Unable to move files in repo without breaking Atom

I’ve got an Issue open here: https://github.com/atom/atom/issues/19819 – this issue exists only with a specific repo, and it exists across at least two different computers, both with fresh Atom installs and in safe mode.

My hope is that someone can help me figure out a work around for this problem. I don’t know if this is due to the file structure in the project, or if there is something in the code itself that might be breaking Atom.

Any thoughts?