Thanks everyone for your responses. They were very helpful.
I didn't have to confront him about anything. He could tell I had something on my mind last night and he said, "Don't worry, I'm going to replace them." Apparently he was planning to buy some from a friend and put them back in my bottle. It's unclear whether he was going to tell me that he replaced my prescription pills with ones he bought on the street.
He acted like it was no big deal and said he thought I was done with the pills since my shoulder was feeling a lot better.
He begged me not to be mad at him and said he was sorry and I told him I wasn't sure how to feel about it all. I told him I wanted to be supportive of his personal situation that he's going through but I don't think I can if he's taking pills.
He said he was going to stop completely and that he was glad I was talking to him about it now before it went too far. He said he didn't want to fall back into that again and that I was a good influence in his life.
I accepted that from him. Maybe this is just a line I'm falling for. I don't know. I've already noticed a change in him. He's very moody this morning and I guess it's because he's not taking any pills. He's definitely a lot more pleasant to be around when he's taking them. I don't know what to feel about that right now.
About him moving in with me - it was just a temporary thing until he finds his own place. We live in a place where housing is extremely limited and a lot of people move in together for practical/housing shortage reasons. I'd never let a guy move in with me that soon under normal circumstances. If he can find his own place then I will encourage him to get it.
I realize I haven't known this person very long and that I'm getting involved in a lot of stuff I don't need to be involved in. I guess I will see how things go over the next couple of weeks and whether he's really going to stop taking pills and whether he's capable of being respectful and kind when he's not taking them.