Here are the main JEphem directories :
Main directories

JEphem/data/prefs contains '.prefs' and '.last' files.
The '.prefs' files are used to store preferences of the user, accessible via menu Settings.
The '.last' files are used to memorize the state of graphical components. This permits the user to find the component in the state is used last. This implies I/O, but is (will be) threaded with low priority. So it doesn't slower the execution.
In general, preferences can be associated to a particular class. So the full JEphem package hierarchy is reproduced below data/prefs.

JEphem/data/astro contains data used by the program (java classes). For example, the files containing data for ELP82 or VSOP87. The sub-package hierarchy of jephem.astro is reproduced.

JEphem/data/lang contains the internationalized texts that are loaded to display GUI components.