Fix bd-4oob: Add multi-repo deletion tracking support

- Added getMultiRepoJSONLPaths() helper to enumerate all JSONL files
- Updated daemon_sync.go to capture/update snapshots for each repo
- Added TestMultiRepoDeletionTracking to verify fix
- Added TestMultiRepoSnapshotIsolation for isolation guarantees

Previously, deletion tracking only worked for single-repo mode because
snapshot operations were hardcoded to the primary JSONL path. This fix
ensures snapshots are managed per-repository in multi-repo mode.

cmd/bd/deletion_tracking.go

@@ -10,6 +10,7 @@ import (
 	"path/filepath"
 	"reflect"
 
+	"github.com/steveyegge/beads/internal/config"
 	"github.com/steveyegge/beads/internal/merge"
 	"github.com/steveyegge/beads/internal/storage"
 )
@@ -329,6 +330,33 @@ func initializeSnapshotsIfNeeded(jsonlPath string) error {
 	return nil
 }
 
+// getMultiRepoJSONLPaths returns all JSONL file paths for multi-repo mode
+// Returns nil if not in multi-repo mode
+func getMultiRepoJSONLPaths() []string {
+	multiRepo := config.GetMultiRepoConfig()
+	if multiRepo == nil {
+		return nil
+	}
+
+	var paths []string
+
+	// Primary repo JSONL
+	primaryPath := multiRepo.Primary
+	if primaryPath == "" {
+		primaryPath = "."
+	}
+	primaryJSONL := filepath.Join(primaryPath, ".beads", "issues.jsonl")
+	paths = append(paths, primaryJSONL)
+
+	// Additional repos' JSONLs
+	for _, repoPath := range multiRepo.Additional {
+		jsonlPath := filepath.Join(repoPath, ".beads", "issues.jsonl")
+		paths = append(paths, jsonlPath)
+	}
+
+	return paths
+}
+
 // applyDeletionsFromMerge applies deletions discovered during 3-way merge
 // This is the main entry point for deletion tracking during sync
 func applyDeletionsFromMerge(ctx context.Context, store storage.Storage, jsonlPath string) error {