Fix git.reset() to remove the added files

The combination of git-read-tree and git-checkout-index used in the
git.checkout() function doesn't remove the files added to the index. This
patch adds the file removal support to the git.reset() function. It also
changes the git.apply_diff() call in stack.Series.merged_patches() so that
the the index is always updated (otherwise the reset wouldn't know which
files to remove).

Signed-off-by: Catalin Marinas <catalin.marinas@gmail.com>