The issue I'm observing might be by design but I don't think the default behavior is ideal. We use Maven for our builds, including use of the Maven Android plugin to build our APK modules. When importing our projects we prefer to separate the directory location for IDEA module files from the content root. The Android Maven plugin looks in the project base directory for the gen, res, assets and libs directories. It's also where the AndroidManifest file is located. When separating module files from the module's content root IDEA sets up the Android facet to point at the module file directory instead of the module's content root. It doesn't affect the Maven build but it does impact using the native features of IDEA to build or manage the project without changing the facet configuration to point at the content root instead of the module file location.