In a shallow clone, gitutil.RootCommit (rev-list -n 1 --max-parents=0 HEAD) returns the graft commit, not the repository's root, and every machine-scoped store keyed on it files under that wrong key with no warning: the history ingest (internal/core/history/ingest.go:86), labs (internal/core/lab/lab.go:172), implement runs and loop state (internal/core/implement/load.go:357, internal/core/implement/loop/loop.go:454 and siblings), the report inbox key (internal/core/report/inbox.go:106), the lifeboat probe (internal/core/lifeboat/probe.go:211) and ahoy's managed-repository index (internal/core/ahoy/store.go:68, managed.go:54). A later full clone of the same repository reads a different folder, so the records look lost. CI checks out full history (fetch-depth: 0), so the gates are not affected. Found by review of the ideate private/public fix (iss-2610090740139804), which now refuses a shallow checkout at its own front door.

In a shallow clone, gitutil.RootCommit (rev-list -n 1 --max-parents=0 HEAD) returns the graft commit, not the repository's root, and every machine-scoped store keyed on it files under that wrong key with no warning: the history ingest (internal/core/history/ingest.go:86), labs (internal/core/lab/lab.go:172), implement runs and loop state (internal/core/implement/load.go:357, internal/core/implement/loop/loop.go:454 and siblings), the report inbox key (internal/core/report/inbox.go:106), the lifeboat probe (internal/core/lifeboat/probe.go:211) and ahoy's managed-repository index (internal/core/ahoy/store.go:68, managed.go:54). A later full clone of the same repository reads a different folder, so the records look lost. CI checks out full history (fetch-depth: 0), so the gates are not affected. Found by review of the ideate private/public fix (iss-2610090740139804), which now refuses a shallow checkout at its own front door.

The same lookup is also ambiguous in a full clone whose history has more than one root commit (an unrelated history merged in) or carries local replace refs or grafts: rev-list -n 1 --max-parents=0 HEAD picks one root by commit order, so two checkouts of one repository can key a store differently. A shallow-aware lookup should refuse those shapes too rather than pick one (found by the security review of the same fix).