Cannot delete and upload file of the same name in the Web IDE

Summary

There is no way to upload a file over the top of an existing file. Because of this, the user then must delete the file and then upload, only to discover that they must first commit the deletion and commit the upload separately. This is not convenient. (Please refer to GitLab FOSS Issue # 60859)

Steps to reproduce

1. Opened the project in the Web IDE
2. Deleted a file
3. Upload a new file of the same name to the same directory

Example Project

https://gitlab.com/jramsay/FlappySwift

Using GitLab Enterprise 12.3.0-ee

What is the current bug behavior?

Error: `The name "x" is already taken in this directory"

What is the expected correct behavior?

I should be able to upload the file

Relevant logs and/or screenshots

Output of checks

This bug happens on our personal GitLab server, which has GitLab Enterprise 12.3.0-ee