I've created a project from an external model (Maven). For importing preferences, I checked the first option 'create temporary modules (re-import on project opening and synchronization'. After that, I added some Spring and Hibernate facets, and "all was well" (okay, it didn't work, but see my other bug reports (about Hibernate mappings not detected) for that). After closing IntelliJ, and reopening the project, the facets were gone. I added them, I closed IntelliJ, reopend it, and they were gone again.
So my guess is that IntelliJ is not saving this modules when loading from an Pom. If this is intended, it seems a bit useless, so I'm guessing it's a bug.
Issue was resolved
Wouldn't it be sensible to use a combination of the poms and local project/module files. So that when the pom file is changed the project will pick the external change up but intellij project setting changes are still kept.
As a temporary workaround you can use 'create regular modules' import option.
Maven support is configured to create regular modules files. It seems to me that these settings should be saved in the imls that are generated. Upon synchronization, IDEA could merge the iml with any new data gleaned from pom changes.
we are working on this problem right now.