Fix bd-hv01: Implement deletion tracking for multi-workspace sync

- Add 3-way merge deletion tracking using snapshot files
- Create .beads/beads.base.jsonl and .beads/beads.left.jsonl snapshots
- Integrate into both sync.go and daemon_sync.go
- Add comprehensive test suite in deletion_tracking_test.go
- Update .gitignore to exclude snapshot files

This fixes the resurrection bug where deleted issues come back after
multi-workspace git sync. Uses the beads-merge 3-way merge logic to
detect and apply deletions correctly.

cmd/bd/daemon_sync.go

@@ -499,6 +499,11 @@ func createSyncFunc(ctx context.Context, store storage.Storage, autoCommit, auto
 		}
 		log.log("Exported to JSONL")
 
+		// Capture left snapshot (pre-pull state) for 3-way merge
+		if err := captureLeftSnapshot(jsonlPath); err != nil {
+			log.log("Warning: failed to capture snapshot for deletion tracking: %v", err)
+		}
+
 		if autoCommit {
 			// Try sync branch commit first
 			committed, err := syncBranchCommitAndPush(syncCtx, store, autoPush, log)
@@ -549,6 +554,12 @@ func createSyncFunc(ctx context.Context, store storage.Storage, autoCommit, auto
 			return
 		}
 
+		// Perform 3-way merge and prune deletions
+		if err := applyDeletionsFromMerge(syncCtx, store, jsonlPath); err != nil {
+			log.log("Error during 3-way merge: %v", err)
+			return
+		}
+
 		if err := importToJSONLWithStore(syncCtx, store, jsonlPath); err != nil {
 			log.log("Import failed: %v", err)
 			return
@@ -567,6 +578,11 @@ func createSyncFunc(ctx context.Context, store storage.Storage, autoCommit, auto
 			return
 		}
 
+		// Update base snapshot after successful import
+		if err := updateBaseSnapshot(jsonlPath); err != nil {
+			log.log("Warning: failed to update base snapshot: %v", err)
+		}
+
 		if autoPush && autoCommit {
 			if err := gitPush(syncCtx); err != nil {
 				log.log("Push failed: %v", err)