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/importer/importer.go

@@ -180,7 +180,8 @@ func ImportIssues(ctx context.Context, dbPath string, store storage.Storage, iss
 	}
 
 	// Check and handle prefix mismatches
-	if err := handlePrefixMismatch(ctx, sqliteStore, issues, opts, result); err != nil {
+	issues, err = handlePrefixMismatch(ctx, sqliteStore, issues, opts, result)
+	if err != nil {
 		return result, err
 	}
 
@@ -258,48 +259,90 @@ func getOrCreateStore(ctx context.Context, dbPath string, store storage.Storage)
 	return sqliteStore, true, nil
 }
 
-// handlePrefixMismatch checks and handles prefix mismatches
-func handlePrefixMismatch(ctx context.Context, sqliteStore *sqlite.SQLiteStorage, issues []*types.Issue, opts Options, result *Result) error {
+// handlePrefixMismatch checks and handles prefix mismatches.
+// Returns a filtered issues slice with tombstoned issues having wrong prefixes removed (bd-6pni).
+func handlePrefixMismatch(ctx context.Context, sqliteStore *sqlite.SQLiteStorage, issues []*types.Issue, opts Options, result *Result) ([]*types.Issue, error) {
 	configuredPrefix, err := sqliteStore.GetConfig(ctx, "issue_prefix")
 	if err != nil {
-		return fmt.Errorf("failed to get configured prefix: %w", err)
+		return nil, fmt.Errorf("failed to get configured prefix: %w", err)
 	}
 
 	// Only validate prefixes if a prefix is configured
 	if strings.TrimSpace(configuredPrefix) == "" {
 		if opts.RenameOnImport {
-			return fmt.Errorf("cannot rename: issue_prefix not configured in database")
+			return nil, fmt.Errorf("cannot rename: issue_prefix not configured in database")
 		}
-		return nil
+		return issues, nil
 	}
 
 	result.ExpectedPrefix = configuredPrefix
 
 	// Analyze prefixes in imported issues
+	// Track tombstones separately - they don't count as "real" mismatches (bd-6pni)
+	tombstoneMismatchPrefixes := make(map[string]int)
+	nonTombstoneMismatchCount := 0
+
+	// Also track which tombstones have wrong prefixes for filtering
+	var filteredIssues []*types.Issue
+	var tombstonesToRemove []string
+
 	for _, issue := range issues {
 		prefix := utils.ExtractIssuePrefix(issue.ID)
 		if prefix != configuredPrefix {
-			result.PrefixMismatch = true
-			result.MismatchPrefixes[prefix]++
+			if issue.IsTombstone() {
+				tombstoneMismatchPrefixes[prefix]++
+				tombstonesToRemove = append(tombstonesToRemove, issue.ID)
+				// Don't add to filtered list - we'll remove these
+			} else {
+				result.PrefixMismatch = true
+				result.MismatchPrefixes[prefix]++
+				nonTombstoneMismatchCount++
+				filteredIssues = append(filteredIssues, issue)
+			}
+		} else {
+			// Correct prefix - keep the issue
+			filteredIssues = append(filteredIssues, issue)
 		}
 	}
 
-	// If prefix mismatch detected and not handling it, return error or warning
-	if result.PrefixMismatch && !opts.RenameOnImport && !opts.DryRun && !opts.SkipPrefixValidation {
-		return fmt.Errorf("prefix mismatch detected: database uses '%s-' but found issues with prefixes: %v (use --rename-on-import to automatically fix)", configuredPrefix, GetPrefixList(result.MismatchPrefixes))
+	// bd-6pni: If ALL mismatched prefix issues are tombstones, they're just pollution
+	// from contributor PRs that used different test prefixes. These are safe to remove.
+	if nonTombstoneMismatchCount == 0 && len(tombstoneMismatchPrefixes) > 0 {
+		// Log that we're ignoring tombstoned mismatches
+		var tombstonePrefixList []string
+		for prefix, count := range tombstoneMismatchPrefixes {
+			tombstonePrefixList = append(tombstonePrefixList, fmt.Sprintf("%s- (%d tombstones)", prefix, count))
+		}
+		fmt.Fprintf(os.Stderr, "Ignoring prefix mismatches (all are tombstones): %v\n", tombstonePrefixList)
+		// Clear mismatch flags - no real issues to worry about
+		result.PrefixMismatch = false
+		result.MismatchPrefixes = make(map[string]int)
+		// Return filtered list without the tombstones
+		return filteredIssues, nil
+	}
+
+	// If there are non-tombstone mismatches, we need to include all issues (tombstones too)
+	// but still report the error for non-tombstones
+	if result.PrefixMismatch {
+		// If not handling the mismatch, return error
+		if !opts.RenameOnImport && !opts.DryRun && !opts.SkipPrefixValidation {
+			return nil, fmt.Errorf("prefix mismatch detected: database uses '%s-' but found issues with prefixes: %v (use --rename-on-import to automatically fix)", configuredPrefix, GetPrefixList(result.MismatchPrefixes))
+		}
 	}
 
 	// Handle rename-on-import if requested
 	if result.PrefixMismatch && opts.RenameOnImport && !opts.DryRun {
 		if err := RenameImportedIssuePrefixes(issues, configuredPrefix); err != nil {
-			return fmt.Errorf("failed to rename prefixes: %w", err)
+			return nil, fmt.Errorf("failed to rename prefixes: %w", err)
 		}
 		// After renaming, clear the mismatch flags since we fixed them
 		result.PrefixMismatch = false
 		result.MismatchPrefixes = make(map[string]int)
+		return issues, nil
 	}
 
-	return nil
+	// Return original issues if no filtering needed
+	return issues, nil
 }
 
 // detectUpdates detects same-ID scenarios (which are updates with hash IDs, not collisions)
@@ -1034,14 +1077,17 @@ func purgeDeletedIssues(ctx context.Context, sqliteStore *sqlite.SQLiteStorage,
 			}
 
 			// Backfill the deletions manifest (self-healing)
-			backfillRecord := deletions.DeletionRecord{
-				ID:        id,
-				Timestamp: time.Now().UTC(),
-				Actor:     "git-history-backfill",
-				Reason:    "recovered from git history (pruned from manifest)",
-			}
-			if err := deletions.AppendDeletion(deletionsPath, backfillRecord); err != nil {
-				fmt.Fprintf(os.Stderr, "Warning: failed to backfill deletion record for %s: %v\n", id, err)
+			// bd-ffr9: Skip writing to deletions.jsonl if tombstone migration is complete
+			if !deletions.IsTombstoneMigrationComplete(beadsDir) {
+				backfillRecord := deletions.DeletionRecord{
+					ID:        id,
+					Timestamp: time.Now().UTC(),
+					Actor:     "git-history-backfill",
+					Reason:    "recovered from git history (pruned from manifest)",
+				}
+				if err := deletions.AppendDeletion(deletionsPath, backfillRecord); err != nil {
+					fmt.Fprintf(os.Stderr, "Warning: failed to backfill deletion record for %s: %v\n", id, err)
+				}
 			}
 
 			// Convert to tombstone (bd-dve)