New Maven Resource Compiler
IntelliJ IDEA now uses a special compiler to process Maven resources as specified in the pom file, with includes/excludes and filters.
Resource folders are not set as Source Folders anymore because they do not fit in the IntelliJ IDEA model.
To use the new functionality please either manually reset all your resource folders in the Project Structure dialog or re-import the project from scratch. Although you may skip this step, the native IntelliJ IDEA compiler will interfere with the Maven Compiler and copy unnecessary files or rewrite already processed ones from these folders.