doc: Make progdocs play nice with git

Moved contrib/asterisk-ng-doxygen to doc/asterisk-ng-doxygen.in

Changed /Makefile to copy asterisk-ng-doxygen.in to
asterisk-ng-doxygen then modify it with version instead of
modifying asterisk-ng-doxygen directly.  Updated clean
targets as well.

Updated /.gitignore and doc/.gitignore.

Change-Id: I38712d3e334fa4baec19d30d05de8c6f28137622