fix(skills): stamp manifest before build merge

graphify/skills/agents/references/update.md

@@ -87,12 +87,30 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from pathlib import Path
 from graphify.build import build_merge
+from graphify.cli import _stamped_manifest_files
 from graphify.detect import save_manifest
 
 # Load new extraction and incremental state
 new_extraction = json.loads(Path('graphify-out/.graphify_extract.json').read_text(encoding=\"utf-8\"))
 incremental = json.loads(Path('graphify-out/.graphify_incremental.json').read_text(encoding=\"utf-8\"))
 deleted = list(incremental.get('deleted_files', []))
+
+# Only stamp semantic files (docs/papers/images) that ACTUALLY produced output
+# THIS run (computed from new_extraction BEFORE build_merge() mutates it in place):
+# a changed doc whose chunk failed must stay unstamped so the next --update re-queues
+# it, otherwise it is marked done and its content is lost forever (#2015, #2865).
+# Mirrors the library extract path (cli._stamped_manifest_files + clear_semantic + scan_corpus).
+_manifest_files = _stamped_manifest_files(incremental['files'], new_extraction, Path('INPUT_PATH'))
+# Changed semantic files dispatched this run but NOT stamped had their chunk fail
+# or be omitted; clear any stale semantic_hash so they are re-queued (#1948).
+_sem_types = ('document', 'paper', 'image')
+_dispatched = {f for t, fl in incremental.get('new_files', {}).items() if t in _sem_types for f in fl}
+_stamped = {f for fl in _manifest_files.values() for f in fl}
+_cleared = _dispatched - _stamped
+# scan_corpus = the RAW full corpus so in-root files newly excluded since last run
+# are dropped rather than masquerading as deletions; untouched rows preserved (#1908).
+_scan = {f for fl in incremental['files'].values() for f in fl}
+
 # prune_sources is ONLY for genuinely DELETED files. Changed/re-extracted files are
 # handled by build_merge's replace-on-re-extract (#1344): every source_file in
 # new_chunks is dropped from the base before merge, so old/stale nodes don't survive.
@@ -142,24 +160,6 @@ print(f'[graphify update] Merged extraction written ({len(merged_out[\"nodes\"])
 # root= matches the build_merge call above so the manifest keys stay relative to
 # the scan root — portable across clones/machines, so --update keeps matching
 # cached files instead of missing every one after a move (#1417).
-#
-# Only stamp semantic files (docs/papers/images) that ACTUALLY produced output
-# THIS run (new_extraction is this run's fresh extraction, read above before the
-# merge overwrote the file): a changed doc whose chunk failed must stay unstamped
-# so the next --update re-queues it, otherwise it is marked done and its content
-# is lost forever (#2015). Mirrors the library extract path
-# (cli._stamped_manifest_files + clear_semantic + scan_corpus).
-from graphify.cli import _stamped_manifest_files
-_manifest_files = _stamped_manifest_files(incremental['files'], new_extraction, Path('INPUT_PATH'))
-# Changed semantic files dispatched this run but NOT stamped had their chunk fail
-# or be omitted; clear any stale semantic_hash so they are re-queued (#1948).
-_sem_types = ('document', 'paper', 'image')
-_dispatched = {f for t, fl in incremental.get('new_files', {}).items() if t in _sem_types for f in fl}
-_stamped = {f for fl in _manifest_files.values() for f in fl}
-_cleared = _dispatched - _stamped
-# scan_corpus = the RAW full corpus so in-root files newly excluded since last run
-# are dropped rather than masquerading as deletions; untouched rows preserved (#1908).
-_scan = {f for fl in incremental['files'].values() for f in fl}
 save_manifest(_manifest_files, root='INPUT_PATH', scan_corpus=_scan, clear_semantic=_cleared or None)
 print('[graphify update] Manifest saved.')
 "

graphify/skills/amp/references/update.md

@@ -87,12 +87,30 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from pathlib import Path
 from graphify.build import build_merge
+from graphify.cli import _stamped_manifest_files
 from graphify.detect import save_manifest
 
 # Load new extraction and incremental state
 new_extraction = json.loads(Path('graphify-out/.graphify_extract.json').read_text(encoding=\"utf-8\"))
 incremental = json.loads(Path('graphify-out/.graphify_incremental.json').read_text(encoding=\"utf-8\"))
 deleted = list(incremental.get('deleted_files', []))
+
+# Only stamp semantic files (docs/papers/images) that ACTUALLY produced output
+# THIS run (computed from new_extraction BEFORE build_merge() mutates it in place):
+# a changed doc whose chunk failed must stay unstamped so the next --update re-queues
+# it, otherwise it is marked done and its content is lost forever (#2015, #2865).
+# Mirrors the library extract path (cli._stamped_manifest_files + clear_semantic + scan_corpus).
+_manifest_files = _stamped_manifest_files(incremental['files'], new_extraction, Path('INPUT_PATH'))
+# Changed semantic files dispatched this run but NOT stamped had their chunk fail
+# or be omitted; clear any stale semantic_hash so they are re-queued (#1948).
+_sem_types = ('document', 'paper', 'image')
+_dispatched = {f for t, fl in incremental.get('new_files', {}).items() if t in _sem_types for f in fl}
+_stamped = {f for fl in _manifest_files.values() for f in fl}
+_cleared = _dispatched - _stamped
+# scan_corpus = the RAW full corpus so in-root files newly excluded since last run
+# are dropped rather than masquerading as deletions; untouched rows preserved (#1908).
+_scan = {f for fl in incremental['files'].values() for f in fl}
+
 # prune_sources is ONLY for genuinely DELETED files. Changed/re-extracted files are
 # handled by build_merge's replace-on-re-extract (#1344): every source_file in
 # new_chunks is dropped from the base before merge, so old/stale nodes don't survive.
@@ -142,24 +160,6 @@ print(f'[graphify update] Merged extraction written ({len(merged_out[\"nodes\"])
 # root= matches the build_merge call above so the manifest keys stay relative to
 # the scan root — portable across clones/machines, so --update keeps matching
 # cached files instead of missing every one after a move (#1417).
-#
-# Only stamp semantic files (docs/papers/images) that ACTUALLY produced output
-# THIS run (new_extraction is this run's fresh extraction, read above before the
-# merge overwrote the file): a changed doc whose chunk failed must stay unstamped
-# so the next --update re-queues it, otherwise it is marked done and its content
-# is lost forever (#2015). Mirrors the library extract path
-# (cli._stamped_manifest_files + clear_semantic + scan_corpus).
-from graphify.cli import _stamped_manifest_files
-_manifest_files = _stamped_manifest_files(incremental['files'], new_extraction, Path('INPUT_PATH'))
-# Changed semantic files dispatched this run but NOT stamped had their chunk fail
-# or be omitted; clear any stale semantic_hash so they are re-queued (#1948).
-_sem_types = ('document', 'paper', 'image')
-_dispatched = {f for t, fl in incremental.get('new_files', {}).items() if t in _sem_types for f in fl}
-_stamped = {f for fl in _manifest_files.values() for f in fl}
-_cleared = _dispatched - _stamped
-# scan_corpus = the RAW full corpus so in-root files newly excluded since last run
-# are dropped rather than masquerading as deletions; untouched rows preserved (#1908).
-_scan = {f for fl in incremental['files'].values() for f in fl}
 save_manifest(_manifest_files, root='INPUT_PATH', scan_corpus=_scan, clear_semantic=_cleared or None)
 print('[graphify update] Manifest saved.')
 "

graphify/skills/claude/references/update.md

@@ -87,12 +87,30 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from pathlib import Path
 from graphify.build import build_merge
+from graphify.cli import _stamped_manifest_files
 from graphify.detect import save_manifest
 
 # Load new extraction and incremental state
 new_extraction = json.loads(Path('graphify-out/.graphify_extract.json').read_text(encoding=\"utf-8\"))
 incremental = json.loads(Path('graphify-out/.graphify_incremental.json').read_text(encoding=\"utf-8\"))
 deleted = list(incremental.get('deleted_files', []))
+
+# Only stamp semantic files (docs/papers/images) that ACTUALLY produced output
+# THIS run (computed from new_extraction BEFORE build_merge() mutates it in place):
+# a changed doc whose chunk failed must stay unstamped so the next --update re-queues
+# it, otherwise it is marked done and its content is lost forever (#2015, #2865).
+# Mirrors the library extract path (cli._stamped_manifest_files + clear_semantic + scan_corpus).
+_manifest_files = _stamped_manifest_files(incremental['files'], new_extraction, Path('INPUT_PATH'))
+# Changed semantic files dispatched this run but NOT stamped had their chunk fail
+# or be omitted; clear any stale semantic_hash so they are re-queued (#1948).
+_sem_types = ('document', 'paper', 'image')
+_dispatched = {f for t, fl in incremental.get('new_files', {}).items() if t in _sem_types for f in fl}
+_stamped = {f for fl in _manifest_files.values() for f in fl}
+_cleared = _dispatched - _stamped
+# scan_corpus = the RAW full corpus so in-root files newly excluded since last run
+# are dropped rather than masquerading as deletions; untouched rows preserved (#1908).
+_scan = {f for fl in incremental['files'].values() for f in fl}
+
 # prune_sources is ONLY for genuinely DELETED files. Changed/re-extracted files are
 # handled by build_merge's replace-on-re-extract (#1344): every source_file in
 # new_chunks is dropped from the base before merge, so old/stale nodes don't survive.
@@ -142,24 +160,6 @@ print(f'[graphify update] Merged extraction written ({len(merged_out[\"nodes\"])
 # root= matches the build_merge call above so the manifest keys stay relative to
 # the scan root — portable across clones/machines, so --update keeps matching
 # cached files instead of missing every one after a move (#1417).
-#
-# Only stamp semantic files (docs/papers/images) that ACTUALLY produced output
-# THIS run (new_extraction is this run's fresh extraction, read above before the
-# merge overwrote the file): a changed doc whose chunk failed must stay unstamped
-# so the next --update re-queues it, otherwise it is marked done and its content
-# is lost forever (#2015). Mirrors the library extract path
-# (cli._stamped_manifest_files + clear_semantic + scan_corpus).
-from graphify.cli import _stamped_manifest_files
-_manifest_files = _stamped_manifest_files(incremental['files'], new_extraction, Path('INPUT_PATH'))
-# Changed semantic files dispatched this run but NOT stamped had their chunk fail
-# or be omitted; clear any stale semantic_hash so they are re-queued (#1948).
-_sem_types = ('document', 'paper', 'image')
-_dispatched = {f for t, fl in incremental.get('new_files', {}).items() if t in _sem_types for f in fl}
-_stamped = {f for fl in _manifest_files.values() for f in fl}
-_cleared = _dispatched - _stamped
-# scan_corpus = the RAW full corpus so in-root files newly excluded since last run
-# are dropped rather than masquerading as deletions; untouched rows preserved (#1908).
-_scan = {f for fl in incremental['files'].values() for f in fl}
 save_manifest(_manifest_files, root='INPUT_PATH', scan_corpus=_scan, clear_semantic=_cleared or None)
 print('[graphify update] Manifest saved.')
 "

graphify/skills/claw/references/update.md

@@ -87,12 +87,30 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from pathlib import Path
 from graphify.build import build_merge
+from graphify.cli import _stamped_manifest_files
 from graphify.detect import save_manifest
 
 # Load new extraction and incremental state
 new_extraction = json.loads(Path('graphify-out/.graphify_extract.json').read_text(encoding=\"utf-8\"))
 incremental = json.loads(Path('graphify-out/.graphify_incremental.json').read_text(encoding=\"utf-8\"))
 deleted = list(incremental.get('deleted_files', []))
+
+# Only stamp semantic files (docs/papers/images) that ACTUALLY produced output
+# THIS run (computed from new_extraction BEFORE build_merge() mutates it in place):
+# a changed doc whose chunk failed must stay unstamped so the next --update re-queues
+# it, otherwise it is marked done and its content is lost forever (#2015, #2865).
+# Mirrors the library extract path (cli._stamped_manifest_files + clear_semantic + scan_corpus).
+_manifest_files = _stamped_manifest_files(incremental['files'], new_extraction, Path('INPUT_PATH'))
+# Changed semantic files dispatched this run but NOT stamped had their chunk fail
+# or be omitted; clear any stale semantic_hash so they are re-queued (#1948).
+_sem_types = ('document', 'paper', 'image')
+_dispatched = {f for t, fl in incremental.get('new_files', {}).items() if t in _sem_types for f in fl}
+_stamped = {f for fl in _manifest_files.values() for f in fl}
+_cleared = _dispatched - _stamped
+# scan_corpus = the RAW full corpus so in-root files newly excluded since last run
+# are dropped rather than masquerading as deletions; untouched rows preserved (#1908).
+_scan = {f for fl in incremental['files'].values() for f in fl}
+
 # prune_sources is ONLY for genuinely DELETED files. Changed/re-extracted files are
 # handled by build_merge's replace-on-re-extract (#1344): every source_file in
 # new_chunks is dropped from the base before merge, so old/stale nodes don't survive.
@@ -142,24 +160,6 @@ print(f'[graphify update] Merged extraction written ({len(merged_out[\"nodes\"])
 # root= matches the build_merge call above so the manifest keys stay relative to
 # the scan root — portable across clones/machines, so --update keeps matching
 # cached files instead of missing every one after a move (#1417).
-#
-# Only stamp semantic files (docs/papers/images) that ACTUALLY produced output
-# THIS run (new_extraction is this run's fresh extraction, read above before the
-# merge overwrote the file): a changed doc whose chunk failed must stay unstamped
-# so the next --update re-queues it, otherwise it is marked done and its content
-# is lost forever (#2015). Mirrors the library extract path
-# (cli._stamped_manifest_files + clear_semantic + scan_corpus).
-from graphify.cli import _stamped_manifest_files
-_manifest_files = _stamped_manifest_files(incremental['files'], new_extraction, Path('INPUT_PATH'))
-# Changed semantic files dispatched this run but NOT stamped had their chunk fail
-# or be omitted; clear any stale semantic_hash so they are re-queued (#1948).
-_sem_types = ('document', 'paper', 'image')
-_dispatched = {f for t, fl in incremental.get('new_files', {}).items() if t in _sem_types for f in fl}
-_stamped = {f for fl in _manifest_files.values() for f in fl}
-_cleared = _dispatched - _stamped
-# scan_corpus = the RAW full corpus so in-root files newly excluded since last run
-# are dropped rather than masquerading as deletions; untouched rows preserved (#1908).
-_scan = {f for fl in incremental['files'].values() for f in fl}
 save_manifest(_manifest_files, root='INPUT_PATH', scan_corpus=_scan, clear_semantic=_cleared or None)
 print('[graphify update] Manifest saved.')
 "

graphify/skills/codex/references/update.md

@@ -87,12 +87,30 @@ $(cat graphify-out/.graphify_python) -c "
 import json
 from pathlib import Path
 from graphify.build import build_merge
+from graphify.cli import _stamped_manifest_files
 from graphify.detect import save_manifest
 
 # Load new extraction and incremental state
 new_extraction = json.loads(Path('graphify-out/.graphify_extract.json').read_text(encoding=\"utf-8\"))
 incremental = json.loads(Path('graphify-out/.graphify_incremental.json').read_text(encoding=\"utf-8\"))
 deleted = list(incremental.get('deleted_files', []))
+
+# Only stamp semantic files (docs/papers/images) that ACTUALLY produced output
+# THIS run (computed from new_extraction BEFORE build_merge() mutates it in place):
+# a changed doc whose chunk failed must stay unstamped so the next --update re-queues
+# it, otherwise it is marked done and its content is lost forever (#2015, #2865).
+# Mirrors the library extract path (cli._stamped_manifest_files + clear_semantic + scan_corpus).
+_manifest_files = _stamped_manifest_files(incremental['files'], new_extraction, Path('INPUT_PATH'))
+# Changed semantic files dispatched this run but NOT stamped had their chunk fail
+# or be omitted; clear any stale semantic_hash so they are re-queued (#1948).
+_sem_types = ('document', 'paper', 'image')
+_dispatched = {f for t, fl in incremental.get('new_files', {}).items() if t in _sem_types for f in fl}
+_stamped = {f for fl in _manifest_files.values() for f in fl}
+_cleared = _dispatched - _stamped
+# scan_corpus = the RAW full corpus so in-root files newly excluded since last run
+# are dropped rather than masquerading as deletions; untouched rows preserved (#1908).
+_scan = {f for fl in incremental['files'].values() for f in fl}
+
 # prune_sources is ONLY for genuinely DELETED files. Changed/re-extracted files are
 # handled by build_merge's replace-on-re-extract (#1344): every source_file in
 # new_chunks is dropped from the base before merge, so old/stale nodes don't survive.
@@ -142,24 +160,6 @@ print(f'[graphify update] Merged extraction written ({len(merged_out[\"nodes\"])
 # root= matches the build_merge call above so the manifest keys stay relative to
 # the scan root — portable across clones/machines, so --update keeps matching
 # cached files instead of missing every one after a move (#1417).
-#
-# Only stamp semantic files (docs/papers/images) that ACTUALLY produced output
-# THIS run (new_extraction is this run's fresh extraction, read above before the
-# merge overwrote the file): a changed doc whose chunk failed must stay unstamped
-# so the next --update re-queues it, otherwise it is marked done and its content
-# is lost forever (#2015). Mirrors the library extract path
-# (cli._stamped_manifest_files + clear_semantic + scan_corpus).
-from graphify.cli import _stamped_manifest_files
-_manifest_files = _stamped_manifest_files(incremental['files'], new_extraction, Path('INPUT_PATH'))
-# Changed semantic files dispatched this run but NOT stamped had their chunk fail
-# or be omitted; clear any stale semantic_hash so they are re-queued (#1948).
-_sem_types = ('document', 'paper', 'image')
-_dispatched = {f for t, fl in incremental.get('new_files', {}).items() if t in _sem_types for f in fl}
-_stamped = {f for fl in _manifest_files.values() for f in fl}
-_cleared = _dispatched - _stamped
-# scan_corpus = the RAW full corpus so in-root files newly excluded since last run
-# are dropped rather than masquerading as deletions; untouched rows preserved (#1908).
-_scan = {f for fl in incremental['files'].values() for f in fl}
 save_manifest(_manifest_files, root='INPUT_PATH', scan_corpus=_scan, clear_semantic=_cleared or None)
 print('[graphify update] Manifest saved.')
 "