The test applet (which produced most of the performance measurements on the OV-chip progress page, and a test frame for our Bignat library for big integers on Java Card are not affected by patent issues. They can always be build and run.
If you really want to compile everything you can apply this patch. The patch will give you syntactically correct Java code, but the missing method bodies will still be missing. Therefore some of the applets and programs won't run correctly.
For Windows users a zip file containing generated and preprocessed sources is provided as ov-chip-2-2010-09-20.zip, see file README.WINDOWS.
The hacker guide contains already a lot of information, but it currently is still very incomplete.