[tools] Add apply_patch tool (#2303)

## Summary
We've been seeing a number of issues and reports with our synthetic
`apply_patch` tool, e.g. #802. Let's make this a real tool - in my
anecdotal testing, it's critical for GPT-OSS models, but I'd like to
make it the standard across GPT-5 and codex models as well.

## Testing
- [x] Tested locally
- [x] Integration test

codex-rs/mcp-server/src/codex_tool_config.rs

@@ -160,6 +160,7 @@ impl CodexToolCallParam {
             codex_linux_sandbox_exe,
             base_instructions,
             include_plan_tool,
+            include_apply_patch_tool: None,
             disable_response_storage: None,
             show_raw_agent_reasoning: None,
         };