We have nearly a perfect Maven structure, but we have an additional directory level at the top of several directory trees. So, instead of just src/main/java, it's somdir/src/main/java. That's enough to confuse Maven or the IDEs we've tried (Eclipse and Intellij). The IDE doesn't recognize this as a Maven project.
This issue is now solved. The trick for us was to just create multiple Maven modules within the IDE. Simple, but not intuitive considering the pre-defined archetypes do the work for you.