sudo cp /usr/lib/jvm/default-java/include/* /usr/local/include/
sudo cp /usr/lib/jvm/default-java/include/linux/* /usr/local/include/
This step is not necessary, since cmake can find them on its own by replacing the following line in CMakeLists.txt:
include_directories("${PROJECT_SOURCE_DIR}/srcs" "${ODE_ROOT_DIR}/include")
with:
find_package(Java)
include_directories("${PROJECT_SOURCE_DIR}/srcs" "${ODE_ROOT_DIR}/include" ${JAVA_INCLUDE_PATH} ${JAVA_INCLUDE_PATH2})
SIGServer is then able to be compiled directly.