Both of these will stage all files, including new files (which
git commit -a misses) and deleted files.
The difference is that
git add -A also stages files in higher directories that still belong to the same git repository. Here's an example:
/my-repo .git/ subfolder/ nestedfile.txt rootfile.txt
If your current working directory is
/my-repo, and that's the root of this git repo (thus the
.git/ folder), these two commands will do the same thing.
But if you
rm rootfile.txt, then
git add . will not stage the change that
../rootfile.txt has been deleted, because
git add . only affects the current directory and subdirectories.
git add -A, on the other hand, will stage this change.