Knee issues?

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I've noticed my knees have become sensitive suddenly. I used to run and exercise regularly, and then took a long break because I was stressed out with school. Recently I have gotten back into working out with running and the elliptical, pilates ect. I don't think I'm over doing it, but I can't do these exercises that long because my knees feel crappy. They don't hurt persay, they just feel uncomfortable. I'm not sure if that may be diet related or if I just need to slow down even more, which is annoying but whatever. I also don't get much calcium anymore so I am hoping to bump that up somehow. I have some vitamins I need to start taking again, but as for food there is little that I actually like that has calcium. I usually got enough calcium in smoothies, but since it's winter I don't really like smoothies much, I used to have them for breakfast but it's just too cold imo so I don't. I'm not a huge fan of eating dark leafy greens otherwise unless mixed in a salad, but like I said, cold food in cold weather. Not a fan. I also couldn't eat any dairy even if I wanted because I realized a few months ago I am allergic.