Custom java classes and folders disappearing when updating

Not applicable
Issue description

So I have had this happen two times now. I take a duplicate of my workspace and try to update it to one of the snapshots. And it works except any of my custom classes that are not made using the custom code element are deleted while updating. The reason I don't use the custom code element is because I want my classes in a specific folder not the main mod folder but in a folder within it

If I need to explane more please tell me.

Issue comments

Since the change in the way generator works in 2020.2, we can not really distinguish user files from generated files. If we did not clear files on the workspace rebuild, there could old ghost files remain. The approach to this is to make a package for mcreator, say:


in workspace settings, and then add custom files to


MCreator will only clear the files in "my.package.generated".

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