This program uses a rather complicated SQLite driver linking procedure with two phases. During editing and compilation, a driver JAR file is linked into the environment. For release, the same driver content is copied into the intermediate class-file directory as class files (because one JAR file cannot placed inside another, and a ZIP file delivery scheme is unworkable) for inclusion in the production JAR file, which is created by the install script.

So avoid disturbing the contents of the jdbc-libraries directory until you've refamiliarized yourself with its intricacies.
