Ignore configured hooks in git helpers (#22843)

## What
- Internal Git helper commands now ignore configured hook directories
during repository bookkeeping.

## Why
- These helper flows should stay consistent even when a repository has
hook-directory configuration of its own.

## How
- Pass a command-local `core.hooksPath` override in the shared helper
path and the Git-info helper path.
- Add regressions for the baseline index rewrite flow and the metadata
status flow.

## Validation
- `cargo fmt --manifest-path
/Users/bookholt/code/codex/codex-rs/Cargo.toml --all --check`
- `cargo test --manifest-path
/Users/bookholt/code/codex/codex-rs/Cargo.toml -p codex-git-utils`
- `cargo test --manifest-path
/Users/bookholt/code/codex/codex-rs/Cargo.toml -p codex-core
test_get_has_changes_`

codex-rs/core/src/git_info_tests.rs

@@ -379,6 +379,50 @@ async fn test_get_has_changes_ignores_repo_fsmonitor_config() {
     );
 }
 
+#[cfg(unix)]
+#[tokio::test]
+async fn test_get_has_changes_ignores_configured_hooks_path() {
+    let temp_dir = TempDir::new().expect("Failed to create temp dir");
+    let repo_path = create_test_git_repo(&temp_dir).await;
+    let hooks_dir = repo_path.join(".git/hooks-path-test");
+    let hook_path = hooks_dir.join("post-index-change");
+    let marker_path = repo_path.join("hook-ran");
+
+    fs::create_dir_all(&hooks_dir).expect("create hook dir");
+    fs::write(
+        &hook_path,
+        format!(
+            "#!/bin/sh\nprintf ran > \"{}\"\n",
+            marker_path.to_string_lossy()
+        ),
+    )
+    .expect("write post-index-change hook");
+    let mut permissions = fs::metadata(&hook_path)
+        .expect("read hook metadata")
+        .permissions();
+    permissions.set_mode(0o755);
+    fs::set_permissions(&hook_path, permissions).expect("mark hook executable");
+
+    Command::new("git")
+        .args([
+            "config",
+            "core.hooksPath",
+            hooks_dir.to_string_lossy().as_ref(),
+        ])
+        .current_dir(&repo_path)
+        .output()
+        .await
+        .expect("configure hooks path");
+
+    fs::write(repo_path.join("test.txt"), "test content").expect("refresh tracked file");
+
+    assert_eq!(get_has_changes(&repo_path).await, Some(false));
+    assert!(
+        !marker_path.exists(),
+        "metadata collection should not invoke configured hook directories"
+    );
+}
+
 #[tokio::test]
 async fn test_get_git_working_tree_state_clean_repo() {
     let temp_dir = TempDir::new().expect("Failed to create temp dir");