A DESCRIPTION OF THE PROBLEM :
A java shebang script starts as a single class, and grows so that it would be reasonable to have multiple packages.
We need a single-file format that would be equivalent to a directory tree, and this format must be human-readable, human-writable, and human-editable.
Something like:

//==Foo.java
package com.foo;
public class Foo {
}
//==Bar.java
package com.foo.bar;
public class Bar {
}

(The full path is not needed because there is a package statement at the top of every source file)

(Note that the full path will be needed if you decide to extend this proposal with support of base64-encoded resource files.)