I see in the new version of XOOPS the pm is now a module, is this the same for notifications.

what happens to:

View Account
Edit Account
Notifications
Logout
Inbox

Does this mean we have to say bye to the user menu, this is one thing my users love, but now the profiles and pm will get all mixed up with the main menu and other modules installed.

why was the profile and pm not kept part of the core?

Even though the profiles and PM are moved to modules, they will still be linked to the user menu.

The reason for the separation was to make it easier to add features, and eventually there will probably be a choice of profile and pm modules with different features to choose from.

But through the API it will be mapped to the user menu as before. The links created in the main menu can be hidden by giving the modules a weight of "0" in the modules administration page.

HTH.