If you want to change some of your configuration settings, for example to use MySQL rather than SQLite, we strongly recommend you make those modifications in the local_jaxer folder. When you use Jaxer within Aptana Studio, or when you use the standalone Jaxer Package, a folder called local_jaxer is created for you automatically, as a peer of your jaxer folder. It already contains templates for files you can use to override Jaxer's default settings. When you upgrade Jaxer you'll get a new version of the jaxer folder, but your local_jaxer folder will be preserved, and its settings will override those in the jaxer folder.