[git] Apply .gitignore on an existing repository already tracking large number of files

If you added your .gitignore too late, git will continue to track already commited files regardless. To fix this, you can always remove all cached instances of the unwanted files.

First, to check what files are you actually tracking, you can run:

git ls-tree --name-only --full-tree -r HEAD

Let say that you found unwanted files in a directory like cache/ so, it's safer to target that directory instead of all of your files.

So instead of:

git rm -r --cached .

It's safer to target the unwanted file or directory:

git rm -r --cached cache/

Then proceed to add all changes,

git add .

and commit...

git commit -m ".gitignore is now working"

Reference: https://amyetheredge.com/code/13.html