CubeMX 6.0.1 has a new bug with project setting
I posted previous for 6.0 that there was a bug where it would change your ProjectManager settings from 'Add necessary library files' to 'Copy only the necessary library files'. (https://community.st.com/s/question/0D53W00000DffOTSAZ/updating-from-cubemx-53-to-6-results-in-some-project-settings-changing)
That bug is technically fixed, as it no longer updates the .ioc file and keeps whatever setting you previously had. The new bug is that is just completely ignores that setting and always chooses "Copy only the necessary library files"
This is what my .ioc files says:
ProjectManager.LibraryCopy=2
This is what my project file does when I open it

Regardless of what changes I make to the project and that setting, the .ioc file never changes and it always opens up with "Copy only the necessary library files". So like, we're half way there I guess?
This happens on an H7 project and an L4 project I tested. The H7 was a 6.0 project and the L4 was a 5.0.1 project.
