speculate that the issue is that with do_java=1 we compile the java sources in two places, in the Makefile and in the t4ht system calls.
Well, you created the Makefile invocations. Change it as you like. I certainly agree it is wrong to compile things in two places. If it's too much work to rip out the compilations from the *.tex files (nothing I'm ever going to tackle), then maybe the Makefile compilations should be deleted. Whatever you wish. As make can run several processes in parallel this may create some Our Makefile is not set up to consider make -j anything. Just stick to serial make run please. Another thing is that in general make is not so good for java, because the same file.java can generate several file*.class files, That is not a problem in principle. A given source file can be specified to generate multiple outputs. foo.class bar.class: foo.java javac ... delegating java compilation to ant would be preferable. Definitely not. -k