add Request namespace for request dispatching
add listcmp into Core modules

	modified:   modules/Core/MANIFEST
	new file:   modules/Core/lib/CoGe/Core/List.pm
	modified:   modules/MANIFEST
	modified:   web/CoGeBlast_new.pl
	modified:   web/CoGeBlast_old.pl
	modified:   web/NotebookView.pl
	modified:   web/Notebooks.pl
	modified:   web/SynFind_new.pl
	modified:   web/User.pl
add support for posting json content

A request can now set the content type as application/json and the
POSTDATA will be parsed as a json string. If the data is not valid json
a PAYLOAD error is returned. If the PAYLOAD can not be properly routed
a NOT_FOUND error is returned. When successful the json object will
submitted as the arguments to the dispatch function.

	modified:   modules/Accessory/lib/CoGe/Accessory/Web.pm
add job submission and gff exporting

	modified:   modules/MANIFEST
	new file:   modules/Pipelines/MANIFEST
	modified:   modules/Pipelines/Misc/lib/CoGe/Pipelines/Misc/Gff.pm
	new file:   modules/Pipelines/lib/CoGe/Pipelines/PipelineFactory.pm
	new file:   modules/Requests/lib/CoGe/Requests/GffRequest.pm
	modified:   modules/Requests/lib/CoGe/Requests/Request.pm
	modified:   modules/Requests/lib/CoGe/Requests/RequestFactory.pm
	modified:   modules/Services/lib/CoGe/Services/Data/Job.pm
	modified:   modules/Services/lib/CoGe/Services/Routes.pm
add script to create results file
add results file generation
add a Buildable interface for workflow creation

	modified:   modules/MANIFEST
	modified:   modules/Pipelines/MANIFEST
	new file:   modules/Pipelines/lib/CoGe/Builder/Buildable.pm
	new file:   modules/Pipelines/lib/CoGe/Builder/GffBuilder.pm
	modified:   modules/Pipelines/lib/CoGe/Pipelines/PipelineFactory.pm
add irods export option to gff exporting

	new file:   modules/Pipelines/Misc/lib/CoGe/Pipelines/Misc/IPut.pm
	modified:   modules/Pipelines/lib/CoGe/Builder/GffBuilder.pm
cleanup code and use get_workflow_path
get the irods base path for a user
add no execute option to irods_put
symlink result files into the result directory

	new file:   scripts/link_results.pl
add downloading of results
update workflow to generate results

	modified:   Pipelines/Misc/lib/CoGe/Pipelines/Misc/Gff.pm
	modified:   Pipelines/Misc/lib/CoGe/Pipelines/Misc/IPut.pm
	modified:   Pipelines/lib/CoGe/Builder/GffBuilder.pm
restructure modules into a shared package

	modified:   modules/MANIFEST
	modified:   modules/Pipelines/MANIFEST
	deleted:    modules/Pipelines/Misc/MANIFEST
	deleted:    modules/Pipelines/Misc/Makefile.PL
	deleted:    modules/Pipelines/SNP/MANIFEST
	deleted:    modules/Pipelines/SNP/Makefile.PL
	deleted:    modules/Pipelines/SynMap/MANIFEST
	deleted:    modules/Pipelines/SynMap/Makefile.PL
	renamed:    modules/Pipelines/SNP/lib/CoGe/Pipelines/FindSNPs.pm -> modules/Pipelines/lib/CoGe/Pipelines/FindSNPs.pm
	renamed:    modules/Pipelines/Misc/lib/CoGe/Pipelines/Misc/Bed.pm -> modules/Pipelines/lib/CoGe/Pipelines/Misc/Bed.pm
	renamed:    modules/Pipelines/Misc/lib/CoGe/Pipelines/Misc/Copy.pm -> modules/Pipelines/lib/CoGe/Pipelines/Misc/Copy.pm
	renamed:    modules/Pipelines/Misc/lib/CoGe/Pipelines/Misc/Features.pm -> modules/Pipelines/lib/CoGe/Pipelines/Misc/Features.pm
	renamed:    modules/Pipelines/Misc/lib/CoGe/Pipelines/Misc/Gff.pm -> modules/Pipelines/lib/CoGe/Pipelines/Misc/Gff.pm
	renamed:    modules/Pipelines/Misc/lib/CoGe/Pipelines/Misc/IPut.pm -> modules/Pipelines/lib/CoGe/Pipelines/Misc/IPut.pm
	renamed:    modules/Pipelines/Misc/lib/CoGe/Pipelines/Misc/Tbl.pm -> modules/Pipelines/lib/CoGe/Pipelines/Misc/Tbl.pm
	renamed:    modules/Pipelines/SynMap/lib/CoGe/Pipelines/SynMap.pm -> modules/Pipelines/lib/CoGe/Pipelines/SynMap.pm
	renamed:    modules/Pipelines/qTeller/lib/CoGe/Pipelines/qTeller.pm -> modules/Pipelines/lib/CoGe/Pipelines/qTeller.pm
	new file:   modules/Pipelines/lib/CoGe/Requests/FastaRequest.pm
	renamed:    modules/Requests/lib/CoGe/Requests/GffRequest.pm -> modules/Pipelines/lib/CoGe/Requests/GffRequest.pm
	renamed:    modules/Requests/lib/CoGe/Requests/Request.pm -> modules/Pipelines/lib/CoGe/Requests/Request.pm
	renamed:    modules/Requests/lib/CoGe/Requests/RequestFactory.pm -> modules/Pipelines/lib/CoGe/Requests/RequestFactory.pm
	deleted:    modules/Pipelines/qTeller/MANIFEST
	deleted:    modules/Pipelines/qTeller/Makefile.PL
	deleted:    modules/Requests/MANIFEST
	deleted:    modules/Requests/Makefile.PL
move factories into factory namespace

	modified:   modules/MANIFEST
	modified:   modules/Pipelines/MANIFEST
	renamed:    modules/Pipelines/lib/CoGe/Pipelines/PipelineFactory.pm -> modules/Pipelines/lib/CoGe/Factory/PipelineFactory.pm
	renamed:    modules/Pipelines/lib/CoGe/Requests/RequestFactory.pm -> modules/Pipelines/lib/CoGe/Factory/RequestFactory.pm
	modified:   modules/Services/lib/CoGe/Services/Data/Job.pm
add fasta export to request factory

Create generic GenomeRequest to check access to genomes.
fail when no workflow is given
add fasta exporting to job submission
add generic request for experiments