Use HashMap for AlignmentDataManager.loadedDataMap

We were using MapMaker with softValues, which was forcing reloads during batch testing. Since this really is a cache, it might make sense to use Guavas Cache
Have CommandExecutor garbagecollect when "clearing caches"
Misc. cleanup of CoverageCounter.

Add some better comments, remove unused code
Merge branch 'AlignmentCaching'
Update IGVSessionReaderTestHeaded to use data file which exists
Update IGVCommandBarTest now that we no longer throw spurious events