Fixed all problems with type removal.

Fixed the last two problems with type removal (at least for the MonoGame
library) - the library is now fully verifiable after piranha.exe
remove-code-members-types.
Nested types have different visibility attributes. It's perfectly fine
to expose a protected internal type via a protected member.
You must not remove the "<Module>" class.
Replacing references seems to work a bit better.

Replacing references seems to work a bit better than removing and adding
them.