All of you java source should go at src/main/java. All of your resource files should go in src/main/resources. When the build runs, during the process-resources phase the resource are copied to target/classes. Similarly, during the compile phase, the Java source are compiled into target/classes. Then during the package phase, all of the files in target/classes (both resource files and class files) are packaged into a JAR file. This standard Maven practice and you should not try to subvert that (unless you like causing yourself much grief and anguish.)
If you are trying to use the assembly plugin to create the JAR file, you are doing it wrong. The assembly plugin is meant to create an installation or distribution package of your product, it is not meant to build the artifact (JAR file) for the project.