Hi Davide,
I'm very glad to hear that you like the idea of EMF Profiles and that you plan to use it for your research!
I've to admit that you are right -- the documentation is out of date very much :) However, I try to create a new documentation that is more up to date, unfortunately, I didn't manage to write up more that a documentation on how to create profiles so far. Here is the documentation for creating profiles:
I'll write up another article documenting how to apply profiles soon -- hopefully :)
In the meanwhile, I hope the following short description helps you to get started:
To apply a profile, you need to open the model to which you want to apply the profile, open the EMF Profile > Profile Application View and hit the green plus button in that view. Then, you may choose the file to which you want to save the profile application and select the profile to be applied. Once the profile application is displayed in the profile application view, you can right-click any element in the model to which you want to apply the profile and select "Apply Stereotype".
If you have any questions, don't hesitate to ask! In case, you don't know that paper yet, maybe this is also a help to you:
Good luck with your research!
Best wishes,
Philip