I also dissent from the majority here and have to say that the relationship isn't over, but you definitely cannot sit back and do nothing about this situation or it will be. The fact alone that she said she wishes you hadn't lived together tells me that she still loves the relationship you two had before and would like it to be that way again. Maybe that's something as simple as just not living together. On the other hand, maybe it's going to concern her that a relationship where living together brings her discomfort and awkwardness doesn't seem like it can move forward.
You've got to let her know how you feel and show that you really care about the state of your relationship. By that, I don't mean show you really care by buying her a gift or simply saying that you want to make this work. It sounds like she has been clear about what is bothering her and why. If there is something not clear then you need to ask. Once you know what's exactly the things that are bothering her, both in theory and in practice, you need to let her know that want to address her concerns and are willing to bend a little, change a little, to be the kind of boyfriend she deserves and you want to be (assuming this is true, of course). Don't let her off scott-free either though, she needs to know that her behavior is hurtful to you and that she needs to not imagine pressure where there is none. That is just another level of trust and she needs to be able to give you the benefit of the doubt that your motives are on the up-and-up otherwise what does that say about the kind of person she thinks she is with?
It seems to me that what has happened her is that by living together you have both learned a lot more about each other and, at least for her, enough of it didn't fit into the mold she created in her mind about you from dating that she is starting to reevaluate her image of the man she came to love. It's possible she already has and if that's the case then you will have a lot more work ahead of you to change that image to a good one again. In the end, you need to show her that you either are 1) still the same guy you were before you moved in; this will be difficult because you will essentially be telling her that she is just wrong about her opinion which she has been forming over some time or 2) that you truly want to be that person she wants you to be to have a successful and growing relationship AND that you are committed to doing so. But one last word of advice on this, make sure you do not lie are exaggerate your commitment. If the things she wants from you are just not things you are willing to give then let her know and talk through how important it is to both of you and why. Maybe you both just want different things for yourselves and each other now and if that's the case you are both going to have to be willing to compromise to get there together or else you both ought to split so you can get there on your own.
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"The courts that first rode the warhorse of virtual representation into battle on the res judicata front invested their steed with near-magical properties." ~27 F.3d 751
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