Perhaps classes with identical names inside different projects.
I might know this problem. I just recreated the structure that I created and I called it number 2. Many classes had the same name and the same method inside packages with the same name. This seemed to really confuse the IDE and / or JRE.
I managed to solve the problem, making sure that they were not imported inside the same project! This still gives me weird warnings, but it seems to be working correctly. What I would eventually suggest, if so, would be to remove duplicates from the project together.
user2820531
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