updated version, fixing method to parse args, fixing conversion writing \r and \n, other fixes
commit
Merge branch 'master' of https://github.com/USDBioinformatics/BETS-CLI

Conflicts:
	BETS-WORKING/BETS-CLI/build/built-jar.properties
	BETS-WORKING/BETS-CLI/build/classes/org/usd/edu/btl/cli/Conversion.class
	BETS-WORKING/BETS-CLI/build/classes/org/usd/edu/btl/cli/runCLI.class
	BETS-WORKING/BETS-CLI/nbproject/private/private.properties
	BETS-WORKING/BETS-CLI/nbproject/private/private.xml
	BETS-WORKING/BETS-CLI/src/org/usd/edu/btl/cli/Conversion.java
	BETS-WORKING/BETS-CLI/src/org/usd/edu/btl/cli/runCLI.java