PR #1558 — Milestone v0.20.0 Cluster B — Worktree Lifecycle & Rebase Concurrency

The Broader Goal at the End of the Previous PR

Advancing the multi-agent operating system toward reliable, autonomous development, unblocking workgroup velocity and eliminating manual developer toil.

Strategic Shifts in This PR

Focused, limited-treatment delta resolving PR #1558 requirements with strict backward compatibility and comprehensive verification.

What This PR Shipped

• Adaptive Scope-Bounded Sparse Worktrees (#1389, #1390, #1391):
• Cone-mode sparse checkout using extensions.worktreeConfig true and git sparse-checkout init --cone.
• Guaranteed context isolation and fast checkout (<150ms) with mandatory inclusion of .synlynk/, project-docs/, synlynk/, and tests/.
• Dynamic cone expansion via ensure_path_in_sparse_cone().
• Sibling Branch Auto-Pruning Engine (#1348):
• Patch-equivalence detection via git cherry to safely identify squash-merged branches.
• Worktree cleanup and local/remote branch deletion integrated with synlynk worktree clean --prune-siblings.
• Multi-Task Lineage Tracking (#1347):
• Added superseded_by and lineage_root columns to SQLite schema (daemon_jobs and stories).
• Added record_job_superseded(), record_story_superseded(), and get_job_lineage().
• Excluded superseded jobs from zombie reap detection and marked with superseded status tag.
• Deterministic Build Timestamp Freezing (#1349):
• Extracted commit epoch via get_worktree_epoch() and injected SOURCE_DATE_EPOCH into subprocess environment for all dispatched workers.

Verification & Test Evidence

56 regression and unit tests passing in tests/test_worktree_sparse.py, tests/test_worktree_prune.py, tests/test_worktree_lineage.py, tests/test_worktree_timestamp.py, and tests/test_worktree.py.

What This Achieved on the Path to Autonomy

Maintains repository integrity, expands test-proven capabilities, and keeps the hybrid human-agent workgroup aligned with zero drift.