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 cd subfolder, 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.