Maven integration has suddenly stopped managing dependencies for new maven projects created via the project import facility. For newly imported maven projects there are no dependencies listed in the maven tool window and all imports for classes provided by maven dependencies are broken. I have worked around this by manually adding dependencies for small projects, but that is obviously not feasible for large ones.
This problem started after having deleted all files in a project root directory from a terminal while IDEA was open. (That's a fairly standard flow for projects using GitHub pages where you effectively have two different branches with entirely different contents, and only one is a Java source project.) After this incident, all attempts to recreate the project, even from backups, will not restore maven dependency management features. Additionally, the ability to import new maven-based projects is similarly impaired.
Has anyone else seen this? Suggestions to fix? This feels like a bug, but I thought I would mention it in case there's some configuration knobs I can turn to fix.
I should note this is IntelliJ IDEA 12.1.6.