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/memory.test.ts

@@ -84,7 +84,7 @@ test('an empty note is refused', async () => {
 test('long text is truncated', async () => {
   const m = new Memory('/repo');
   const entry = await m.add('fact', 'x'.repeat(2000));
-  expect(entry?.text.length).toBe(400);
+  expect(entry?.text.length).toBe(600);
 });
 
 test('search requires every term and records a hit', async () => {