Close the XML doc

This will add a new line at the end of the file (and would close all the
open elements if such would exist).
Change defaults for AutoStacking and .kim export
i18n: remove contractions
Fix group count

Thanks to Robert Krawitz discovering the bug and sending a patch for it.
Removing unneeded loop

Thanks to Robert Krawitz for the fix
Update coding standards.

 - Prefer m_foo instance variables over _foo.
 - Add recipe for debug messages.