@harkanwar1313 , I don't know what your config file looks like, but the conflict isn't with your *.config (app if it's console app or web if it's a web app) referencing your .edmx file but that your DbContext is attempting to initialize a model using POCO classes. Check your DbContext.context.tt file. The .tt file is text transform file that generates the classes EF uses for your model. It's been a while since I've used it but somewhere in that file will determine how DbSet<T> or EntitySet<T> is getting generated inside the context.
However, the latest versions of Ef Core doesn't support edmx files. To address this issue, what I would suggest is migrating your edmx file to scaffolding a new DbContext into a code-first approach.