Just read Marek's blog post
http://grendello.blogspot.com/2007/12/runtime-mapping-of-aspnet-configuration.html
see the documentation here:
http://mono-project.com/ASP.NET_Settings_Mapping
I will be implementing the use of this new Mono feature so we don't have to make manual modifications to the config file for use on Mono.
If everyone puts there appSettings like connection string in user.config then there won;t be much need for touching Web.config when working with the code from svn.
Joe