I am searching for hierarchy standard for Java projects and only found this link:
http://java.sun.com/blueprints/code/projectconventions.html
I think that Ant, Maven, Gradle like SE, ME, EE must have silimar structure so it is not sufficient which project type you use...
Use maven structure (details):
my-app
|-- pom.xml
`-- src
|-- main
| `-- java
| `-- com
| `-- mycompany
| `-- app
| `-- App.java
`-- test
`-- java
`-- com
`-- mycompany
`-- app
`-- AppTest.java
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