warning: You ran 'git add' with neither '-A (--all)' or '--ignore-removal'

It is saying that you should use either git add -A or git add --ignore-removal ., because git add . will have a different behavior in the newer version of git. Since it says the current version will ignore deleted paths, my best guess is that the next version will default to including them.

It wants you to be explicit about what whether you want to stage deleted paths in the current directory.

If you want to add deleted paths, you should use git add -A.

If you do not want to add deleted paths, you should use git add --ignore-removal .

I think it is merely trying to warn you so that you will know that your command will do something unexpected (ie different from now) if you upgrade git, so you can take one of the above two options or just make a note of the coming change and move on, with the understanding that you are currently ignoring deleted paths.