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danusha2345
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`codegraph index` rebuilds through `CodeGraph.recreate()`, which unlinks `.codegraph/codegraph.db` and creates a new file at the same path. A running MCP daemon kept its handle on the unlinked inode and its watcher kept "auto-syncing" into it, so no edit reached the on-disk index. The #925 self-heal only ran on the tool-call path and ran no catch-up after reopening. - `sync()` now checks, once it holds the index mutex and the write lock, whether the database was replaced on disk (one stat, the same inode check `reopenIfReplaced` uses). If so it reopens the live file in place and widens a scoped sync to a full reconcile. A failed reopen (rebuild mid-way) returns the lock-busy shape so the watcher keeps its pending files and retries. - `reopenIfReplaced()` refuses while an index/sync holds the mutex, so the tool-call path never closes the handle an in-flight sync writes through. - When a tool call's `freshen()` does reopen, the engine runs its existing catch-up sync (serialized on the same mutex), but only for its own watched instance, so an engine that is not the project's writer never writes. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>