Call her! It doesn't sound as though she is pining away for you, after all, so I doubt that a mere phone call or an invite out for a burger would send her into a tizzy of wedding fantasies. If the breakup was as friendly and mutual as it sounds, then I'm sure she'd love to catch up and see how you are, as well as fill you in on her college adventures. And as you said, you two were friends first. Just because you had a mistimed or ill-fated dalliance late in the friendship doesn't mean you should forego it entirely...

I think you should definitely call her, and I don't think you have to "make your intentions clear". It's casual, you two like each other, so you should enjoy each other's company...
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if you get the sense that she wants a relationship with you, and wants to sleep with you, then you should tell her how you really feel -- but if you just want to call her and hang out with her, I think to declare your intentions would only make things a bit awkward...