Well, she doesn’t sound like a friend, honestly. She sounds like a user who is trading on your alleged friendship to do whatever she wants, concerning everything, from taking over your part of the apartment to ignoring her pets and letting you deal with the fallout. She gets all the space, help, etc. and you get nothing in return. I don’t see how you can even call that a friendship.
She also sounds like she has no business being a pet owner. She doesn’t care for them, doesn’t medicate them properly, doesn’t take care of the little box, and doesn’t even see them much. Plus, your apartment doesn’t even allow them.
I think you have to sit her down and insist that she remove her junk from your space, that she take care of her cats or find them a new home, and that she stop using you. You might have to threaten to turn her into the apartment management-if fleas went untreated for so long, there’s a good chance that they’ve gotten into other apartments and the management might already be looking for the owners of whatever pets caused the problem. You could both have to pay hefty damage fees. My older D has an apartment and 2 cats and she pays higher rent AND security deposits. Having unapproved pets is grounds for eviction.