Directly overwrite with fixed doctests
call git directly and from the right directory
Add newline at end of file and fix cmdline help
Also fix the cmdline doctest
Trac #16992: Direct Fixdoctests

Now that we are actually using a versions control system as it is
intended, the `sage --fixdoctests` workflow is a bit antiquated:

* Run `sage --fixdoctests src/sage/foo.py`
* Get a diff printed to stdout
* copy `src/sage/foo.py.out` to `src/sage/foo.py`
* Run `git diff` to get the same diff again

Instead, just overwrite the file directly. Use version control for the
rest.

URL: http://trac.sagemath.org/16992
Reported by: vbraun
Ticket author(s): Volker Braun
Reviewer(s): Jeroen Demeyer