Fixed Jbrowse workflow (removed runtime str parameter altogether) plus some formatting and code cleaning

jinja templating, more workflow changes, trying fixes for the jbrowse gmod tool using API (in progress)

run_workflow changes (functional again), some optimisation in gga_init, gga_load and run_workflow, more validation steps in gga_init

more config options (host, passwords, tripal themes), adapted methods to handle several histories in the same instance

Modifications for multiple histories in the same gaalxy instance, some changes for swarm architecture