IGV-1945

Use log4j loggers instead of System.out in many places. Abstract message writer in others so we can easily use System.err (or different stream) for user info, rather than System.out
IGV-1945

Set PrintStream as a field in CommandLineStatusMonitor
IGV-1945

Remove System.out.println calls in converters and parsers where necessary
IGV-1945

Remove System.out.println calls in sorters where necessary
IGV-1945

Allow wig output of igvtools count to be directed to stdout, write test for same. Not implemented for TDF yet
IGV-1945

Allow output of igvtools sort to be directed to stdout, write test for same.
Updates for Java 8. Update JIDE library, remove references to external DTD

Should revisit the DTD thing, not sure why that's necessary but it's easy enough for now.

IGV-1950
Implement custom decoding codec for cufflinks cli_plugin

IGV-1908 IGV-1909
Change FpkmTrackingCodec -> FPKMTrackingCodec pt 1

IGV-1908 IGV-1909
Change FpkmTrackingCodec -> FPKMTrackingCodec pt 2

IGV-1908 IGV-1909
Replace references to DTD in plugin XML files

 Apparently need them for default values
Fix potential NPE in FPKMTrackingSampleCodec

IGV-1908 IGV-1909
Uncomment some tests which should be allowed for BEDToolsPlugin

Rename method in RunPlugin
Merge pull request #47 from broadinstitute/IgvToolsStdout

Igv tools stdout
Region command now accepts an optional description, which cannot contain spaces

Syntax:
region <chr> <start> <end> <desc>

OR

region <chr:start-end> <desc>

IGV-1893
Begin writing snapshot stress test for batch

IGV-1946