fix: fixed bootstrap overwrtting .env file and improved bool handling for js use

alfred/settings_bootstrap.py

@@ -359,10 +359,9 @@ class SettingsBootstrap:
                         value = "true" if value else "false"
 
                     output_lines.append(f"{key}={value}\n")
-                else:
                 # Variable not in schema
                 # If it exists in current .env, use that value, otherwise keep template
-                    if key in self.existing_env:
+                elif key in self.existing_env:
                     output_lines.append(f"{key}={self.existing_env[key]}\n")
                 else:
                     output_lines.append(line)
@@ -371,7 +370,9 @@ class SettingsBootstrap:
                 output_lines.append(line)
 
         # Append custom variables from existing .env that aren't in .env.example
-        custom_vars = {k: v for k, v in self.existing_env.items() if k not in processed_keys}
+        custom_vars = {
+            k: v for k, v in self.existing_env.items() if k not in processed_keys
+        }
         if custom_vars:
             output_lines.append("\n# --- CUSTOM VARIABLES ---\n")
             output_lines.append("# Variables added manually (not in .env.example)\n")

tests/test_settings_bootstrap_advanced.py

@@ -150,7 +150,9 @@ class TestTemplatePreservation:
 class TestSecretPreservation:
     """Test that secrets are never overwritten."""
 
-    def test_preserves_existing_secrets(self, test_toml_with_all_types, test_env_example):
+    def test_preserves_existing_secrets(
+        self, test_toml_with_all_types, test_env_example
+    ):
         """Test that existing secrets are preserved across multiple bootstraps."""
         from alfred.settings_schema import load_schema