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fix(skills): prune excluded files during update #2909

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14 changes: 9 additions & 5 deletions graphify/skills/agents/references/update.md
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -17,11 +17,14 @@ 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\")
deleted = list(result.get('deleted_files', []))
if new_total == 0 and not deleted:
excluded = list(result.get('excluded_files', []))
if new_total == 0 and not deleted and not excluded:
print('No files changed since last run. Nothing to update.')
raise SystemExit(0)
if deleted:
print(f'{len(deleted)} deleted file(s) to prune.')
if excluded:
print(f'{len(excluded)} excluded file(s) to prune.')
if new_total > 0:
print(f'{new_total} new/changed file(s) to re-extract.')
"
Expand Down Expand Up @@ -93,13 +96,14 @@ from graphify.detect import save_manifest
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', []))
# 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.
excluded = list(incremental.get('excluded_files', []))
# prune_sources is ONLY for genuinely DELETED and EXCLUDED files (#1908/#2908). 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.
# Do NOT add `changed` here: with root= passed, prune_set relativizes to the same base
# as the freshly merged nodes and would DELETE the re-extracted content (#1178 is moot
# now that replace — not the dedup pass — reconciles changed files).
prune = list(deleted) or None
prune = deleted + excluded or None

# Use build_merge() — reads graph.json directly without NetworkX round-trip
# so edge direction (calls, implements, imports) is always preserved (#801).
Expand Down
14 changes: 9 additions & 5 deletions graphify/skills/amp/references/update.md
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -17,11 +17,14 @@ 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\")
deleted = list(result.get('deleted_files', []))
if new_total == 0 and not deleted:
excluded = list(result.get('excluded_files', []))
if new_total == 0 and not deleted and not excluded:
print('No files changed since last run. Nothing to update.')
raise SystemExit(0)
if deleted:
print(f'{len(deleted)} deleted file(s) to prune.')
if excluded:
print(f'{len(excluded)} excluded file(s) to prune.')
if new_total > 0:
print(f'{new_total} new/changed file(s) to re-extract.')
"
Expand Down Expand Up @@ -93,13 +96,14 @@ from graphify.detect import save_manifest
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', []))
# 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.
excluded = list(incremental.get('excluded_files', []))
# prune_sources is ONLY for genuinely DELETED and EXCLUDED files (#1908/#2908). 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.
# Do NOT add `changed` here: with root= passed, prune_set relativizes to the same base
# as the freshly merged nodes and would DELETE the re-extracted content (#1178 is moot
# now that replace — not the dedup pass — reconciles changed files).
prune = list(deleted) or None
prune = deleted + excluded or None

# Use build_merge() — reads graph.json directly without NetworkX round-trip
# so edge direction (calls, implements, imports) is always preserved (#801).
Expand Down
14 changes: 9 additions & 5 deletions graphify/skills/claude/references/update.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -17,11 +17,14 @@ 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\")
deleted = list(result.get('deleted_files', []))
if new_total == 0 and not deleted:
excluded = list(result.get('excluded_files', []))
if new_total == 0 and not deleted and not excluded:
print('No files changed since last run. Nothing to update.')
raise SystemExit(0)
if deleted:
print(f'{len(deleted)} deleted file(s) to prune.')
if excluded:
print(f'{len(excluded)} excluded file(s) to prune.')
if new_total > 0:
print(f'{new_total} new/changed file(s) to re-extract.')
"
Expand Down Expand Up @@ -93,13 +96,14 @@ from graphify.detect import save_manifest
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', []))
# 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.
excluded = list(incremental.get('excluded_files', []))
# prune_sources is ONLY for genuinely DELETED and EXCLUDED files (#1908/#2908). 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.
# Do NOT add `changed` here: with root= passed, prune_set relativizes to the same base
# as the freshly merged nodes and would DELETE the re-extracted content (#1178 is moot
# now that replace — not the dedup pass — reconciles changed files).
prune = list(deleted) or None
prune = deleted + excluded or None

# Use build_merge() — reads graph.json directly without NetworkX round-trip
# so edge direction (calls, implements, imports) is always preserved (#801).
Expand Down
14 changes: 9 additions & 5 deletions graphify/skills/claw/references/update.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -17,11 +17,14 @@ 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\")
deleted = list(result.get('deleted_files', []))
if new_total == 0 and not deleted:
excluded = list(result.get('excluded_files', []))
if new_total == 0 and not deleted and not excluded:
print('No files changed since last run. Nothing to update.')
raise SystemExit(0)
if deleted:
print(f'{len(deleted)} deleted file(s) to prune.')
if excluded:
print(f'{len(excluded)} excluded file(s) to prune.')
if new_total > 0:
print(f'{new_total} new/changed file(s) to re-extract.')
"
Expand Down Expand Up @@ -93,13 +96,14 @@ from graphify.detect import save_manifest
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', []))
# 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.
excluded = list(incremental.get('excluded_files', []))
# prune_sources is ONLY for genuinely DELETED and EXCLUDED files (#1908/#2908). 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.
# Do NOT add `changed` here: with root= passed, prune_set relativizes to the same base
# as the freshly merged nodes and would DELETE the re-extracted content (#1178 is moot
# now that replace — not the dedup pass — reconciles changed files).
prune = list(deleted) or None
prune = deleted + excluded or None

# Use build_merge() — reads graph.json directly without NetworkX round-trip
# so edge direction (calls, implements, imports) is always preserved (#801).
Expand Down
14 changes: 9 additions & 5 deletions graphify/skills/codex/references/update.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -17,11 +17,14 @@ 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\")
deleted = list(result.get('deleted_files', []))
if new_total == 0 and not deleted:
excluded = list(result.get('excluded_files', []))
if new_total == 0 and not deleted and not excluded:
print('No files changed since last run. Nothing to update.')
raise SystemExit(0)
if deleted:
print(f'{len(deleted)} deleted file(s) to prune.')
if excluded:
print(f'{len(excluded)} excluded file(s) to prune.')
if new_total > 0:
print(f'{new_total} new/changed file(s) to re-extract.')
"
Expand Down Expand Up @@ -93,13 +96,14 @@ from graphify.detect import save_manifest
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', []))
# 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.
excluded = list(incremental.get('excluded_files', []))
# prune_sources is ONLY for genuinely DELETED and EXCLUDED files (#1908/#2908). 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.
# Do NOT add `changed` here: with root= passed, prune_set relativizes to the same base
# as the freshly merged nodes and would DELETE the re-extracted content (#1178 is moot
# now that replace — not the dedup pass — reconciles changed files).
prune = list(deleted) or None
prune = deleted + excluded or None

# Use build_merge() — reads graph.json directly without NetworkX round-trip
# so edge direction (calls, implements, imports) is always preserved (#801).
Expand Down
14 changes: 9 additions & 5 deletions graphify/skills/copilot/references/update.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -17,11 +17,14 @@ 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\")
deleted = list(result.get('deleted_files', []))
if new_total == 0 and not deleted:
excluded = list(result.get('excluded_files', []))
if new_total == 0 and not deleted and not excluded:
print('No files changed since last run. Nothing to update.')
raise SystemExit(0)
if deleted:
print(f'{len(deleted)} deleted file(s) to prune.')
if excluded:
print(f'{len(excluded)} excluded file(s) to prune.')
if new_total > 0:
print(f'{new_total} new/changed file(s) to re-extract.')
"
Expand Down Expand Up @@ -93,13 +96,14 @@ from graphify.detect import save_manifest
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', []))
# 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.
excluded = list(incremental.get('excluded_files', []))
# prune_sources is ONLY for genuinely DELETED and EXCLUDED files (#1908/#2908). 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.
# Do NOT add `changed` here: with root= passed, prune_set relativizes to the same base
# as the freshly merged nodes and would DELETE the re-extracted content (#1178 is moot
# now that replace — not the dedup pass — reconciles changed files).
prune = list(deleted) or None
prune = deleted + excluded or None

# Use build_merge() — reads graph.json directly without NetworkX round-trip
# so edge direction (calls, implements, imports) is always preserved (#801).
Expand Down
14 changes: 9 additions & 5 deletions graphify/skills/droid/references/update.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -17,11 +17,14 @@ 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\")
deleted = list(result.get('deleted_files', []))
if new_total == 0 and not deleted:
excluded = list(result.get('excluded_files', []))
if new_total == 0 and not deleted and not excluded:
print('No files changed since last run. Nothing to update.')
raise SystemExit(0)
if deleted:
print(f'{len(deleted)} deleted file(s) to prune.')
if excluded:
print(f'{len(excluded)} excluded file(s) to prune.')
if new_total > 0:
print(f'{new_total} new/changed file(s) to re-extract.')
"
Expand Down Expand Up @@ -93,13 +96,14 @@ from graphify.detect import save_manifest
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', []))
# 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.
excluded = list(incremental.get('excluded_files', []))
# prune_sources is ONLY for genuinely DELETED and EXCLUDED files (#1908/#2908). 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.
# Do NOT add `changed` here: with root= passed, prune_set relativizes to the same base
# as the freshly merged nodes and would DELETE the re-extracted content (#1178 is moot
# now that replace — not the dedup pass — reconciles changed files).
prune = list(deleted) or None
prune = deleted + excluded or None

# Use build_merge() — reads graph.json directly without NetworkX round-trip
# so edge direction (calls, implements, imports) is always preserved (#801).
Expand Down
14 changes: 9 additions & 5 deletions graphify/skills/kilo/references/update.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -17,11 +17,14 @@ 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\")
deleted = list(result.get('deleted_files', []))
if new_total == 0 and not deleted:
excluded = list(result.get('excluded_files', []))
if new_total == 0 and not deleted and not excluded:
print('No files changed since last run. Nothing to update.')
raise SystemExit(0)
if deleted:
print(f'{len(deleted)} deleted file(s) to prune.')
if excluded:
print(f'{len(excluded)} excluded file(s) to prune.')
if new_total > 0:
print(f'{new_total} new/changed file(s) to re-extract.')
"
Expand Down Expand Up @@ -93,13 +96,14 @@ from graphify.detect import save_manifest
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', []))
# 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.
excluded = list(incremental.get('excluded_files', []))
# prune_sources is ONLY for genuinely DELETED and EXCLUDED files (#1908/#2908). 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.
# Do NOT add `changed` here: with root= passed, prune_set relativizes to the same base
# as the freshly merged nodes and would DELETE the re-extracted content (#1178 is moot
# now that replace — not the dedup pass — reconciles changed files).
prune = list(deleted) or None
prune = deleted + excluded or None

# Use build_merge() — reads graph.json directly without NetworkX round-trip
# so edge direction (calls, implements, imports) is always preserved (#801).
Expand Down
14 changes: 9 additions & 5 deletions graphify/skills/kiro/references/update.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -17,11 +17,14 @@ 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\")
deleted = list(result.get('deleted_files', []))
if new_total == 0 and not deleted:
excluded = list(result.get('excluded_files', []))
if new_total == 0 and not deleted and not excluded:
print('No files changed since last run. Nothing to update.')
raise SystemExit(0)
if deleted:
print(f'{len(deleted)} deleted file(s) to prune.')
if excluded:
print(f'{len(excluded)} excluded file(s) to prune.')
if new_total > 0:
print(f'{new_total} new/changed file(s) to re-extract.')
"
Expand Down Expand Up @@ -93,13 +96,14 @@ from graphify.detect import save_manifest
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', []))
# 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.
excluded = list(incremental.get('excluded_files', []))
# prune_sources is ONLY for genuinely DELETED and EXCLUDED files (#1908/#2908). 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.
# Do NOT add `changed` here: with root= passed, prune_set relativizes to the same base
# as the freshly merged nodes and would DELETE the re-extracted content (#1178 is moot
# now that replace — not the dedup pass — reconciles changed files).
prune = list(deleted) or None
prune = deleted + excluded or None

# Use build_merge() — reads graph.json directly without NetworkX round-trip
# so edge direction (calls, implements, imports) is always preserved (#801).
Expand Down
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