Update IGV to use new FeatureCodec API
Have MUTCodec load read header in constructor, as before
User LineIterator.peek() when reading headers so we don't read beyond header region
Override VCFWrapperCodec.decodeLoc to call through to wrapped Codec

The default implementation didn't work with VCFVariant, because we adjust the start positions of indels to remove redundant reference bases

IGV-1903
Add in additional flag in session file to determine if sequence track is loaded.

This is especially important for fasta-only genomes, where there is no gene track. Previously we had been treating them as either both-present or both-absent.

IGV-2011
Make sure that loading VCF files is case-insensitive to the extension

Add test for same

IGV-2012
Update ConfirmDialog to not show in headless mode
Merge branch 'TribbleVCF'
Merge remote-tracking branch: upstream/master