create standalone script for order contigs

	new file:   scripts/synmap/order_contigs_to_chromosome.pl
Add jex support for generating pseudo assembly

New generate_assembly end point will submit a generate pseudo assembly
task to be run.

	modified:   modules/MANIFEST
	new file:   modules/Pipelines/SynMap/MANIFEST
	new file:   modules/Pipelines/SynMap/Makefile.PL
	new file:   modules/Pipelines/SynMap/lib/CoGe/Pipelines/SynMap.pm
	modified:   scripts/synmap/order_contigs_to_chromosome.pl
	modified:   web/SynMap.pl
add pseudo assembly generation dialog

Switch pseudo assembly to new workflow submission endpoint. Add
dialog to notify user the assembly is being generated.

	modified:   web/SynMap.pl
	modified:   web/css/coge.css
	modified:   web/js/synmap.js
	modified:   web/tmpl/SynMap.tmpl