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docs(skill): save_manifest at end of --update merge step (#545)

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Closes #538.

The full-pipeline path's Step 9 already calls save_manifest, so the
NEXT --update can diff against the full-rebuild's baseline.

But the --update flow itself does NOT save the manifest after merging
the incremental result. Consequence: a file deleted between
--update #1 and --update #2 keeps reappearing in #2's deleted_files
list (since the manifest still records its old mtime), generating a
spurious ghost-node prune attempt every run.

Add save_manifest(incremental['files']) at the end of the --update
merge step in both skill.md and skill-copilot.md (the only two skill
files carrying the merge step verbatim). The 'incremental' dict is
already in scope from the prune block above; its 'files' key is the
full current file list, which is exactly what save_manifest needs.

Pure prompt edit — no code changes, no test impact.
This commit is contained in:
saxster
2026-05-02 14:14:52 +01:00
committed by GitHub
parent 8b41440ad1
commit e1636a0e88
2 changed files with 16 additions and 0 deletions
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graphify/skill-copilot.md
+8
View File
@@ -827,6 +827,14 @@ if deleted:
# Merge: new nodes/edges into existing graph
G_existing.update(G_new)
print(f'Merged: {G_existing.number_of_nodes()} nodes, {G_existing.number_of_edges()} edges')
# Save manifest with the CURRENT full file list so the next --update
# diffs against today's filesystem state, not the prior --update's
# baseline. Without this, deleted files get reported as ghosts again
# on every subsequent --update until a full rebuild runs.
from graphify.detect import save_manifest
save_manifest(incremental['files'])
print('[graphify update] Manifest saved.')
"
```
graphify/skill.md
+8
View File
@@ -942,6 +942,14 @@ merged_out = {
}
Path('graphify-out/.graphify_extract.json').write_text(json.dumps(merged_out))
print(f'[graphify update] Merged extraction written ({len(merged_out[\"nodes\"])} nodes, {len(merged_out[\"edges\"])} edges)')
# Save manifest with the CURRENT full file list so the next --update
# diffs against today's filesystem state, not the prior --update's
# baseline. Without this, deleted files get reported as ghosts again
# on every subsequent --update until a full rebuild runs.
from graphify.detect import save_manifest
save_manifest(incremental['files'])
print('[graphify update] Manifest saved.')
"
```