fix: reconcile disconnected local/remote metadata branches on enable

[dvydra]

Problem

When a user hit the empty-orphan bug (#511) and then worked normally, the CLI recorded checkpoints onto the local orphan. Now the local entire/checkpoints/v1 has real data on a completely disconnected history from the remote — no common ancestor, both containing real checkpoint data.

Neither #511 (fresh clone fix) nor #516 (empty orphan update) handle this case because the local branch isn't empty.

Discussion: https://entireio.slack.com/archives/C0A095SNK32/p1772083910982219?thread_ts=1772052543.300359&cid=C0A095SNK32

Fix

EnsureMetadataBranch() now detects when local and remote metadata branches have real data but differ, and uses git merge-base --is-ancestor to determine the relationship:

1. Remote is ancestor of local → already synced, nothing to do
2. Local is ancestor of remote → fast-forward local to remote
3. Neither (disconnected/diverged) → merge both trees into a merge commit

The merge is safe because checkpoint data is sharded by random ID (<id[:2]>/<id[2:]>/) with no shared index or manifest — different checkpoints never write to the same paths.

Uses the same tree-merge pattern as fetchAndMergeSessionsCommon() in push_common.go: flatten both trees via FlattenTree(), combine entries, rebuild via BuildTreeFromEntries(), create merge commit with both parents.

Test plan

• TestEnsureMetadataBranch_ReconcilesDisconnectedBranches — creates disconnected orphan with local data, verifies merge contains both sides
• TestEnsureMetadataBranch_FastForwardsWhenBehind — local behind remote, verifies fast-forward
• Existing tests still pass (fresh clone, empty orphan, no remote)
• mise run fmt && mise run lint && mise run test:ci clean

🤖 Generated with Claude Code

[cursor]

PR Summary

Medium Risk
Touches git ref/commit manipulation for the metadata branch and shells out to git merge-base, so failures could impact checkpoint syncing or create unexpected merge commits if assumptions about tree merging change.

Overview
Fixes EnsureMetadataBranch() so that when both local and origin/entire/checkpoints/v1 exist with non-empty but different histories, the CLI determines ancestry via git merge-base --is-ancestor and either does nothing, fast-forwards the local ref, or creates a merge commit that combines both checkpoint trees.

Adds syncMetadataBranch/isAncestorCLI helpers (uses git CLI with a timeout) and expands tests to cover disconnected-history reconciliation and the “local behind remote” fast-forward case, plus a small test utility for cloning with git identity.

^{Written by Cursor Bugbot for commit 32ad256. Configure here.}

[Copilot]

Pull request overview

This PR fixes a critical bug where users who encountered the empty-orphan bug (#511) and then continued working would have disconnected local and remote metadata branches with real checkpoint data but no common ancestor. The fix adds logic to detect and reconcile such disconnected branches through merging.

Changes:

• Added syncMetadataBranch() function to handle disconnected/diverged local and remote metadata branches using git merge-base for ancestry checks
• Added isAncestorCLI() helper to check commit ancestry via git CLI (avoiding go-git depth limits)
• Added comprehensive test coverage for branch reconciliation scenarios including disconnected branches and fast-forward cases

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated no comments.

File	Description
cmd/entire/cli/strategy/common.go	Implements branch reconciliation logic with ancestry detection and tree merging for disconnected metadata branches
cmd/entire/cli/strategy/common_test.go	Adds test helper and comprehensive tests for reconciliation scenarios (disconnected branches, fast-forward, existing tests)

[dvydra]

superceded by #533