Add support for specifying coverage path in html links
Update AlignmentDataManagerTest.testQueryLargeFile2

For manual timing comparisons
Fix MotifFinderBug where negative strand box disabled improperly
Add logging statement for OS
Update TrackLoader to treat cufflinks files specially

They were being parsed as feature tracks
Add "DIRECT" option for proxy settings

IGV-2066
Merge remote-tracking branch: upstream/master