Fix problem with prepare-refseqs.pl.t test failing due to the /conf file being missing
Convert color names to hexadecimal values because _AlignmentsMixin parser expects either hexadecimal or rgb/hsl strings for colors. The deletion remains unchanged for aesthetic reasons
Fix regression where the histogram color would not be customized due to HighDPI settings. See issue #456
Merge branch 'master' into jbrowse-1.11.4-test