The java directory contains only .js files that for whatever reason must be hand-crafted and used directly, not created at build time.
Most of the java files used by SwingJS come from the /j2s/java project directory and were created by the Java2Script project. Those that are here are replacements to those files to fix issues of one sort or another.
Note that all files in the jsjava package will be moved to j2s/java as well, as the build script will drop the "js" from all references to "jsjava".