Fix Web IDE deleting newly added files
What does this MR do?
This MR fixes a bug where deleting a newly added file was not removed from staging (and left the commit tab around).
Does this MR meet the acceptance criteria?
- Changelog entry
- Documentation (if required)
- Code review guidelines
- Merge request performance guidelines
- Style guides
- Database guides
- Separation of EE specific content
- Related to #213239 (closed)