External import stubs (#2873) are minted without an _origin stamp. On
the next update the #2334 tier backfill stamped them by shape, and a
stub has no L<line> location, so it became `semantic`. Reconcile keeps
semantic nodes, so once the last file importing a module stopped
importing it, the stub stayed in graph.json forever with no edge. It
also made a rebuild of an unchanged tree differ from the first build.
A stub is derived from its import edges and minted again on every
write, so it has no tier. The backfill (now one helper shared by
_load_existing_graph and the reconcile path) skips stubs and removes a
stamp an earlier run gave one; every tier decision reads an unstamped
stub exactly as before. Reconcile drops a preserved stub that no fresh
or preserved edge references.
On graphify's own repo a warm rebuild now equals the cold build (125
stub nodes differed), a long-lived graph heals to the cold node set
(8 ghost stubs removed), and the changed-files path equals the full
rebuild for edits and additions.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
