SandBox linked to Github; renamed files commited as new files

🐛 bug report

Preflight Checklist

• I have read the
  Contributing Guidelines
  for this project.
• I agree to follow the
  Code of Conduct
  that this project adheres to.
• I have searched the issue tracker for an issue that matches the one I want
  to file, without success.

Description of the problem

I created a sandbox , linked it to my github repo. After initial commit, I renamed few files. Later found that on github, both files exist, ones with old name, and renamed ones.

How has this issue affected you? What are you trying to accomplish?

Despite, code working fine on CSB website, it contained duplicate files.
I expected that the original file would be replaced by the renamed files.

To Reproduce

1. Create a sandbox on CSB website
2. Link it to a github repo and initial commit
3. rename one or more files (e.g. change file extension)
4. commit again
5. go to github repo and observe the files such as original file and renamed file

Link to sandbox: link (provided)

Your Environment

Start by reproducing the problem with the linked sandbox: create a GitHub-linked sandbox, commit it, rename a file, and commit again. Trace the GitHub synchronization flow responsible for file renames, then verify that the repository contains the renamed file without the obsolete filename.