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.
saxster
e1636a0e88