Solved this issue, by replacing reference:$file_uri:$workspace_loc:/MagicDraw/MAGIC_DRAW_INSTALL_DIRECTORY/lib/bundles/com.nomagic.magicdraw.osgi.fragment with the actual path and enabling com.nomagic.magicdraw.platform.feature in the bundles tab of the run configuration.
The problem is that I have a hidden .magicdraw folder which has not been updated after the new installation, and I need it to be updated, since I messed with the files that were inside it and it's completely useless now.
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