[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_message_processor.rs

@@ -367,6 +367,7 @@ fn derive_config_from_params(
         config: cli_overrides,
         base_instructions,
         include_plan_tool,
+        include_apply_patch_tool,
     } = params;
     let overrides = ConfigOverrides {
         model,
@@ -378,6 +379,7 @@ fn derive_config_from_params(
         codex_linux_sandbox_exe,
         base_instructions,
         include_plan_tool,
+        include_apply_patch_tool,
         disable_response_storage: None,
         show_raw_agent_reasoning: None,
     };