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>
Add debug and parallel flags to evaluation script
Add build instructions for Debian
Update TSK to 4.1.0
Keep version number up-to-date with master