Fix staging and unstaging of added and deleted files (#25631)

* When staging in a buffer whose file has been deleted, do not save the
file
* Fix logic for writing to index when file is deleted

Release Notes:

- N/A

crates/editor/src/editor_tests.rs

@@ -16510,6 +16510,7 @@ fn assert_hunk_revert(
 ) {
     cx.set_state(not_reverted_text_with_selections);
     cx.set_head_text(base_text);
+    cx.clear_index_text();
     cx.executor().run_until_parked();
 
     let actual_hunk_statuses_before = cx.update_editor(|editor, window, cx| {