Upgrade slick to 2.1.0

Also contains some starts to refactors. Making this PR now as to match up with the upgrade to slick 2.1.0 in GeoTrellis and the gtfs-parser project.

Feel free to ask questions about the work-in-progress refactor on this PR. I'm making comments to point out a couple of things that I changed.
As you can see here, the Database is a dependency that needs to be injected through a couple different levels. I feel like this code needs some refactoring, and afterwards this database pass-through won't be so blatant (i.e. adding this parameter was a code smell that I'm looking into getting rid of).