[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/exec/src/lib.rs

@@ -146,6 +146,7 @@ pub async fn run_main(cli: Cli, codex_linux_sandbox_exe: Option<PathBuf>) -> any
         codex_linux_sandbox_exe,
         base_instructions: None,
         include_plan_tool: None,
+        include_apply_patch_tool: None,
         disable_response_storage: oss.then_some(true),
         show_raw_agent_reasoning: oss.then_some(true),
     };