fix: resolve P2 sync noise and cleanup issues

- bd-6pni: Auto-filter tombstoned issues with mismatched prefixes during
  import instead of failing. Tombstones from contributor PRs with different
  test prefixes are pollution and safe to ignore.

- bd-ffr9: Stop recreating deletions.jsonl after tombstone migration.
  Added IsTombstoneMigrationComplete() check to all code paths that write
  to the legacy deletions manifest.

- bd-admx: Fix perpetual "JSONL file hash mismatch" warning. Now clears
  both export_hashes AND jsonl_file_hash when mismatch detected, so the
  warning doesn't repeat.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

cmd/bd/autoflush.go

@@ -401,11 +401,15 @@ func validateJSONLIntegrity(ctx context.Context, jsonlPath string) (bool, error)
 	jsonlData, err := os.ReadFile(jsonlPath)
 	if err != nil {
 		if os.IsNotExist(err) {
-			// JSONL doesn't exist but we have a stored hash - clear export_hashes
+			// JSONL doesn't exist but we have a stored hash - clear export_hashes and jsonl_file_hash
 			fmt.Fprintf(os.Stderr, "⚠️  WARNING: JSONL file missing but export_hashes exist. Clearing export_hashes.\n")
 			if err := store.ClearAllExportHashes(ctx); err != nil {
 				return false, fmt.Errorf("failed to clear export_hashes: %w", err)
 			}
+			// Also clear jsonl_file_hash to prevent perpetual mismatch warnings (bd-admx)
+			if err := store.SetJSONLFileHash(ctx, ""); err != nil {
+				return false, fmt.Errorf("failed to clear jsonl_file_hash: %w", err)
+			}
 			return true, nil // Signal full export needed
 		}
 		return false, fmt.Errorf("failed to read JSONL file: %w", err)
@@ -421,11 +425,15 @@ func validateJSONLIntegrity(ctx context.Context, jsonlPath string) (bool, error)
 		fmt.Fprintf(os.Stderr, "⚠️  WARNING: JSONL file hash mismatch detected (bd-160)\n")
 		fmt.Fprintf(os.Stderr, "  This indicates JSONL and export_hashes are out of sync.\n")
 		fmt.Fprintf(os.Stderr, "  Clearing export_hashes to force full re-export.\n")
-		
+
 		// Clear export_hashes to force full re-export
 		if err := store.ClearAllExportHashes(ctx); err != nil {
 			return false, fmt.Errorf("failed to clear export_hashes: %w", err)
 		}
+		// Also clear jsonl_file_hash to prevent perpetual mismatch warnings (bd-admx)
+		if err := store.SetJSONLFileHash(ctx, ""); err != nil {
+			return false, fmt.Errorf("failed to clear jsonl_file_hash: %w", err)
+		}
 		return true, nil // Signal full export needed
 	}
 	

cmd/bd/delete.go

@@ -685,7 +685,14 @@ func getDeletionsPath() string {
 // recordDeletion appends a deletion record to the deletions manifest.
 // This MUST be called BEFORE deleting from the database to ensure
 // deletion records are never lost.
+// After tombstone migration (bd-ffr9), this is a no-op since inline tombstones
+// are used instead of deletions.jsonl.
 func recordDeletion(id, deleteActor, reason string) error {
+	// bd-ffr9: Skip writing to deletions.jsonl if tombstone migration is complete
+	beadsDir := filepath.Dir(dbPath)
+	if deletions.IsTombstoneMigrationComplete(beadsDir) {
+		return nil
+	}
 	record := deletions.DeletionRecord{
 		ID:        id,
 		Timestamp: time.Now().UTC(),
@@ -698,7 +705,14 @@ func recordDeletion(id, deleteActor, reason string) error {
 // recordDeletions appends multiple deletion records to the deletions manifest.
 // This MUST be called BEFORE deleting from the database to ensure
 // deletion records are never lost.
+// After tombstone migration (bd-ffr9), this is a no-op since inline tombstones
+// are used instead of deletions.jsonl.
 func recordDeletions(ids []string, deleteActor, reason string) error {
+	// bd-ffr9: Skip writing to deletions.jsonl if tombstone migration is complete
+	beadsDir := filepath.Dir(dbPath)
+	if deletions.IsTombstoneMigrationComplete(beadsDir) {
+		return nil
+	}
 	path := getDeletionsPath()
 	for _, id := range ids {
 		record := deletions.DeletionRecord{

cmd/bd/delete_recording_test.go

@@ -62,6 +62,39 @@ func TestRecordDeletion(t *testing.T) {
 	}
 }
 
+// TestRecordDeletion_SkipsAfterMigration tests that recordDeletion is a no-op after tombstone migration (bd-ffr9)
+func TestRecordDeletion_SkipsAfterMigration(t *testing.T) {
+	tmpDir := t.TempDir()
+
+	// Set up dbPath so getDeletionsPath() works
+	oldDbPath := dbPath
+	dbPath = filepath.Join(tmpDir, "beads.db")
+	defer func() { dbPath = oldDbPath }()
+
+	// Create the .beads directory
+	if err := os.MkdirAll(tmpDir, 0750); err != nil {
+		t.Fatalf("failed to create directory: %v", err)
+	}
+
+	// Create the .migrated marker file to indicate tombstone migration is complete
+	migratedPath := filepath.Join(tmpDir, "deletions.jsonl.migrated")
+	if err := os.WriteFile(migratedPath, []byte("{}"), 0644); err != nil {
+		t.Fatalf("failed to create migrated marker: %v", err)
+	}
+
+	// Test recordDeletion - should be a no-op
+	err := recordDeletion("test-abc", "test-user", "test reason")
+	if err != nil {
+		t.Fatalf("recordDeletion failed: %v", err)
+	}
+
+	// Verify deletions.jsonl was NOT created
+	deletionsPath := getDeletionsPath()
+	if _, err := os.Stat(deletionsPath); !os.IsNotExist(err) {
+		t.Error("deletions.jsonl should not be created after tombstone migration")
+	}
+}
+
 // TestRecordDeletions tests that recordDeletions creates multiple deletion manifest entries
 func TestRecordDeletions(t *testing.T) {
 	tmpDir := t.TempDir()

cmd/bd/doctor/fix/deletions.go

@@ -16,12 +16,21 @@ import (
 // HydrateDeletionsManifest populates deletions.jsonl from git history.
 // It finds all issue IDs that were ever in the JSONL but are no longer present,
 // and adds them to the deletions manifest.
+// Note (bd-ffr9): After tombstone migration, this is a no-op since inline tombstones
+// are used instead of deletions.jsonl.
 func HydrateDeletionsManifest(path string) error {
 	if err := validateBeadsWorkspace(path); err != nil {
 		return err
 	}
 
 	beadsDir := filepath.Join(path, ".beads")
+
+	// bd-ffr9: Skip hydrating deletions.jsonl if tombstone migration is complete
+	if deletions.IsTombstoneMigrationComplete(beadsDir) {
+		fmt.Println("  Tombstone migration complete - skipping deletions.jsonl hydration")
+		return nil
+	}
+
 	// bd-6xd: issues.jsonl is the canonical filename
 	jsonlPath := filepath.Join(beadsDir, "issues.jsonl")
 

cmd/bd/jsonl_integrity_test.go

@@ -100,12 +100,12 @@ func TestJSONLIntegrityValidation(t *testing.T) {
 		if err := os.WriteFile(jsonlPath, []byte(`{"id":"bd-1","title":"Modified"}`+"\n"), 0644); err != nil {
 			t.Fatalf("failed to modify JSONL: %v", err)
 		}
-		
+
 		// Add an export hash to verify it gets cleared
 		if err := testStore.SetExportHash(ctx, "bd-1", "dummy-hash"); err != nil {
 			t.Fatalf("failed to set export hash: %v", err)
 		}
-		
+
 		// Validate should detect mismatch and clear export_hashes
 		needsFullExport, err := validateJSONLIntegrity(ctx, jsonlPath)
 		if err != nil {
@@ -114,7 +114,7 @@ func TestJSONLIntegrityValidation(t *testing.T) {
 		if !needsFullExport {
 			t.Fatalf("expected needsFullExport=true after clearing export_hashes")
 		}
-		
+
 		// Verify export_hashes were cleared
 		hash, err := testStore.GetExportHash(ctx, "bd-1")
 		if err != nil {
@@ -123,6 +123,15 @@ func TestJSONLIntegrityValidation(t *testing.T) {
 		if hash != "" {
 			t.Fatalf("expected export hash to be cleared, got %q", hash)
 		}
+
+		// Verify jsonl_file_hash was also cleared (bd-admx fix)
+		fileHash, err := testStore.GetJSONLFileHash(ctx)
+		if err != nil {
+			t.Fatalf("failed to get JSONL file hash: %v", err)
+		}
+		if fileHash != "" {
+			t.Fatalf("expected jsonl_file_hash to be cleared to prevent perpetual warnings, got %q", fileHash)
+		}
 	})
 	
 	// Test 3: Missing JSONL file
@@ -131,17 +140,17 @@ func TestJSONLIntegrityValidation(t *testing.T) {
 		if err := testStore.SetJSONLFileHash(ctx, "some-hash"); err != nil {
 			t.Fatalf("failed to set JSONL file hash: %v", err)
 		}
-		
+
 		// Add an export hash
 		if err := testStore.SetExportHash(ctx, "bd-1", "dummy-hash"); err != nil {
 			t.Fatalf("failed to set export hash: %v", err)
 		}
-		
+
 		// Remove JSONL file
 		if err := os.Remove(jsonlPath); err != nil {
 			t.Fatalf("failed to remove JSONL: %v", err)
 		}
-		
+
 		// Validate should detect missing file and clear export_hashes
 		needsFullExport, err := validateJSONLIntegrity(ctx, jsonlPath)
 		if err != nil {
@@ -150,7 +159,7 @@ func TestJSONLIntegrityValidation(t *testing.T) {
 		if !needsFullExport {
 			t.Fatalf("expected needsFullExport=true after clearing export_hashes")
 		}
-		
+
 		// Verify export_hashes were cleared
 		hash, err := testStore.GetExportHash(ctx, "bd-1")
 		if err != nil {
@@ -159,6 +168,15 @@ func TestJSONLIntegrityValidation(t *testing.T) {
 		if hash != "" {
 			t.Fatalf("expected export hash to be cleared, got %q", hash)
 		}
+
+		// Verify jsonl_file_hash was also cleared (bd-admx fix)
+		fileHash, err := testStore.GetJSONLFileHash(ctx)
+		if err != nil {
+			t.Fatalf("failed to get JSONL file hash: %v", err)
+		}
+		if fileHash != "" {
+			t.Fatalf("expected jsonl_file_hash to be cleared to prevent perpetual warnings, got %q", fileHash)
+		}
 	})
 }