A cross-directory rename added the new parent's Contains edge but skipped
removing the old one (a 'not critical' shortcut), leaving the moved entity
a child of BOTH directories: readdir(oldDir) kept listing it, re-creating
the old path showed the name twice, and tree-walking consumers saw the
file in two places. Reported live by a production deployment (37 stale
containment ghosts; blocks tree-sync integrations).
- rename() now removes the old parent's vfs containment edge(s) by edge
id resolved from the graph's own adjacency (the removal law: removal
never requires reading the removed thing), and a move to the root gets
its containment edge (previously skipped -> orphaned from readdir('/')).
- New vfs.repairContainment(): reconciles every VFS entity's containment
edges against canonical metadata.path — removes stale/duplicate vfs
edges, restores missing ones, never touches user knowledge edges. Wired
into repairIndex() so the one operator ritual heals existing ghosts.
- Regression: tests/integration/vfs-rename-containment.test.ts (7).
