For git version 1.x use
git add -u
Which enables git to automatically stage tracked files -- including the deletion of previously staged files.
For git version 2.0 use the commands
To stage a whole working tree
git add -u :/
For current path
git add -u.
These commands will add the staged files and delete the files that are not present on a local disk.
For more information please go through the following tutorial to get more info about git: