You should probably take a look at Jhipster ( http://jhipster.imtqy.com/ )
By the way, for my projects, I clearly prefer to separate client code from server code. The project-client directory for the JS code, next to the project-server directory with Java code.
The first has obviously a “standard Java file structure”.
For the first, JS has its own standards. Well, they are not very stable;), but still. Your JS source code may be half or more - your source, its place is probably not in a subdirectory of your Java project ...
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