refactor: unify tree modification to use ApplyTreeChanges

[dvydra]

Summary

• Adds DiffTrees helper to checkpoint/parse_tree.go that computes []TreeChange from two flat entry maps
• Converts 2 call sites from FlattenTree + BuildTreeFromEntries (flatten entire tree, rebuild from scratch) to DiffTrees + ApplyTreeChanges (surgical tree modification):
  • fetchAndMergeSessionsCommon in push_common.go — separate flattens + surgical apply
  • DeleteOrphanedCheckpoints in cleanup.go — flatten to discover paths + surgical delete
• All tree modification sites now use the same primitive as WriteCommitted, reducing cognitive overhead
• cherryPickOnto in metadata_reconcile.go should be converted separately when PR fix: detect and repair disconnected metadata branches at read/write time #533 merges

Test plan

• 7 new unit tests for DiffTrees including equivalence test with ApplyTreeChanges
• mise run fmt && mise run lint passes clean
• mise run test:ci passes (unit + integration)

🤖 Generated with Claude Code

[cursor]

PR Summary

Medium Risk
Moderate risk because it changes how git trees are merged/deleted in session log syncing, checkpoint cleanup, and metadata-branch repair; bugs here could drop or fail to merge metadata. Added unit tests reduce risk, but behavior differences around deletions/empty dirs remain the main concern.

Overview
Introduces checkpoint.DiffTrees to compute file-level []TreeChange deltas between two flattened trees.

Refactors session log merge (fetchAndMergeSessionsCommon) and orphaned checkpoint cleanup to stop rebuilding full trees and instead apply computed deltas/deletions via checkpoint.ApplyTreeChanges.

Adds ReconcileDisconnectedMetadataBranch to detect a disconnected local/remote entire/checkpoints/v1 history (via git merge-base) and repair it by cherry-picking local commit deltas onto the remote tip using DiffTrees + ApplyTreeChanges.

Adds focused unit tests for DiffTrees, including an equivalence test ensuring DiffTrees + ApplyTreeChanges matches a flatten+rebuild result (when no full-directory deletions are involved).

^{Written by Cursor Bugbot for commit 913f497. Configure here.}

[Copilot]

Pull request overview

Refactors session/checkpoint tree mutation to rely on a single “tree surgery” primitive (ApplyTreeChanges) and introduces DiffTrees to compute []TreeChange deltas from flattened entry maps, reducing full-tree rebuilds across strategy operations.

Changes:

• Added checkpoint.DiffTrees(base, target) to compute file-level add/modify/delete changes from flattened trees.
• Updated session-log merge (fetchAndMergeSessionsCommon) and cleanup (DeleteOrphanedCheckpoints) to apply targeted tree changes via ApplyTreeChanges.
• Added metadata branch reconciliation logic to cherry-pick disconnected local metadata commits onto the remote tip using DiffTrees + ApplyTreeChanges, plus unit tests for DiffTrees.

Reviewed changes

Copilot reviewed 5 out of 5 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
cmd/entire/cli/strategy/push_common.go	Switches remote/local session-log merging from flatten+rebuild to diff+apply tree surgery.
cmd/entire/cli/strategy/metadata_reconcile.go	Adds disconnected metadata-branch reconciliation via cherry-pick using tree diffs and surgical apply.
cmd/entire/cli/strategy/cleanup.go	Converts orphaned checkpoint deletion to generate TreeChange deletions and apply surgically.
cmd/entire/cli/checkpoint/parse_tree.go	Introduces DiffTrees helper to produce []TreeChange from two flattened entry maps.
cmd/entire/cli/checkpoint/parse_tree_test.go	Adds unit tests validating DiffTrees behavior and equivalence with ApplyTreeChanges.

[Copilot]

In this merge path we need to preserve local-only session log entries and add remote entries on top. Using DiffTrees(localEntries, remoteEntries) computes deletions for any path present locally but absent remotely, which can drop local session logs when the remote isn't a strict superset (common after a non-fast-forward push rejection). Consider diffing against a union map (local + remote, with remote overwriting collisions) or otherwise filtering out deletions so the result is an additive/overwrite merge rather than “make local identical to remote”.

Suggested change

	// DiffTrees computes changes to transform local into remote (remote wins on collision)
	changes := checkpoint.DiffTrees(localEntries, remoteEntries)
	// Build a union of local and remote entries where remote overwrites on collision.
	// This ensures we only add/update entries and never delete local-only session logs.
	unionEntries := make(map[string]object.TreeEntry, len(localEntries)+len(remoteEntries))
	for path, entry := range localEntries {
	unionEntries[path] = entry
	}
	for path, entry := range remoteEntries {
	unionEntries[path] = entry
	}
	// DiffTrees computes changes to transform local into the union (remote wins on collision),
	// preserving local-only entries.
	changes := checkpoint.DiffTrees(localEntries, unionEntries)

[Copilot]

DiffTrees only compares TreeEntry.Hash when deciding whether an entry changed. Git tree entries also encode the file mode (e.g., regular vs executable), so a pure mode change with identical blob content would be missed and not applied. Include entry.Mode (and any other relevant metadata) in the equality check so mode-only changes produce a TreeChange.