Genomic align tree display

This is a follow-up from #67
I've made the changes suggested by Ridwan and Dan. I think the result looks good, but as it is a bigger change, I'm making another PR to give you the choice of which one you want to include

show_warnings() is now in Shared, and all the messages have a "severity" field.
The last commit (Kathryn's) is identical to the previous PR. I've only refactored the handling of warnings / errors

Matthieu