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

alfred/settings_bootstrap.py

@@ -311,7 +311,7 @@ class SettingsBootstrap:
     def _write_env(self) -> None:
         """
         Write .env file using .env.example as template.
-        
+
         This preserves the structure, comments, and formatting of .env.example
         while updating only the values of variables defined in the schema.
         Custom variables from existing .env are appended at the end.
@@ -335,43 +335,44 @@ class SettingsBootstrap:
         output_lines = []
         for line in template_lines:
             stripped = line.strip()
-            
+
             # Keep comments and empty lines as-is
             if not stripped or stripped.startswith("#"):
                 output_lines.append(line)
                 continue
-            
+
             # Check if line contains a variable assignment
             if "=" in line:
                 key, _ = line.split("=", 1)
                 key = key.strip()
                 processed_keys.add(key)
-                
+
                 # Check if this variable is in our schema
                 definition = self.schema.get(key)
-                
+
                 if definition:
                     # Update with resolved value (including computed settings)
                     value = self.resolved_settings.get(key, "")
-                    
+
                     # Convert Python booleans to lowercase for .env compatibility
                     if isinstance(value, bool):
                         value = "true" if value else "false"
-                    
+
                     output_lines.append(f"{key}={value}\n")
+                # Variable not in schema
+                # If it exists in current .env, use that value, otherwise keep template
+                elif key in self.existing_env:
+                    output_lines.append(f"{key}={self.existing_env[key]}\n")
                 else:
-                    # Variable not in schema
+                    output_lines.append(line)
-                    # If it exists in current .env, use that value, otherwise keep template
-                    if key in self.existing_env:
-                        output_lines.append(f"{key}={self.existing_env[key]}\n")
-                    else:
-                        output_lines.append(line)
             else:
                 # Keep any other lines as-is
                 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