How do the Doctor and his Companions take care of their basic biological needs while they’re traveling in the TARDIS? It’s a question perhaps less pressing when considering Clara than most others, as she seems to spend little time at all there. We’ve seen her changing clothes after an adventure, but on-screen evidence suggests (to me, at least) that she rarely, if ever, so much as spends one night aboard.
Even as recently as Rory and Amy, though—another pair who treated their time on the TARDIS more like a commuter than a residential lifestyle—it was clear that long stretches of time passed between their visits home. Historically, Companions lived in the TARDIS more like a dormitory or a commune, presumably spending their time between adventures in its halls.
So where do they sleep? Eat? Relieve themselves?
I suppose one obvious answer is that they stop off at various planets (or space stations, or whatever) to get supplies, have a picnic, or find a place to crash. (After all, Rose and Nine talked in The Empty Child about needing to stop for milk: “All the species in all the universe, and it has to come out of a cow,” he quips.) It makes a certain amount of sense that part of exploring the universe is exploring various species’ cuisines, for example.
I don’t think that’s how it works, though. We saw early on (in The Daleks, the second-ever story to be broadcast) that the TARDIS was equipped with a food machine that could produce (rather unappetizing looking) blocks of nutritional matter, programmed to taste like whatever one liked. Although it barely ever showed up again, that seeded the idea that the crew had everything they needed without ever leaving the ship.