fix: harden API, DB, and web layer from audit findings

- Cap list API limit at 200 to prevent unbounded queries
- Sanitize markdown output with DOMPurify to prevent XSS
- Add v4 migration with indexes on deleted_at and modified_at
- Fix v2 migration swallowed ALTER TABLE errors
- Tighten ~/.nib directory permissions to 0o700

internal/api/entities.go

@@ -92,6 +92,9 @@ func listEntities(store *db.Store) http.HandlerFunc {
 				writeError(w, http.StatusBadRequest, "invalid_input", "limit must be a positive integer")
 				return
 			}
+			if limit > 200 {
+				limit = 200
+			}
 			p.Limit = limit
 		}
 		if offsetStr := r.URL.Query().Get("offset"); offsetStr != "" {

internal/db/db.go

@@ -51,7 +51,7 @@ func (s *Store) Close() error {
 	return s.db.Close()
 }
 
-const currentSchema = 3
+const currentSchema = 4
 
 var migrations = []func(db *sql.DB) error{
 	// v1: initial schema
@@ -92,8 +92,12 @@ var migrations = []func(db *sql.DB) error{
 
 	// v2: add title and description columns
 	func(db *sql.DB) error {
-		db.Exec(`ALTER TABLE entities ADD COLUMN title TEXT`)
-		db.Exec(`ALTER TABLE entities ADD COLUMN description TEXT`)
+		if _, err := db.Exec(`ALTER TABLE entities ADD COLUMN title TEXT`); err != nil {
+			return fmt.Errorf("add title column: %w", err)
+		}
+		if _, err := db.Exec(`ALTER TABLE entities ADD COLUMN description TEXT`); err != nil {
+			return fmt.Errorf("add description column: %w", err)
+		}
 		return nil
 	},
 
@@ -166,6 +170,19 @@ var migrations = []func(db *sql.DB) error{
 
 		return tx.Commit()
 	},
+
+	// v4: add indexes for common query filters
+	func(db *sql.DB) error {
+		for _, idx := range []string{
+			`CREATE INDEX IF NOT EXISTS idx_entities_deleted ON entities(deleted_at)`,
+			`CREATE INDEX IF NOT EXISTS idx_entities_modified ON entities(modified_at DESC) WHERE deleted_at IS NULL`,
+		} {
+			if _, err := db.Exec(idx); err != nil {
+				return fmt.Errorf("create index: %w", err)
+			}
+		}
+		return nil
+	},
 }
 
 func (s *Store) migrate() error {
@@ -200,7 +217,7 @@ func DefaultPath() (string, error) {
 		return "", err
 	}
 	dir := filepath.Join(home, ".nib")
-	if err := os.MkdirAll(dir, 0o755); err != nil {
+	if err := os.MkdirAll(dir, 0o700); err != nil {
 		return "", err
 	}
 	return filepath.Join(dir, "nib.db"), nil