Multiple installations on the same domain.

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We are facing a problem with multiple Concrete installations.
The main domain use to had a WordPress website and several folder with Concrete websites. Each of the folders contains standalone websites and they where working just fine.
To be more precise we had a website on mydomain.com and another website on mydomain.com/wesbite1 and another for mydomain.com/website2. I know the regular setup would be with sub domains, but they are started like this long time ago and want to keep that way.
Lately we also rebuilt the main website in Concrete and facing the following problem: If someone logs into the main website he is also logged in into the other websites too, installed in the folders. Is there a way to isolate this installations so there be no interference between the websites? I would like to keep the structure like I mentioned.
Sub domains could solve the issue, but this is not our scope.

Thanks.

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