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>

internal/deletions/deletions.go

@@ -181,6 +181,17 @@ func DefaultPath(beadsDir string) string {
 	return filepath.Join(beadsDir, "deletions.jsonl")
 }
 
+// IsTombstoneMigrationComplete checks if the tombstone migration has been completed.
+// After running `bd migrate-tombstones`, the deletions.jsonl file is archived to
+// deletions.jsonl.migrated. This function checks for that marker file.
+// When migration is complete, new deletion records should NOT be written to
+// deletions.jsonl (bd-ffr9).
+func IsTombstoneMigrationComplete(beadsDir string) bool {
+	migratedPath := filepath.Join(beadsDir, "deletions.jsonl.migrated")
+	_, err := os.Stat(migratedPath)
+	return err == nil
+}
+
 // Count returns the number of lines in the deletions manifest.
 // This is a fast operation that doesn't parse JSON, just counts lines.
 // Returns 0 if the file doesn't exist or is empty.

internal/deletions/deletions_test.go

@@ -290,6 +290,38 @@ func TestDefaultPath(t *testing.T) {
 	}
 }
 
+func TestIsTombstoneMigrationComplete(t *testing.T) {
+	t.Run("no migrated file", func(t *testing.T) {
+		tmpDir := t.TempDir()
+		if IsTombstoneMigrationComplete(tmpDir) {
+			t.Error("expected false when no .migrated file exists")
+		}
+	})
+
+	t.Run("migrated file exists", func(t *testing.T) {
+		tmpDir := t.TempDir()
+		migratedPath := filepath.Join(tmpDir, "deletions.jsonl.migrated")
+		if err := os.WriteFile(migratedPath, []byte("{}"), 0644); err != nil {
+			t.Fatalf("failed to create migrated file: %v", err)
+		}
+		if !IsTombstoneMigrationComplete(tmpDir) {
+			t.Error("expected true when .migrated file exists")
+		}
+	})
+
+	t.Run("deletions.jsonl exists without migrated", func(t *testing.T) {
+		tmpDir := t.TempDir()
+		deletionsPath := filepath.Join(tmpDir, "deletions.jsonl")
+		if err := os.WriteFile(deletionsPath, []byte("{}"), 0644); err != nil {
+			t.Fatalf("failed to create deletions file: %v", err)
+		}
+		// Should return false because the .migrated marker doesn't exist
+		if IsTombstoneMigrationComplete(tmpDir) {
+			t.Error("expected false when only deletions.jsonl exists (not migrated)")
+		}
+	})
+}
+
 func TestLoadDeletions_EmptyLines(t *testing.T) {
 	tmpDir := t.TempDir()
 	path := filepath.Join(tmpDir, "deletions.jsonl")