Update packaging for ShabbyX repo/4.0.0

* Updates for RTAI-4.0.0 and ShabbyX git repo
  - acinclude.m4 file moved
  - configure.in -> configure.ac
  - makefile -> GNUmakefile
  - Arch is now 'x86', not 'amd64' and 'i.86'
  - Add Build-Depends: autoconf, automake, libtool
  - Deal with missing depcomp/config.sub/etc.
  - Remove non-module directories for module package
    - *FIXME* These directories need to be packaged elsewhere
* Bug fixes
  - Fix ./configure command line typo
  - Fix race condition with build-arch-stamp