[Gmod-ajax] Some recent changes to the JBrowse command-line scripts

[Mitch S. <mit...@be...>]

JBrowse work is ongoing, but I'd like to highlight a few specific recent 
changes, since they affect people who run JBrowse instances.

One big change was adding support for BED flat files; because of that, I 
changed the name of gff-to-json.pl to flatfile-to-json.pl.  Some of the 
command line arguments for that script have also changed; see the usage 
message for details.

Also, since a few people were confused about exactly how to run 
generate-names.pl, that script no longer needs any command line 
arguments.  It now figures out what files to operate on by itself.

Regards,
Mitch