Perch to Perch Runway upgrade instructions

Quick clarification question.

I was following the instructions here for upgrading and probably missed a step about how to update the database.

https://docs.grabaperch.com/runway/upgrading/

Should we use the setup files outside core to upgrade the database on local site to add the collections tables and then remove the setup files like we would on a clean install? Or are they not required to run an upgrade on the db?

Besides this small issue the upgrade instructions for the conversion to Runway worked smoothly. We see collections in Perch Admin but can't add new collections b/c of the small issue with the database upgrade.