Better solution for tools depending on internal services

This means stuff like https://github.com/intermine/bluegenes-jbrowse-tool which depends on https://jbrowse.intermine.org/?data= and https://github.com/intermine/bluegenes-msa-viewer/ which depends on http://sequencealignment.apps.intermine.org

Start by reviewing the bluegenes-jbrowse-tool and bluegenes-msa-viewer repositories, along with the jbrowse.intermine.org and sequencealignment.apps.intermine.org service URLs they depend on. Clarify the desired approach for handling these internal service dependencies and define how the tools should work without their current assumptions. Done means the dependency strategy is agreed and both affected tools follow it.

Written by the indexing model from the issue text.