From what you described and assuming she knew you were in lecture, the most likely thing that happened is that she was worried that you were cheating on her and that’s why she broke into your apartment. Afterwards she tried to find evidence and she cleaned up in order to cover for changing the placement of your stuff. I’m sorry but it is best you break up, now that she did something like this i doubt she will respect any kind of limits or boundaries.
Did she break in through a window or something
Not overreacting, this is fucking bizarre and CONTROLLING ASF. Just because she cleaned your apartment (was probably snooping) doesn’t make this ok/normal. Her behaviour is invasive and unacceptable.