This is a straight refactor, moving apply-patch-related code from
`codex.rs` and into the new `apply_patch.rs` file. The only "logical"
change is inlining `#[allow(clippy::unwrap_used)]` instead of declaring
`#![allow(clippy::unwrap_used)]` at the top of the file (which is
currently the case in `codex.rs`).
---
[//]: # (BEGIN SAPLING FOOTER)
Stack created with [Sapling](https://sapling-scm.com). Best reviewed
with [ReviewStack](https://reviewstack.dev/openai/codex/pull/1703).
* #1705
* __->__ #1703
* #1702
* #1698
* #1697
