when you run git clone
it creates a new dir..
cd into that dir, make changes then do your commit
the -m is handy for short commit messages, leave it off and you get a 'full' editor ( using $EDITOR )
-a commits ALL changes ( and only changes, new files will still not be 'seen' )
git add file1 file2 path/to/file3 dir1 path/to/dir2