refactor modes implementation and improve validation handling

refactor `code` and `hybrid` modes for better type safety and configuration flexibility. add `_isProd` helper to standardize environment checks and improve plugin syncing warnings. adjust validation logic for clean JSON schema handling and enhance test coverage for modes.

app/src/modules/ModuleManager.ts

@@ -223,7 +223,7 @@ export class ModuleManager {
    }
 
    extractSecrets() {
-      const moduleConfigs = structuredClone(this.configs());
+      const moduleConfigs = JSON.parse(JSON.stringify(this.configs()));
       const secrets = { ...this.options?.secrets };
       const extractedKeys: string[] = [];