When the target of the compare is a scripts folder, SQL Compare will create new items with the schema name as part of the file name, such as "person.Contact.sql".
Could this be made optional?
It doesn't affect the filename when altering, only creating.
This behaviour causes us issues because we use Visual Studio database projects where the schema is part of the path, not the filename. For example such as "AdventureWorks\Person\Tables\Contact.sql"