fix(cleanup): resolve CHECK constraint failure and add tombstone pruning

- Fix bd-tnsq: executeDelete now sets closed_at=NULL when creating
  tombstones, satisfying the CHECK constraint that requires
  closed_at IS NULL when status != 'closed'

- Fix bd-08ea: cleanup command now also prunes expired tombstones
  (older than 30 days) after converting closed issues to tombstones

- Add regression test for batch deletion of closed issues

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

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

cmd/bd/cleanup.go

@@ -13,23 +13,26 @@ import (
 
 var cleanupCmd = &cobra.Command{
 	Use:   "cleanup",
-	Short: "Delete closed issues from database to free up space",
+	Short: "Delete closed issues and prune expired tombstones",
-	Long: `Delete closed issues from the database to reduce database size.
+	Long: `Delete closed issues and prune expired tombstones to reduce database size.
+
+This command:
+1. Converts closed issues to tombstones (soft delete)
+2. Prunes expired tombstones (older than 30 days) from issues.jsonl
 
-This command permanently removes closed issues from beads.db and issues.jsonl.
 It does NOT remove temporary files - use 'bd clean' for that.
 
 By default, deletes ALL closed issues. Use --older-than to only delete
 issues closed before a certain date.
 
 EXAMPLES:
-Delete all closed issues:
+Delete all closed issues and prune tombstones:
   bd cleanup --force
 
 Delete issues closed more than 30 days ago:
   bd cleanup --older-than 30 --force
 
-Preview what would be deleted:
+Preview what would be deleted/pruned:
   bd cleanup --dry-run
   bd cleanup --older-than 90 --dry-run
 
@@ -40,7 +43,8 @@ SAFETY:
 - Use --json for programmatic output
 
 SEE ALSO:
-  bd clean      Remove temporary git merge artifacts`,
+  bd clean      Remove temporary git merge artifacts
+  bd compact    Run compaction on issues`,
 	Run: func(cmd *cobra.Command, args []string) {
 		force, _ := cmd.Flags().GetBool("force")
 		dryRun, _ := cmd.Flags().GetBool("dry-run")
@@ -128,6 +132,37 @@ SEE ALSO:
 
 		// Use the existing batch deletion logic
 		deleteBatch(cmd, issueIDs, force, dryRun, cascade, jsonOutput, "cleanup")
+
+		// Also prune expired tombstones (bd-08ea)
+		// This runs after closed issues are converted to tombstones, cleaning up old ones
+		if dryRun {
+			// Preview what tombstones would be pruned
+			tombstoneResult, err := previewPruneTombstones()
+			if err != nil {
+				if !jsonOutput {
+					fmt.Fprintf(os.Stderr, "Warning: failed to check tombstones: %v\n", err)
+				}
+			} else if tombstoneResult != nil && tombstoneResult.PrunedCount > 0 {
+				if !jsonOutput {
+					fmt.Printf("\nExpired tombstones that would be pruned: %d (older than %d days)\n",
+						tombstoneResult.PrunedCount, tombstoneResult.TTLDays)
+				}
+			}
+		} else if force {
+			// Actually prune expired tombstones
+			tombstoneResult, err := pruneExpiredTombstones()
+			if err != nil {
+				if !jsonOutput {
+					fmt.Fprintf(os.Stderr, "Warning: failed to prune expired tombstones: %v\n", err)
+				}
+			} else if tombstoneResult != nil && tombstoneResult.PrunedCount > 0 {
+				if !jsonOutput {
+					green := color.New(color.FgGreen).SprintFunc()
+					fmt.Printf("\n%s Pruned %d expired tombstone(s) (older than %d days)\n",
+						green("✓"), tombstoneResult.PrunedCount, tombstoneResult.TTLDays)
+				}
+			}
+		}
 	},
 }
 

cmd/bd/compact.go

@@ -1076,6 +1076,58 @@ func pruneExpiredTombstones() (*TombstonePruneResult, error) {
 	}, nil
 }
 
+// previewPruneTombstones checks what tombstones would be pruned without modifying files.
+// Used for dry-run mode in cleanup command (bd-08ea).
+func previewPruneTombstones() (*TombstonePruneResult, error) {
+	beadsDir := filepath.Dir(dbPath)
+	issuesPath := filepath.Join(beadsDir, "issues.jsonl")
+
+	// Check if issues.jsonl exists
+	if _, err := os.Stat(issuesPath); os.IsNotExist(err) {
+		return &TombstonePruneResult{}, nil
+	}
+
+	// Read all issues
+	// nolint:gosec // G304: issuesPath is controlled from beadsDir
+	file, err := os.Open(issuesPath)
+	if err != nil {
+		return nil, fmt.Errorf("failed to open issues.jsonl: %w", err)
+	}
+	defer file.Close()
+
+	var allIssues []*types.Issue
+	decoder := json.NewDecoder(file)
+	for {
+		var issue types.Issue
+		if err := decoder.Decode(&issue); err != nil {
+			if err.Error() == "EOF" {
+				break
+			}
+			// Skip corrupt lines
+			continue
+		}
+		allIssues = append(allIssues, &issue)
+	}
+
+	// Determine TTL
+	ttl := types.DefaultTombstoneTTL
+	ttlDays := int(ttl.Hours() / 24)
+
+	// Count expired tombstones
+	var prunedIDs []string
+	for _, issue := range allIssues {
+		if issue.IsExpired(ttl) {
+			prunedIDs = append(prunedIDs, issue.ID)
+		}
+	}
+
+	return &TombstonePruneResult{
+		PrunedCount: len(prunedIDs),
+		PrunedIDs:   prunedIDs,
+		TTLDays:     ttlDays,
+	}, nil
+}
+
 func init() {
 	compactCmd.Flags().BoolVar(&compactDryRun, "dry-run", false, "Preview without compacting")
 	compactCmd.Flags().IntVar(&compactTier, "tier", 1, "Compaction tier (1 or 2)")

internal/storage/sqlite/queries.go

@@ -1202,12 +1202,15 @@ func (s *SQLiteStorage) executeDelete(ctx context.Context, tx *sql.Tx, inClause
 	_ = rows.Close()
 
 	// 3. Convert issues to tombstones (only for issues that exist)
+	// Note: closed_at must be set to NULL because of CHECK constraint:
+	// (status = 'closed') = (closed_at IS NOT NULL)
 	now := time.Now()
 	deletedCount := 0
 	for id, originalType := range issueTypes {
 		execResult, err := tx.ExecContext(ctx, `
 			UPDATE issues
 			SET status = ?,
+			    closed_at = NULL,
 			    deleted_at = ?,
 			    deleted_by = ?,
 			    delete_reason = ?,

internal/storage/sqlite/tombstone_test.go

@@ -3,6 +3,7 @@ package sqlite
 import (
 	"context"
 	"testing"
+	"time"
 
 	"github.com/steveyegge/beads/internal/types"
 )
@@ -299,6 +300,67 @@ func TestDeleteIssuesCreatesTombstones(t *testing.T) {
 		}
 	})
 
+	t.Run("batch deletion of closed issues creates tombstones (bd-tnsq)", func(t *testing.T) {
+		// Regression test: batch deletion of closed issues was failing with
+		// CHECK constraint: (status = 'closed') = (closed_at IS NOT NULL)
+		// because closed_at wasn't being set to NULL when creating tombstones
+		store := newTestStore(t, "file::memory:?mode=memory&cache=private")
+
+		now := time.Now()
+		closedAt := now.Add(-24 * time.Hour)
+
+		// Create closed issues (with closed_at set)
+		issue1 := &types.Issue{
+			ID:        "bd-closed-10",
+			Title:     "Closed Issue 1",
+			Status:    types.StatusClosed,
+			Priority:  1,
+			IssueType: types.TypeBug,
+			ClosedAt:  &closedAt,
+		}
+		issue2 := &types.Issue{
+			ID:        "bd-closed-11",
+			Title:     "Closed Issue 2",
+			Status:    types.StatusClosed,
+			Priority:  1,
+			IssueType: types.TypeTask,
+			ClosedAt:  &closedAt,
+		}
+
+		if err := store.CreateIssue(ctx, issue1, "test"); err != nil {
+			t.Fatalf("Failed to create closed issue1: %v", err)
+		}
+		if err := store.CreateIssue(ctx, issue2, "test"); err != nil {
+			t.Fatalf("Failed to create closed issue2: %v", err)
+		}
+
+		// Batch delete closed issues - this was failing before the fix
+		result, err := store.DeleteIssues(ctx, []string{"bd-closed-10", "bd-closed-11"}, false, true, false)
+		if err != nil {
+			t.Fatalf("DeleteIssues on closed issues failed: %v", err)
+		}
+		if result.DeletedCount != 2 {
+			t.Errorf("Expected 2 deletions, got %d", result.DeletedCount)
+		}
+
+		// Verify tombstones have closed_at = NULL (required by CHECK constraint)
+		tombstone1, _ := store.GetIssue(ctx, "bd-closed-10")
+		if tombstone1 == nil || tombstone1.Status != types.StatusTombstone {
+			t.Error("bd-closed-10 should be tombstone")
+		}
+		if tombstone1.ClosedAt != nil {
+			t.Error("bd-closed-10 tombstone should have closed_at = NULL")
+		}
+
+		tombstone2, _ := store.GetIssue(ctx, "bd-closed-11")
+		if tombstone2 == nil || tombstone2.Status != types.StatusTombstone {
+			t.Error("bd-closed-11 should be tombstone")
+		}
+		if tombstone2.ClosedAt != nil {
+			t.Error("bd-closed-11 tombstone should have closed_at = NULL")
+		}
+	})
+
 	t.Run("cascade deletion creates tombstones", func(t *testing.T) {
 		store := newTestStore(t, "file::memory:?mode=memory&cache=private")