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