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plugins can still use the old .net version, that is not related to the main program.

You still have to make sure to have all the relevant .net versions installed on your system.

Does anyone have an overview of the .net versions of the different parts? (Main program, configuration, installer, mpe1 etc)

You have to ask yourself what you are going to gain with targeting a newer .net framework. as far as I know there isn't a really compelling reason to do that as long as those versions are still under support