refactor: improve agent file model validation and settings source deduplication

- Enhanced model parsing in agent discovery to validate against allowed values and log warnings for invalid models.
- Refactored settingSources construction in AgentService to utilize Set for automatic deduplication, simplifying the merging of user and project settings with skills sources.
- Updated tests to reflect changes in allowedTools for improved functionality.

These changes enhance the robustness of agent configuration and streamline settings management.

apps/server/tests/unit/providers/claude-provider.test.ts

@@ -96,7 +96,17 @@ describe('claude-provider.ts', () => {
       expect(sdk.query).toHaveBeenCalledWith({
         prompt: 'Test',
         options: expect.objectContaining({
-          allowedTools: ['Read', 'Write', 'Edit', 'Glob', 'Grep', 'Bash', 'WebSearch', 'WebFetch'],
+          allowedTools: [
+            'Read',
+            'Write',
+            'Edit',
+            'Glob',
+            'Grep',
+            'Bash',
+            'WebSearch',
+            'WebFetch',
+            'Skill',
+          ],
         }),
       });
     });