Fix for work on SEQWARE-1434
Add fix for SEQWARE-1444, needs tests.
Fixes for SEQWARE-1444 and associated tests.
Warning message for SEQWARE-1471
Further testing relating to launching of bundles (as opposed to scheduling or installating) also revealed an ini parsing error.

Details at wiki.oicr.on.ca/display/SEQWARE/2013/01/22/Jan+22%2C+2013%3A+ini+file+issues
Merge pull request #45 from SeqWare/feature/SEQWARE-1434_ini_files

Feature/seqware 1434 ini files