From e1636a0e8808b35545730286d415455398ace013 Mon Sep 17 00:00:00 2001
From: saxster <119735920+saxster@users.noreply.github.com>
Date: Sat, 2 May 2026 18:44:52 +0530
Subject: [PATCH] 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.
---
 graphify/skill-copilot.md | 8 ++++++++
 graphify/skill.md         | 8 ++++++++
 2 files changed, 16 insertions(+)

diff --git a/graphify/skill-copilot.md b/graphify/skill-copilot.md
index 62992f977..468279891 100644
--- a/graphify/skill-copilot.md
+++ b/graphify/skill-copilot.md
@@ -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.')
 " 
 ```
 
diff --git a/graphify/skill.md b/graphify/skill.md
index f04d71ff6..58cb22c42 100644
--- a/graphify/skill.md
+++ b/graphify/skill.md
@@ -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.')
 " 
 ```