Enhance roadmap and documentation with new features and optimizations

- Add optimization pass details including subagent model override, system prompt caching, and memory recall improvements.
- Document per-path permission matching for apply_patch and read_many_files.
- Update configuration to include subagentModel for cost-effective task handling.
- Implement atomic config writes to prevent half-written JSON on crashes.
- Introduce empty-report subagent retry mechanism for improved reliability.
- Adjust memory entry limits and search functionality for better performance.
- Add tests for new features and ensure existing functionality remains intact.

test/permission.test.ts

@@ -45,7 +45,8 @@ test('file tools are matched on their path', () => {
 
 test('a batch read is matched on every path it asks for', () => {
   const subject = subjectOf('read_many_files', { files: [{ path: 'a.ts' }, { path: 'b.ts' }] });
-  expect(subject).toBe('a.ts b.ts');
+  // One subject per path, newline-separated so a path containing spaces stays whole.
+  expect(subject).toBe('a.ts\nb.ts');
 });
 
 test('search tools are matched on the pattern, git_show on the ref', () => {