You have done a pet hate,
I have spent 20 years trying to get people to use version control systems right.
when you rename or move a file, please please do it inside the VCS.
if you rename or move a file outside your VCS, the VCS does not know what you have done, so you loss history.
without the history it can be hard to see why something has changed.
in git you should use “git mv”
(also if you want to delete something done not delete files, you need to move (using the VCS) them to a deleted folder, do the data/info/history etc is not lost)
Roger
(I am really a clearcase person, by far the best VCS but you do pay for it 5->100K per user per year, I have worked on projects that have had 5000+ dev, running for 10+ years)