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'