chore: update ESLint configuration and improve TypeScript type handling

- Added additional test file patterns to ESLint configuration for better coverage.
- Introduced new rule to ignore unused TypeScript variables starting with an underscore.
- Updated `PermissionController` to set approval mode correctly.
- Refactored timeout constants in `Query` class for better maintainability.
- Enhanced E2E tests for permission control and multi-turn conversations with clearer prompts and expectations.
- Removed outdated simple query test file and added new single-turn test suite for better organization.

packages/core/src/config/config.ts

@@ -293,27 +293,6 @@ export interface ConfigParameters {
   inputFormat?: InputFormat;
   outputFormat?: OutputFormat;
   skipStartupContext?: boolean;
-  inputFormat?: InputFormat;
-  outputFormat?: OutputFormat;
-}
-
-function normalizeConfigOutputFormat(
-  format: OutputFormat | undefined,
-): OutputFormat | undefined {
-  if (!format) {
-    return undefined;
-  }
-  switch (format) {
-    case 'stream-json':
-      return OutputFormat.STREAM_JSON;
-    case 'json':
-    case OutputFormat.JSON:
-      return OutputFormat.JSON;
-    case 'text':
-    case OutputFormat.TEXT:
-    default:
-      return OutputFormat.TEXT;
-  }
 }
 
 function normalizeConfigOutputFormat(