- Restricted number of threads for long server jobs to MedSavantServerEngine.MAX_THREADS (default: # virtual cores - 1)
- Added IO controller to limit # of threads doing IO to MedSavantServerEngine.MAX_IO_JOBS (default: MAX_THREADS -- so it's effectively off)
- Fixed file handle issue #164
Merge branch 'master' of https://github.com/compbio-UofT/medsavant

Conflicts:
	MedSavantServerEngine/src/main/java/org/ut/biolab/medsavant/server/db/variants/VariantManagerUtils.java
- Uncommented code that cleans up working directories.