In Brazil, this "arruma" can be both. "Set up" and "clean up"
Literally, "arrumar" means "to arrange". If you "arrange" the table before lunch, then you set it up for lunch. If you "arrange" the table after lunch, then you are cleaning it up, removing food and dishes, to let it as it was before lunch.
There are also "pôr a mesa" (verb pôr = to put), which is "set up" the table. (Ela põe a mesa)
And "tirar a mesa" (verb tirar: take off), which is "clean up" the table after lunch. (Ela tira a mesa)