I use the payments manual credit card processor for testing. I go to config/local plugins and then edit and set it to only show for administrators. I later published a site update from Visual Studio and noticed in some order checks that people were using it to make purchases. How??? I go back and see the role assignment is not set. I don't know where it's persisted but this was a close call, fortunately only about a dozen orders as a feature I added wasn't working, thankfully in another area.
So where are the roles persisted for a plugin such as the Payments.Manual plugin? and why isn't it persisted between Visual Studio publishing?