fix(core): resolve 500 errors with gemini-3-flash-preview model

- Refactor default model configs to prevent Flash models from inheriting thinkingConfig
- Add synthetic model turn to initial chat history to enforce alternating user/model roles required by gemini-3-flash-preview
- Fix trailing newline assertion error in file-system integration test

packages/core/src/utils/environmentContext.ts

@@ -96,6 +96,10 @@ export async function getInitialChatHistory(
       role: 'user',
       parts: [{ text: envContextString }],
     },
+    {
+      role: 'model',
+      parts: [{ text: 'Understood. I am ready.' }],
+    },
     ...(extraHistory ?? []),
   ];
 }