chore: merge git crates (#5909)

Merge `git-apply` and `git-tooling` into `utils/`

codex-rs/utils/git/README.md

@@ -0,0 +1,33 @@
+# codex-git
+
+Helpers for interacting with git, including patch application and worktree
+snapshot utilities.
+
+```rust,no_run
+use std::path::Path;
+
+use codex_git::{
+    apply_git_patch, create_ghost_commit, restore_ghost_commit, ApplyGitRequest,
+    CreateGhostCommitOptions,
+};
+
+let repo = Path::new("/path/to/repo");
+
+// Apply a patch (omitted here) to the repository.
+let request = ApplyGitRequest {
+    cwd: repo.to_path_buf(),
+    diff: String::from("...diff contents..."),
+    revert: false,
+    preflight: false,
+};
+let result = apply_git_patch(&request)?;
+
+// Capture the current working tree as an unreferenced commit.
+let ghost = create_ghost_commit(&CreateGhostCommitOptions::new(repo))?;
+
+// Later, undo back to that state.
+restore_ghost_commit(repo, &ghost)?;
+```
+
+Pass a custom message with `.message("…")` or force-include ignored files with
+`.force_include(["ignored.log".into()])`.