Since they are in different directories, they need to be special cased
This is needed to support wpilibsuite/WPILibInstaller-Avalonia#492,
since those are currently handled by special scripts.
Putting an early exit if statement at the top instead of wrapping the
whole file contents unbreaks unit test configs, as was discovered for
SysId. It reduces nesting as well.
Unused plugins were removed from the beginnings of files as well.
