Enzo,
You can use the Apache Commons Compress library.
Use the answer given here: https://stackoverflow.com/questions/4834721/java-read-bz2-file-and-uncompress-parse-on-the-fly/
The inputstreem needed as described in the answers' code can be obtained using the Core.getSystemFileDocumentContent() method.
The answer assumes that the zip contains txt files, so you might need other handling for your zipfile.