It's currently not possible to ignore a certain folder within SQL Source Control.
Is it possible to move your "upgrade" folder to a higher level that is not within the SQL Source Control directory? Maybe you could have a structure like:
- Database - high level root folder
-- SchemaChanges - Point SQL Source Control here
-- Upgrade - Use for your patch files
Have you tried using SQL Compare to deploy your changes? You can use SQL Compare to compare a scripts folder (if you get a version using your source control system) or your development database to a target database (e.g., Test/QA). SQL Compare will show you all the differences. You can then automatically generate a syncrhonization script, which will create all the ALTER statements for you. It will take care of dependencies and order as well. This can be ran directly on the target db or it can generate a script that you can open in SSMS and review yourself before executing.
I hope this helps!
Stephanie M. Herr
SQL Source Control Project Manager