Java J2EE Application Conversion - Windows/MSSql to Linux/MySQL

Currently have a Java package that is a data router. The router conducts the following 3 steps. 1) Sweeper - Sweeps designated directories (stored in a db table) and stores those files from the sweep into the applications working directories, then log the files in the database table as being new and unprocessed. 2) Splitter - The second process splits the original file up in such a way that only one transaction exists per file, as the original file may contain many transactions to many different destinations. Stores those files from the split into the applications working directories, then log the files in a database table as being new and unprocessed. 3) Router - The third process reads the header of each file, determines the end destination and copies each file to it's approperate location. Project Scope: Convert application to read and write files on a Linux (Ubuntu 8.04) file system and read and log entires to and from a MySQL database.