Add tutorial for running "modern" pathogen workflows

[joverlee521]

We already have the Running a phylogenetic workflow tutorial that is based on the simple zika-tutorial repo. However, we do not have a tutorial for the "modern" phylo workflows that are slightly more complex.

Potential location in docs

• an extension of Pathogens
• under Using a pathogen repository

Things we should highlight in the tutorial (feel free to edit and add more to the list):

• nextstrain run instructions (original discussion)
• multiple inputs configuration (originally suggested by @kimandrews)
• explain output of the run_config.yaml to prevent user error