Вот что выходит:
$ git add .
warning: You ran 'git add' with neither '-A (--all)' or '--ignore-removal',
whose behaviour will change in Git 2.0 with respect to paths you removed.
Paths like 'workspace/.metadata/.plugins/org.eclipse.core.resources/.projects/Re
moteSystemsTempFiles/.markers.snap' that are
removed from your working tree are ignored with this version of Git.
* 'git add --ignore-removal ', which is the current default,
ignores paths you removed from your working tree.
* 'git add --all ' will let you also record the removals.
Run 'git status' to check the paths you removed from your working tree.
