detect import detect
 from pathlib import Path
-result = detect(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 # Write the sidecar from Python, not a shell redirect, so the same block renders
 # on PowerShell hosts without console-encoding drift (#2528).
 Path('graphify-out/.graphify_detect.json').write_text(json.dumps(result, ensure_ascii=False), encoding=\"utf-8\")

tools/skillgen/expected/graphify__skill-codex.md

@@ -117,7 +117,9 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.detect import detect
 from pathlib import Path
-result = detect(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 # Write the sidecar from Python, not a shell redirect, so the same block renders
 # on PowerShell hosts without console-encoding drift (#2528).
 Path('graphify-out/.graphify_detect.json').write_text(json.dumps(result, ensure_ascii=False), encoding=\"utf-8\")

tools/skillgen/expected/graphify__skill-copilot.md

@@ -117,7 +117,9 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.detect import detect
 from pathlib import Path
-result = detect(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 # Write the sidecar from Python, not a shell redirect, so the same block renders
 # on PowerShell hosts without console-encoding drift (#2528).
 Path('graphify-out/.graphify_detect.json').write_text(json.dumps(result, ensure_ascii=False), encoding=\"utf-8\")

tools/skillgen/expected/graphify__skill-devin.md

@@ -124,7 +124,9 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.detect import detect
 from pathlib import Path
-result = detect(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 print(json.dumps(result))
 " > graphify-out/.graphify_detect.json
 ```
@@ -911,7 +913,9 @@ import sys, json
 from graphify.detect import detect_incremental, save_manifest
 from pathlib import Path
 
-result = detect_incremental(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect_incremental(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 new_total = result.get('new_total', 0)
 print(json.dumps(result, indent=2))
 Path('graphify-out/.graphify_incremental.json').write_text(json.dumps(result))

tools/skillgen/expected/graphify__skill-droid.md

@@ -117,7 +117,9 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.detect import detect
 from pathlib import Path
-result = detect(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 # Write the sidecar from Python, not a shell redirect, so the same block renders
 # on PowerShell hosts without console-encoding drift (#2528).
 Path('graphify-out/.graphify_detect.json').write_text(json.dumps(result, ensure_ascii=False), encoding=\"utf-8\")

tools/skillgen/expected/graphify__skill-kilo.md

@@ -117,7 +117,9 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.detect import detect
 from pathlib import Path
-result = detect(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 # Write the sidecar from Python, not a shell redirect, so the same block renders
 # on PowerShell hosts without console-encoding drift (#2528).
 Path('graphify-out/.graphify_detect.json').write_text(json.dumps(result, ensure_ascii=False), encoding=\"utf-8\")

tools/skillgen/expected/graphify__skill-kiro.md

@@ -117,7 +117,9 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.detect import detect
 from pathlib import Path
-result = detect(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 # Write the sidecar from Python, not a shell redirect, so the same block renders
 # on PowerShell hosts without console-encoding drift (#2528).
 Path('graphify-out/.graphify_detect.json').write_text(json.dumps(result, ensure_ascii=False), encoding=\"utf-8\")

tools/skillgen/expected/graphify__skill-opencode.md

@@ -117,7 +117,9 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.detect import detect
 from pathlib import Path
-result = detect(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 # Write the sidecar from Python, not a shell redirect, so the same block renders
 # on PowerShell hosts without console-encoding drift (#2528).
 Path('graphify-out/.graphify_detect.json').write_text(json.dumps(result, ensure_ascii=False), encoding=\"utf-8\")

tools/skillgen/expected/graphify__skill-pi.md

@@ -117,7 +117,9 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.detect import detect
 from pathlib import Path
-result = detect(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 # Write the sidecar from Python, not a shell redirect, so the same block renders
 # on PowerShell hosts without console-encoding drift (#2528).
 Path('graphify-out/.graphify_detect.json').write_text(json.dumps(result, ensure_ascii=False), encoding=\"utf-8\")

tools/skillgen/expected/graphify__skill-trae.md

@@ -117,7 +117,9 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.detect import detect
 from pathlib import Path
-result = detect(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 # Write the sidecar from Python, not a shell redirect, so the same block renders
 # on PowerShell hosts without console-encoding drift (#2528).
 Path('graphify-out/.graphify_detect.json').write_text(json.dumps(result, ensure_ascii=False), encoding=\"utf-8\")

tools/skillgen/expected/graphify__skill-vscode.md

@@ -117,7 +117,9 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.detect import detect
 from pathlib import Path
-result = detect(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 # Write the sidecar from Python, not a shell redirect, so the same block renders
 # on PowerShell hosts without console-encoding drift (#2528).
 Path('graphify-out/.graphify_detect.json').write_text(json.dumps(result, ensure_ascii=False), encoding=\"utf-8\")

tools/skillgen/expected/graphify__skill-windows.md

@@ -145,7 +145,9 @@ If the import succeeds, print nothing and move straight to Step 2.
 import json
 from graphify.detect import detect
 from pathlib import Path
-result = detect(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 # Write the sidecar from Python, not a shell redirect, so the same block renders
 # on PowerShell hosts without console-encoding drift (#2528).
 Path('graphify-out/.graphify_detect.json').write_text(json.dumps(result, ensure_ascii=False), encoding="utf-8")

tools/skillgen/expected/graphify__skill.md

@@ -117,7 +117,9 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.detect import detect
 from pathlib import Path
-result = detect(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 # Write the sidecar from Python, not a shell redirect, so the same block renders
 # on PowerShell hosts without console-encoding drift (#2528).
 Path('graphify-out/.graphify_detect.json').write_text(json.dumps(result, ensure_ascii=False), encoding=\"utf-8\")

tools/skillgen/expected/graphify__skills__agents__references__update.md

@@ -12,7 +12,9 @@ import sys, json
 from graphify.detect import detect_incremental, save_manifest
 from pathlib import Path
 
-result = detect_incremental(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect_incremental(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 new_total = result.get('new_total', 0)
 print(json.dumps(result, indent=2, ensure_ascii=False))
 Path('graphify-out/.graphify_incremental.json').write_text(json.dumps(result, ensure_ascii=False), encoding=\"utf-8\")

tools/skillgen/expected/graphify__skills__amp__references__update.md

@@ -12,7 +12,9 @@ import sys, json
 from graphify.detect import detect_incremental, save_manifest
 from pathlib import Path
 
-result = detect_incremental(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect_incremental(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 new_total = result.get('new_total', 0)
 print(json.dumps(result, indent=2, ensure_ascii=False))
 Path('graphify-out/.graphify_incremental.json').write_text(json.dumps(result, ensure_ascii=False), encoding=\"utf-8\")

tools/skillgen/expected/graphify__skills__claude__references__update.md

@@ -12,7 +12,9 @@ import sys, json
 from graphify.detect import detect_incremental, save_manifest
 from pathlib import Path
 
-result = detect_incremental(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect_incremental(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 new_total = result.get('new_total', 0)
 print(json.dumps(result, indent=2, ensure_ascii=False))
 Path('graphify-out/.graphify_incremental.json').write_text(json.dumps(result, ensure_ascii=False), encoding=\"utf-8\")

tools/skillgen/expected/graphify__skills__claw__references__update.md

@@ -12,7 +12,9 @@ import sys, json
 from graphify.detect import detect_incremental, save_manifest
 from pathlib import Path
 
-result = detect_incremental(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect_incremental(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 new_total = result.get('new_total', 0)
 print(json.dumps(result, indent=2, ensure_ascii=False))
 Path('graphify-out/.graphify_incremental.json').write_text(json.dumps(result, ensure_ascii=False), encoding=\"utf-8\")

tools/skillgen/expected/graphify__skills__codex__references__update.md

@@ -12,7 +12,9 @@ import sys, json
 from graphify.detect import detect_incremental, save_manifest
 from pathlib import Path
 
-result = detect_incremental(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect_incremental(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 new_total = result.get('new_total', 0)
 print(json.dumps(result, indent=2, ensure_ascii=False))
 Path('graphify-out/.graphify_incremental.json').write_text(json.dumps(result, ensure_ascii=False), encoding=\"utf-8\")

tools/skillgen/expected/graphify__skills__copilot__references__update.md

@@ -12,7 +12,9 @@ import sys, json
 from graphify.detect import detect_incremental, save_manifest
 from pathlib import Path
 
-result = detect_incremental(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect_incremental(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 new_total = result.get('new_total', 0)
 print(json.dumps(result, indent=2, ensure_ascii=False))
 Path('graphify-out/.graphify_incremental.json').write_text(json.dumps(result, ensure_ascii=False), encoding=\"utf-8\")

tools/skillgen/expected/graphify__skills__droid__references__update.md

@@ -12,7 +12,9 @@ import sys, json
 from graphify.detect import detect_incremental, save_manifest
 from pathlib import Path
 
-result = detect_incremental(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect_incremental(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 new_total = result.get('new_total', 0)
 print(json.dumps(result, indent=2, ensure_ascii=False))
 Path('graphify-out/.graphify_incremental.json').write_text(json.dumps(result, ensure_ascii=False), encoding=\"utf-8\")

tools/skillgen/expected/graphify__skills__kilo__references__update.md

@@ -12,7 +12,9 @@ import sys, json
 from graphify.detect import detect_incremental, save_manifest
 from pathlib import Path
 
-result = detect_incremental(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect_incremental(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 new_total = result.get('new_total', 0)
 print(json.dumps(result, indent=2, ensure_ascii=False))
 Path('graphify-out/.graphify_incremental.json').write_text(json.dumps(result, ensure_ascii=False), encoding=\"utf-8\")

tools/skillgen/expected/graphify__skills__kiro__references__update.md

@@ -12,7 +12,9 @@ import sys, json
 from graphify.detect import detect_incremental, save_manifest
 from pathlib import Path
 
-result = detect_incremental(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect_incremental(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 new_total = result.get('new_total', 0)
 print(json.dumps(result, indent=2, ensure_ascii=False))
 Path('graphify-out/.graphify_incremental.json').write_text(json.dumps(result, ensure_ascii=False), encoding=\"utf-8\")

tools/skillgen/expected/graphify__skills__opencode__references__update.md

@@ -12,7 +12,9 @@ import sys, json
 from graphify.detect import detect_incremental, save_manifest
 from pathlib import Path
 
-result = detect_incremental(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect_incremental(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 new_total = result.get('new_total', 0)
 print(json.dumps(result, indent=2, ensure_ascii=False))
 Path('graphify-out/.graphify_incremental.json').write_text(json.dumps(result, ensure_ascii=False), encoding=\"utf-8\")

tools/skillgen/expected/graphify__skills__pi__references__update.md

@@ -12,7 +12,9 @@ import sys, json
 from graphify.detect import detect_incremental, save_manifest
 from pathlib import Path
 
-result = detect_incremental(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect_incremental(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 new_total = result.get('new_total', 0)
 print(json.dumps(result, indent=2, ensure_ascii=False))
 Path('graphify-out/.graphify_incremental.json').write_text(json.dumps(result, ensure_ascii=False), encoding=\"utf-8\")

tools/skillgen/expected/graphify__skills__trae__references__update.md

@@ -12,7 +12,9 @@ import sys, json
 from graphify.detect import detect_incremental, save_manifest
 from pathlib import Path
 
-result = detect_incremental(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect_incremental(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 new_total = result.get('new_total', 0)
 print(json.dumps(result, indent=2, ensure_ascii=False))
 Path('graphify-out/.graphify_incremental.json').write_text(json.dumps(result, ensure_ascii=False), encoding=\"utf-8\")

tools/skillgen/expected/graphify__skills__vscode__references__update.md

@@ -12,7 +12,9 @@ import sys, json
 from graphify.detect import detect_incremental, save_manifest
 from pathlib import Path
 
-result = detect_incremental(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect_incremental(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 new_total = result.get('new_total', 0)
 print(json.dumps(result, indent=2, ensure_ascii=False))
 Path('graphify-out/.graphify_incremental.json').write_text(json.dumps(result, ensure_ascii=False), encoding=\"utf-8\")

tools/skillgen/expected/graphify__skills__windows__references__update.md

@@ -12,7 +12,9 @@ import sys, json
 from graphify.detect import detect_incremental, save_manifest
 from pathlib import Path
 
-result = detect_incremental(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect_incremental(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 new_total = result.get('new_total', 0)
 print(json.dumps(result, indent=2, ensure_ascii=False))
 Path('graphify-out/.graphify_incremental.json').write_text(json.dumps(result, ensure_ascii=False), encoding=\"utf-8\")

tools/skillgen/fragments/core/aider.md

@@ -111,7 +111,9 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.detect import detect
 from pathlib import Path
-result = detect(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 print(json.dumps(result))
 " > .graphify_detect.json
 ```
@@ -772,7 +774,9 @@ import sys, json
 from graphify.detect import detect_incremental, save_manifest
 from pathlib import Path
 
-result = detect_incremental(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect_incremental(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 new_total = result.get('new_total', 0)
 print(json.dumps(result, indent=2))
 Path('.graphify_incremental.json').write_text(json.dumps(result))

tools/skillgen/fragments/core/core.md

@@ -70,7 +70,9 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.detect import detect
 from pathlib import Path
-result = detect(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 # Write the sidecar from Python, not a shell redirect, so the same block renders
 # on PowerShell hosts without console-encoding drift (#2528).
 Path('graphify-out/.graphify_detect.json').write_text(json.dumps(result, ensure_ascii=False), encoding=\"utf-8\")

tools/skillgen/fragments/core/devin.md

@@ -124,7 +124,9 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from graphify.detect import detect
 from pathlib import Path
-result = detect(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 print(json.dumps(result))
 " > graphify-out/.graphify_detect.json
 ```
@@ -911,7 +913,9 @@ import sys, json
 from graphify.detect import detect_incremental, save_manifest
 from pathlib import Path
 
-result = detect_incremental(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect_incremental(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 new_total = result.get('new_total', 0)
 print(json.dumps(result, indent=2))
 Path('graphify-out/.graphify_incremental.json').write_text(json.dumps(result))

tools/skillgen/fragments/references/shared/update.md

@@ -12,7 +12,9 @@ import sys, json
 from graphify.detect import detect_incremental, save_manifest
 from pathlib import Path
 
-result = detect_incremental(Path('INPUT_PATH'))
+from graphify.paths import out_path
+from graphify.watch import _read_build_excludes, _read_build_gitignore
+result = detect_incremental(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))
 new_total = result.get('new_total', 0)
 print(json.dumps(result, indent=2, ensure_ascii=False))
 Path('graphify-out/.graphify_incremental.json').write_text(json.dumps(result, ensure_ascii=False), encoding=\"utf-8\")

tools/skillgen/gen.py

@@ -1197,6 +1197,18 @@ def _is_graph_diff_direction_fix_line(line: str) -> bool:
     )
 
 
+def _is_persisted_scan_options_fix_line(line: str) -> bool:
+    """Skill scans reuse CLI corpus-shaping options without changing detect defaults (#4240)."""
+    return line.strip() in (
+        "from graphify.paths import out_path",
+        "from graphify.watch import _read_build_excludes, _read_build_gitignore",
+        "result = detect(Path('INPUT_PATH'))",
+        "result = detect_incremental(Path('INPUT_PATH'))",
+        "result = detect(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))",
+        "result = detect_incremental(Path('INPUT_PATH'), extra_excludes=_read_build_excludes(out_path()), gitignore=_read_build_gitignore(out_path()))",
+    )
+
+
 # Every line that may differ between a rendered monolith and its pristine v8
 # baseline. Each predicate documents one sanctioned change-class; a blank line is
 # allowed because the multi-line fix blocks insert spacing. Anything else failing
@@ -1221,6 +1233,7 @@ _SANCTIONED_MONOLITH_DIFFS = (
     _is_step1_root_marker_fix_line,
     _is_watch_injection_fix_line,
     _is_graph_diff_direction_fix_line,
+    _is_persisted_scan_options_fix_line,
 )