fix: Add pre-migration orphan cleanup to avoid chicken-and-egg failure (bd-eko4)

When the database has orphaned foreign key references (dependencies or labels
pointing to non-existent issues), the migration invariant check would fail,
preventing the database from opening. This created a chicken-and-egg problem:

1. bd doctor --fix tries to open the database
2. Opening triggers migrations with invariant checks
3. Invariant check fails due to orphaned refs
4. Fix never runs because database won't open

The fix adds CleanOrphanedRefs() that runs BEFORE captureSnapshot() in
RunMigrations. This automatically cleans up orphaned dependencies and labels
(preserving external:* refs), allowing the database to open normally.

Added test coverage for the cleanup function.

internal/storage/sqlite/migration_invariants.go

@@ -205,3 +205,46 @@ func GetInvariantNames() []string {
 	sort.Strings(names)
 	return names
 }
+
+// CleanOrphanedRefs removes orphaned dependencies and labels that reference non-existent issues.
+// This runs BEFORE migrations to prevent the chicken-and-egg problem where:
+// 1. bd doctor --fix tries to open the database
+// 2. Opening triggers migrations with invariant checks
+// 3. Invariant check fails due to orphaned refs from prior tombstone deletion
+// 4. Fix never runs because database won't open
+//
+// Returns counts of cleaned items for logging.
+func CleanOrphanedRefs(db *sql.DB) (deps int, labels int, err error) {
+	// Clean orphaned dependencies (issue_id not in issues)
+	result, err := db.Exec(`
+		DELETE FROM dependencies
+		WHERE NOT EXISTS (SELECT 1 FROM issues WHERE id = issue_id)
+	`)
+	if err != nil {
+		return 0, 0, fmt.Errorf("failed to clean orphaned dependencies (issue_id): %w", err)
+	}
+	depsIssue, _ := result.RowsAffected()
+
+	// Clean orphaned dependencies (depends_on_id not in issues, excluding external refs)
+	result, err = db.Exec(`
+		DELETE FROM dependencies
+		WHERE NOT EXISTS (SELECT 1 FROM issues WHERE id = depends_on_id)
+		  AND depends_on_id NOT LIKE 'external:%'
+	`)
+	if err != nil {
+		return 0, 0, fmt.Errorf("failed to clean orphaned dependencies (depends_on_id): %w", err)
+	}
+	depsDependsOn, _ := result.RowsAffected()
+
+	// Clean orphaned labels (issue_id not in issues)
+	result, err = db.Exec(`
+		DELETE FROM labels
+		WHERE NOT EXISTS (SELECT 1 FROM issues WHERE id = issue_id)
+	`)
+	if err != nil {
+		return 0, 0, fmt.Errorf("failed to clean orphaned labels: %w", err)
+	}
+	labelsCount, _ := result.RowsAffected()
+
+	return int(depsIssue + depsDependsOn), int(labelsCount), nil
+}