Anything to do with modules and prefs is currently under EXPERIMENTAL_MODULE_PREFS and turned off.
We never load 'out of date' modules (but do allow modules to interrogate the current prefs and 'pretend' they are that version. The 'Aurora' plug-ins do that).
If a module is 'out of date' we provide the name in a user-facing message and actual location in the log, just in case the user has a number of versions in different places (untested).
We currently don't remember the users preference for loading each module, but could extend this. We would need an extra button in the ShowMultiDialog of ModuleManager::Initialize and then store the preferences in prefs. That would need a more sophisticated entry in prefs->Modules to enable a user to change their decisions.
Removing duplicate code from LoadModules, at the expense of making ModuleManager::Initialize more monolithic.
Make MultiDialog a bit more general.
Remove a few warnings.
Some logging has been turned back on when loading libs, we could turn it off again.
To test you could compile mod-nyq-bench and make sure it is available on the bottom of the 'View' menu, then unselect it in the Prefs -> Modules an retry.