Among the features omitted from this manual are the Java language bindings for the Adevs simulator. Build instructions for the Java bindings are given in the ``Build and Install" section. How these bindings are used will (I hope) be obvious once you have perused the C++ interface: the interfaces for building models and running simulations with Java are essentially the same as with C++.
The Java bindings have three limitations. First, you pay a (usually unnoticeable) cost in execution time for the extra work that Adevs must to do manage memory associated with input and output objects and models that are orphaned during a change of structure. Second, the facilities for combined simulation of discrete event and continuous models are not implemented for Java. Third, this is not a `pure Java' simulation engine: it uses a great deal of native code to do its work (though this is invisible to the programmer).
There are at least two positive aspects of the Java bindings. The first is it omits the need for explicitly managing memory. The Java garbage collector (plus some extra work by the simulation engine) takes care of this for you. Second, you have access to the nice features and standard libraries of the Java programming language.
Other topics not included in this manual are theory (why the simulator is built as it is) and some experimental features of the simulation engine. Among the latter are support for simulating hybrid differential-algebraic systems and conservative, parallel simulation using multicore processors. If you are interested in any of these subjects, I offer the following (greatly abridged) list of books and articles: