Added sanity checks for PM3 installations.

conf-scripts/bc2-conf

doc/buildsystem.rst

doc/tests/test_doctests.py

extras/sanity_checks/Makefile

extras/sanity_checks/README

extras/sanity_checks/aln.fasta

extras/sanity_checks/prepare_sanity_checks.sh

extras/sanity_checks/run_pipeline.py

extras/sanity_checks/template.pdb

extras/sanity_checks/test_all.py

extras/sanity_checks/test_cpp.cc

extras/sanity_checks/test_module.py