The biggest design mistake I made with Amfora, my first community open source project, was autogenerating config files. On startup, the application looks for a config file, and creates one if it doesn’t exist, full of all the application defaults. At the time, I thought this was great, as it documents all the existing options, and makes them very visible to the user in case they want to change them. In the end, this decision created a lot of headaches and is not something I’d ever do again.

makeworld is right! I had the same problem in Mycorrhiza but didn't suffer great consequences because the configuration design didn't change much.