Your instructions were partially correct. You started:
git rm -r --cached .
which removed junk files from tracked git. But for some reason you decided to add it again using
git add .
This led to the appearance of an unwanted file as a new file:
new file: calc/2_preliminary/1_CFD/7_Calc_Fluent/03_stationary_vof_stationary/mesh_04/run_10000.cas
The reason this is a new file is because you already told Git to forget about it.
The right course of action would be to only scripts that you really want in the repo that exclude files ending in .cas .
Update:
Try running git rm , but this time include only .cas files:
git ls-files | grep '\.cas$' | xargs git rm
Now, if you run git status , you should only see .cas files as deleted. Well, they have not actually been deleted from your local file system, but they will be deleted from the repo.
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