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).

Screenshots

Before	After
20200417_ide_delete_new_file_before	20200417_ide_delete_new_file_fix

Does this MR meet the acceptance criteria?

Conformity

• Changelog entry
• Documentation (if required)
• Code review guidelines
• Merge request performance guidelines
• Style guides
• Database guides
• Separation of EE specific content

References

• Related to #213239 (closed)