My Java program references a lot of data files. I put them in a top level directory called data/, along with src/ and bin/. In Eclipse, references to data/ and ../data/ both s
I'd recommend you access the files in a classpath-relative way, whether in Eclipse or in a compiled JAR.
There are a few ways you might go about it, but a basic JDK-only approach would be to use Class's getResourceAsStream() method, giving you access to an InputStream object that you can read in.