git add -u
The "u" option stands for Update.
This will update the repo and really delete files from the repo that you simply have deleted in your local copy.
git add -u [filename]
to stage a delete to just one file. Once pushed, the file can not be within the repo.
git add -A .
is equivalent to
git add .
git add -u .
Note the additional '.' on git add -A and git add -u. Warning: starting with git 2.0 (mid-2013), this will always stage files on the whole working tree. If you would like to stage files under the current path of your working tree, you would like to use:
git add -A