Add "Group By..." to VCF track menu.  Tweaks to group border display.
Tweak vertical position of feature labels.
Changes to flanking region.
(1) don't use flanking region for single-base jumps
(2) allow entry as a % of feature size
Bug fix -- cannot explicitly turn on default track attributes from View menu
Add permissions and application-name attribute to manifest
Update unit test to point to data file which exists
Modify IGVBEDCodecTest to be more forgiving on Java 6
Merge remote-tracking branch: upstream/master