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897483fc96
After #1361 added root= to the --update build_merge call, build_merge's prune (which runs after the merge) began matching freshly re-extracted changed-file nodes and deleting them — a regression in 0.8.41 where --update on a changed file wiped its nodes. This drops `changed` from prune_sources (replace-on- re-extract from #1344 already reconciles changed files), passes root= to the full build's build_from_json so its node-key base matches the update side, and pins the extraction-spec source_file to the verbatim path so the two runs never drift. Re-blessed skillgen expected/ snapshots. Co-Authored-By: RelywOo <RelywOo@users.noreply.github.com> Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>