rm base/config/kconfig/Makefile.kconfig.orig

Apparently committed by accident, either at the time of the ShabbyX
fork or else in the upstream RTAI tree.

This gets automatically removed by `dh_clean`.  Removing it here
instead of making an exclusion for this file in the packaging.
Fix `distclean` target

Don't remove `./configure`.  GNU coding standards say the `distclean`
target should not remove anything needed to run `./configure`.

Include `doc` directory for build and clean.