Fix: /undo destructively interacts with git staging (#8214) (#8303)

Fixes #8214 by removing the '--staged' flag from the undo git restore
command. This ensures that while the working tree is reverted to the
snapshot state, the user's staged changes (index) are preserved,
preventing data loss. Also adds a regression test.

codex-rs/core/tests/suite/undo.rs

@@ -486,3 +486,65 @@ async fn undo_overwrites_manual_edits_after_turn() -> Result<()> {
 
     Ok(())
 }
+
+#[tokio::test(flavor = "multi_thread", worker_threads = 2)]
+async fn undo_preserves_unrelated_staged_changes() -> Result<()> {
+    skip_if_no_network!(Ok(()));
+
+    let harness = undo_harness().await?;
+    init_git_repo(harness.cwd())?;
+
+    // create a file for user to mess with
+    let user_file = harness.path("user_file.txt");
+    fs::write(&user_file, "user content v1\n")?;
+    git(harness.cwd(), &["add", "user_file.txt"])?;
+    git(harness.cwd(), &["commit", "-m", "add user file"])?;
+
+    // AI turn: modifies a DIFFERENT file (creating ghost commit of baseline)
+    let ai_file = harness.path("ai_file.txt");
+    fs::write(&ai_file, "ai content v1\n")?;
+    git(harness.cwd(), &["add", "ai_file.txt"])?;
+    git(harness.cwd(), &["commit", "-m", "add ai file"])?; // baseline
+
+    let patch = "*** Begin Patch\n*** Update File: ai_file.txt\n@@\n-ai content v1\n+ai content v2\n*** End Patch";
+    run_apply_patch_turn(&harness, "modify ai file", "undo-staging-test", patch, "ok").await?;
+    assert_eq!(fs::read_to_string(&ai_file)?, "ai content v2\n");
+
+    // NOW: User modifies user_file AND stages it
+    fs::write(&user_file, "user content v2 (staged)\n")?;
+    git(harness.cwd(), &["add", "user_file.txt"])?;
+
+    // Verify status before undo
+    let status_before = git_output(harness.cwd(), &["status", "--porcelain"])?;
+    assert!(status_before.contains("M  user_file.txt")); // M in index
+
+    // UNDO
+    let codex = Arc::clone(&harness.test().codex);
+    // checks that undo succeeded
+    expect_successful_undo(&codex).await?;
+
+    // AI file should be reverted
+    assert_eq!(fs::read_to_string(&ai_file)?, "ai content v1\n");
+
+    // User file should STILL be staged with v2
+    let status_after = git_output(harness.cwd(), &["status", "--porcelain"])?;
+
+    // We expect 'M' in the first column (index modified).
+    // The second column will likely be 'M' because the worktree was reverted to v1 while index has v2.
+    // So "MM user_file.txt" is expected.
+    if !status_after.contains("MM user_file.txt") && !status_after.contains("M  user_file.txt") {
+        bail!("Status should contain staged change (M in first col), but was: '{status_after}'");
+    }
+
+    // Disk content is reverted to v1 (snapshot state)
+    assert_eq!(fs::read_to_string(&user_file)?, "user content v1\n");
+
+    // But we can get v2 back from index
+    git(harness.cwd(), &["checkout", "user_file.txt"])?;
+    assert_eq!(
+        fs::read_to_string(&user_file)?,
+        "user content v2 (staged)\n"
+    );
+
+    Ok(())
+}

codex-rs/utils/git/src/ghost_commits.rs

@@ -469,15 +469,18 @@ fn restore_to_commit_inner(
     repo_prefix: Option<&Path>,
     commit_id: &str,
 ) -> Result<(), GitToolingError> {
-    // `git restore` resets both the index and working tree to the snapshot commit.
+    // `git restore` resets the working tree to the snapshot commit.
+    // We intentionally avoid --staged to preserve user's staged changes.
+    // While this might leave some Codex-staged changes in the index (if Codex ran `git add`),
+    // it prevents data loss for users who use the index as a save point.
+    // Data safety > cleanliness.
     // Example:
-    //   git restore --source <commit> --worktree --staged -- <prefix>
+    //   git restore --source <commit> --worktree -- <prefix>
     let mut restore_args = vec![
         OsString::from("restore"),
         OsString::from("--source"),
         OsString::from(commit_id),
         OsString::from("--worktree"),
-        OsString::from("--staged"),
         OsString::from("--"),
     ];
     if let Some(prefix) = repo_prefix {