By default, a model installer built using Repast’s Build Installer functionality will also include your raw source code (not just the bytecode). If you do not want your .java files to be bundled with the model installer, you can change this in the project’s installer/installation_components.xml file. Remove or comment out these lines from that file (near the bottom):
<pack name="Sources" required="no">
<description>The model source code</description>
<file src="repast.simphony.bin_and_src_$REPAST_VERSION/temp/src" targetdir="$INSTALL_PATH/yourModelName"/>
</pack>
After you create the new installer and install the model, the directories of the standalone model should no longer contain your source code. Those directories will only contain the .class files. (Of course, it’s still possible for the user to decompile the .class files back into .java files, but at least removing the raw .java files sends the signal and requires some actual work to get the code on any unscrupulous users’ parts. Use an obfuscator to avoid decompilation if you’re worried.)
Repast uses IzPack to build the software installer for its models. Inside your project’s /installer directory are the .xml and other files that IzPack uses.