6 Configuration Files
GeoServer configuration is currently persisted in a number of xml based files. Early versions of GeoServer were configured entirely by editing the files, but as of 1.2 there is also the web administration tool, which we highly recommend, as it makes configuration much quicker. However, there are times when you will need to work directly with the xml files themselves. If things are not working exactly right through the web admin tool then the files can be quite useful. And many times the latest configuration options will only be available through the files, as it often takes time to implement the changes in STRUTS. One thing to note, if working with files and through the web administration interface the files will often times get mangled. No data should be lost, but comments and formatting can not be persisted. If those things are important then GeoServer should only be configured through the files.
See also the user docs on 2.5 GeoServer Data Directory