Accommodate Ubuntu 12.10's ~/.bashrc like 13.04's
Add missed package for Ubuntu 12.10
Move RE execution into own script

This will make parallelizing the evaluation script easier.
Add optional parallel evaluation
Revise deprecated automake form

From auto-generated warning reference:
<http://www.gnu.org/software/automake/manual/automake.html#Modernize-AM_005fINIT_005fAUTOMAKE-invocation>