status: Show added but not yet committed files.

Seems easy, but git ls-files can't list the right subset of files.
So, I wrote a whole new parser for git status output, and converted the
status command to use that.

There are a few other small behavior changes. The order changed. Unlocked
files show as T. In indirect mode, deleted files were not shown before, and
that's fixed. Regular files checked directly into git and modified
were not shown before, and are now.

doc/todo/make_status_show_staged_files.mdwn

@@ -21,3 +21,5 @@ Using the `git status` command directly will show the added files
 ### What version of git-annex are you using? On what operating system?
 
 git-annex version: 5.20141024-g613f396
+
+> [[done]] --[[Joey]]