strategy: don't treat shallow merge-base miss as disconnected metadata

[Soph]

https://entire.io/gh/entireio/cli/trails/569

On a shallow checkpoint clone, git merge-base reports "no common ancestor" whenever the real ancestor lives below the shallow boundary — git has no objects there. The disconnection check trusted that exit code as proof of disconnection, so an ordinary diverged-but-behind metadata branch on a shallow clone was misread as disconnected. That triggered a full-history cherry-pick reconcile, which then blew MaxCommitTraversalDepth on a deep team branch and aborted both entire push and entire doctor ("commit chain exceeded 1000 commits without reaching root"), leaving doctor looping on a fix that could never succeed.

checkpoint/v1 clones are routinely shallow (resume/explain fetch the tip with --depth=1 via FetchMetadataTreeOnly and nothing deepens them again), so this hit a normal user who fell behind while out of office.

Fix:

• New metadataDisconnected() only trusts a merge-base miss as a genuine disconnection when the repo is NOT shallow; on a shallow clone the verdict is suppressed and the refs are reported connected. Routed through IsMetadataDisconnected (warn hot path + doctor detection) and ReconcileDisconnectedMetadataRef (push + doctor fix), so the warn path stays network-free and the doomed reconcile no longer fires.
• entire doctor now deepens the metadata branch (--unshallow, best-effort, without advancing the local ref) before the check when the repo is shallow, so it can still detect and repair genuine disconnections on an accurate, fully-materialized history.
• Export remote.IsShallowRepository so both packages share one check.

With the false positive gone, push rebases the local-only commits onto the remote tip normally and doctor reports OK instead of erroring. Genuine empty-orphan disconnections are still caught (by doctor after deepening, and on push the rebase cap still refuses to combine unrelated histories).

Entire-Checkpoint: 175693b95a72

---

Note

Medium Risk
Changes metadata disconnection detection and doctor fetch behavior on shallow repos; incorrect logic could miss real disconnections or skip needed repair, but behavior is covered by new tests and doctor still deepens before authoritative checks.

Overview
Fixes false disconnected metadata detection on shallow checkpoint clones, where git merge-base can report no common ancestor even when local and remote still share history below the shallow boundary.

metadataDisconnected only trusts a merge-base miss when the repo is not shallow; on shallow clones it reports refs as connected so push/warn paths skip a doomed full-history cherry-pick reconcile (which could hit MaxCommitTraversalDepth). IsMetadataDisconnected and ReconcileDisconnectedMetadataRef route through this helper.

entire doctor best-effort calls new DeepenMetadataBranch (--unshallow fetch of the metadata branch without advancing the local ref) before the disconnection check when the clone is shallow, so genuine disconnections can still be found after history is materialized.

remote.IsShallowRepository is exported for shared shallow detection; tests cover shallow false-positive suppression and real disconnections on full repos.

^{Reviewed by Cursor Bugbot for commit 7742dd7. Configure here.}

[Copilot]

Pull request overview

This PR fixes false “metadata branch disconnected” detection on shallow checkpoint clones by making the ancestry check shallow-aware, and by teaching entire doctor to deepen metadata history before performing an authoritative disconnection check/repair.

Changes:

• Route metadata disconnection detection through a new metadataDisconnected helper that suppresses merge-base “no common ancestor” results when the repo is shallow.
• Add DeepenMetadataBranch and invoke it from entire doctor (best-effort) to unshallow metadata history before checking/reconciling.
• Export remote.IsShallowRepository for shared shallow detection across packages and add tests for the new behavior.

Reviewed changes

Copilot reviewed 6 out of 6 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
cmd/entire/cli/strategy/metadata_reconcile.go	Adds shallow-aware disconnection detection and uses it in warning + reconcile paths.
cmd/entire/cli/strategy/metadata_reconcile_test.go	Adds coverage for shallow suppression vs genuine disconnection scenarios.
cmd/entire/cli/git_operations.go	Introduces DeepenMetadataBranch to unshallow metadata history without advancing the local primary ref.
cmd/entire/cli/doctor.go	Deepens metadata history on shallow repos before checking for disconnection (best-effort).
cmd/entire/cli/checkpoint/remote/git.go	Exports IsShallowRepository and uses it to gate --unshallow.
cmd/entire/cli/checkpoint/remote/git_test.go	Updates tests to use the exported IsShallowRepository.

[Soph]

close in favor of #1443