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The #2543 heal re-queues any manifest-stamped code file that has a
registered extractor but zero nodes in graph.json, treating it as a
poisoned stamp. A file the extractor declines by design (data JSON such
as .xcassets Contents.json, #1224/#2879) is exactly that shape — stamped,
zero nodes — yet legitimate, so the heal re-queued it on every incremental
run forever.
extract() now surfaces the declined files (skipped_sources), save_manifest
marks their row ast_empty: true (preserved across unchanged incrementals,
dropped once a file starts producing nodes), and the heal skips rows
carrying the marker. A pre-fix manifest has no marker, so such a file is
re-queued exactly once, re-stamped with the marker, and left alone after.
Co-Authored-By: Claude Code <noreply@anthropic.com>
(cherry picked from commit c930591f08)