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/sync.go

@@ -148,6 +148,11 @@ Use --merge to merge the sync branch back to main branch.`,
 				fmt.Fprintf(os.Stderr, "Error exporting: %v\n", err)
 				os.Exit(1)
 			}
+
+			// Capture left snapshot (pre-pull state) for 3-way merge
+			if err := captureLeftSnapshot(jsonlPath); err != nil {
+				fmt.Fprintf(os.Stderr, "Warning: failed to capture snapshot for deletion tracking: %v\n", err)
+			}
 		}
 
 		// Step 2: Check if there are changes to commit
@@ -192,6 +197,14 @@ Use --merge to merge the sync branch back to main branch.`,
 					}
 				}
 
+				// Step 3.5: Perform 3-way merge and prune deletions
+				if err := ensureStoreActive(); err == nil && store != nil {
+					if err := applyDeletionsFromMerge(ctx, store, jsonlPath); err != nil {
+						fmt.Fprintf(os.Stderr, "Error during 3-way merge: %v\n", err)
+						os.Exit(1)
+					}
+				}
+
 				// Step 4: Import updated JSONL after pull
 				fmt.Println("→ Importing updated JSONL...")
 				if err := importFromJSONL(ctx, jsonlPath, renameOnImport); err != nil {
@@ -249,6 +262,11 @@ Use --merge to merge the sync branch back to main branch.`,
 						fmt.Println("→ DB and JSONL in sync, skipping re-export")
 					}
 				}
+
+				// Update base snapshot after successful import
+				if err := updateBaseSnapshot(jsonlPath); err != nil {
+					fmt.Fprintf(os.Stderr, "Warning: failed to update base snapshot: %v\n", err)
+				}
 			}
 		}