Fixed issues with relative paths in some of the test suite, so that it
would use the packaged pnase.txt file regardless of other variables.
Fixed ability to append new start/stop information to
bestPfamLines_pfamToPDB.txt
Unclear to me what is happening with push-pull.  May have lost a family
or added one without knowing?
Would appear that excluding Energenetics.properties has caused issues
Merge branch 'master' of https://github.com/afodor/cobs

Conflicts:
	cobs/Energetics.properties
	cobs/test/SangerPDBpfamMappingTest.class