fix: sync ID counters after import to prevent collisions

When importing issues with explicit high IDs (e.g., bd-100), the
issue_counters table wasn't being updated. This caused the next
auto-generated issue to collide with existing IDs (bd-4 instead of bd-101).

Changes:
- Add SyncAllCounters() to scan all issues and update counters atomically
- Add SyncCounterForPrefix() for granular counter synchronization
- Call SyncAllCounters() in import command after creating issues
- Add comprehensive tests for counter sync functionality
- Update TestImportCounterSyncAfterHighID to verify fix

The fix uses a single efficient SQL query to prevent ID collisions
with subsequently auto-generated issues.

cmd/bd/import.go

@@ -238,6 +238,13 @@ Behavior:
 			}
 		}
 
+		// Phase 4.5: Sync ID counters after importing issues with explicit IDs
+		// This prevents ID collisions with subsequently auto-generated issues
+		if err := sqliteStore.SyncAllCounters(ctx); err != nil {
+			fmt.Fprintf(os.Stderr, "Warning: failed to sync ID counters: %v\n", err)
+			// Don't exit - this is not fatal, just a warning
+		}
+
 		// Phase 5: Process dependencies
 		// Do this after all issues are created to handle forward references
 		var depsCreated, depsSkipped int

cmd/bd/import_collision_test.go

@@ -1023,6 +1023,13 @@ func TestImportCounterSyncAfterHighID(t *testing.T) {
 		t.Fatalf("Failed to import high ID issue: %v", err)
 	}
 
+	// Step 4: Sync counters after import (mimics import command behavior)
+	if err := testStore.SyncAllCounters(ctx); err != nil {
+		t.Fatalf("Failed to sync counters: %v", err)
+	}
+
+	// Step 5: Create another auto-generated issue
+	// This should get bd-101 (counter should have synced to 100), not bd-4
 	newIssue := &types.Issue{
 		Title:     "New issue after import",
 		Status:    types.StatusOpen,

internal/storage/sqlite/sqlite.go

@@ -107,6 +107,22 @@ func (s *SQLiteStorage) getNextIDForPrefix(ctx context.Context, prefix string) (
 	return nextID, nil
 }
 
+// SyncCounterForPrefix synchronizes the counter to be at least the given value
+// This is used after importing issues with explicit IDs to prevent ID collisions
+// with subsequently auto-generated IDs
+func (s *SQLiteStorage) SyncCounterForPrefix(ctx context.Context, prefix string, minValue int) error {
+	_, err := s.db.ExecContext(ctx, `
+		INSERT INTO issue_counters (prefix, last_id)
+		VALUES (?, ?)
+		ON CONFLICT(prefix) DO UPDATE SET
+			last_id = MAX(last_id, ?)
+	`, prefix, minValue, minValue)
+	if err != nil {
+		return fmt.Errorf("failed to sync counter for prefix %s: %w", prefix, err)
+	}
+	return nil
+}
+
 // SyncAllCounters synchronizes all ID counters based on existing issues in the database
 // This scans all issues and updates counters to prevent ID collisions with auto-generated IDs
 func (s *SQLiteStorage) SyncAllCounters(ctx context.Context) error {

internal/storage/sqlite/sqlite_test.go

@@ -479,3 +479,68 @@ func TestMultiProcessIDGeneration(t *testing.T) {
 		t.Errorf("Expected no errors, got %d", len(errors))
 	}
 }
+
+func TestSyncCounterForPrefix(t *testing.T) {
+	store, cleanup := setupTestDB(t)
+	defer cleanup()
+
+	ctx := context.Background()
+
+	// Set config for issue prefix
+	if err := store.SetConfig(ctx, "issue_prefix", "bd"); err != nil {
+		t.Fatalf("Failed to set issue prefix: %v", err)
+	}
+
+	// Create a few auto-generated issues (bd-1, bd-2, bd-3)
+	for i := 0; i < 3; i++ {
+		issue := &types.Issue{
+			Title:     "Auto issue",
+			Status:    types.StatusOpen,
+			Priority:  1,
+			IssueType: types.TypeTask,
+		}
+		if err := store.CreateIssue(ctx, issue, "test"); err != nil {
+			t.Fatalf("Failed to create issue: %v", err)
+		}
+	}
+
+	// Sync counter to 100
+	if err := store.SyncCounterForPrefix(ctx, "bd", 100); err != nil {
+		t.Fatalf("SyncCounterForPrefix failed: %v", err)
+	}
+
+	// Next auto-generated issue should be bd-101
+	issue := &types.Issue{
+		Title:     "After sync",
+		Status:    types.StatusOpen,
+		Priority:  1,
+		IssueType: types.TypeTask,
+	}
+	if err := store.CreateIssue(ctx, issue, "test"); err != nil {
+		t.Fatalf("Failed to create issue after sync: %v", err)
+	}
+
+	if issue.ID != "bd-101" {
+		t.Errorf("Expected ID bd-101 after sync, got %s", issue.ID)
+	}
+
+	// Syncing to a lower value should not decrease the counter
+	if err := store.SyncCounterForPrefix(ctx, "bd", 50); err != nil {
+		t.Fatalf("SyncCounterForPrefix failed: %v", err)
+	}
+
+	// Next issue should still be bd-102, not bd-51
+	issue2 := &types.Issue{
+		Title:     "After lower sync",
+		Status:    types.StatusOpen,
+		Priority:  1,
+		IssueType: types.TypeTask,
+	}
+	if err := store.CreateIssue(ctx, issue2, "test"); err != nil {
+		t.Fatalf("Failed to create issue: %v", err)
+	}
+
+	if issue2.ID != "bd-102" {
+		t.Errorf("Expected ID bd-102 (counter should not decrease), got %s", issue2.ID)
+	}
+}