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)

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

Deploy stacks and load data both working, only phaeoexplorer workflow script to finish. Data loading done directly from the script (not calling the container script anymore). Also some polishing.