Unfortunately it is not possible to define a table as join table and to execute queries directly to the table. If you want to execute queries to the JoinTable you should define the association as 1:m:1 and map the JoinTable to a class.
You can easily get the ids of all entities in one relation from many to many association:
Page page = context.Pages.FirstOrDefault();
> tagsId = page.Tags.Select(c => c.Id);
I hope that helps. If any questions arise do not hesitate to contact us again.
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