You need to set it up in a runtime environment
The script has to include native using -Djava.library.path:
java -Djava.library.path %PATH_TO_NATIVES% -jar app.jar
The classpath in the jar manifest must include relative jar paths
Class-Path: lib/reflections-0.9.10.jar lib/other-library.jar
At runtime, it must look like this:

dir/

app.jar
run.bat or run.sh
lib/

reflections-0.9.10.jar
other-library.jar