Add atomic stack storage and migration primitives

[skarim]

Makes the files that record stacks and interrupted operations safer to save and read. It also prepares the move from separate tracking files in each checkout to one shared stack catalog, without losing existing stack definitions.

Functionality and user impact

• Write each updated file in full before replacing the old one, keeping its permissions. Other commands cannot read a half-written file, and a failed save reports an error rather than deleting the old file first.
• Prepare a migration that combines separate stacks and matching copies of the same stack, keeps backups, and stops when definitions conflict or an older operation still needs recovery. Interrupted migrations can resume.
• Add separate locks for saving the catalog and running a whole command. A save also checks whether another command changed the file since it was loaded.

Boundary: commands still use their existing catalog locations. #528 turns on shared storage and migration. This PR changes how files are saved, not branch contents or worktree layouts. Worktree support requires Git 2.36+ and does not create/remove worktrees or stash changes automatically.

Key areas to review

• internal/stack/atomic.go: WriteAtomic / writeFileAtomic write and flush a temporary file before replacing the saved file. Check that failures are reported and temporary files are cleaned up.
• atomic_unix.go and atomic_windows.go: handle replacement on each platform, including Windows readers that still have the old file open. Creating a backup must never overwrite an existing backup.
• internal/stack/stack.go: Save and checkStale prevent overwriting changes made since loading. SaveNonBlocking lets an optional metadata refresh skip saving when another writer is active.
• internal/stack/lock.go: Lock is held only while saving the catalog. LockOperation can cover a whole command, including branch changes and the final save. Keeping them separate lets the command save without trying to acquire a lock it already holds.
• internal/stack/migration.go: MigrateLegacyState, mergeMigrationCatalogs, and checkMigrationSnapshot decide which definitions can be combined. Follow how original data is saved before the new catalog replaces it, and how interrupted work resumes.

Related issues

• Github stack does not persist across worktrees #459
• gh stack rebase silently succeeds when git rebase --onto fails to start (in branch checked out in another worktree) #35
• sync might not work with worktree #87

Part 2 of the 4-PR split of #520

[Copilot]

Copilot review overview

🟡 Changes recommended

Windows recovery-state readers do not permit delete sharing, so concurrent atomic replacement can fail and leave stale recovery data.

Review effort: Balanced
Findings: 2

Open (2)

• Use share-delete reads when loading rebase state · New
• Use share-delete reads when loading modify state · New

What changed in this PR

Adds atomic state persistence, separate operation/catalog locks, and resumable migration primitives for future shared worktree storage.

Changes:

• Implements cross-platform atomic file replacement.
• Adds migration conflict detection, backups, journaling, and recovery.
• Extends locking and stale-write protection with comprehensive tests.

File	Description
cmd/​rebase.go	Uses atomic rebase-state writes.
internal/​git/​gitops_test.go	Improves rebase failure diagnostics.
internal/​modify/​state.go	Uses atomic modify-state writes.
internal/​stack/​atomic.go	Implements shared atomic-write logic.
internal/​stack/​atomic_unix.go	Adds Unix publication and directory syncing.
internal/​stack/​atomic_windows.go	Adds Windows replacement and share-delete reads.
internal/​stack/​atomic_windows_test.go	Tests Windows reader-safe replacement.
internal/​stack/​lock.go	Separates catalog and operation locks.
internal/​stack/​lock_test.go	Tests locking and atomic publication.
internal/​stack/​migration.go	Implements resumable catalog migration.
internal/​stack/​stack.go	Integrates atomic saves and migration guards.
internal/​stack/​stack_test.go	Tests migration, conflicts, and recovery.

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[Lukeghenco]

New line needed?

[Lukeghenco]

This seems like the biggest core change in this PR right? If I am understanding this correctly we are now writing to a temp file before we replace the pre-existing one (in stack/atomic.go) instead of what appears to be deleting and then replacing the file in the deleted code?