I have a website in Sharepoint 2007. We use a wsp to deploy our projects. We can deploy dlls, usercontrols, features, but i don\'t know how to include new lines in the web.c
I think direct web.config manipulation can get tricky when you have multiple servers. If your entire installation is only on a few servers, it just might be easier doing that than trying to make simple web.config changes via code.
Plus, manipulating the web.config directly ensures you have a complete web.config in your source control system. If you use the API to make changes, all you'll have in source control is a bunch of C# code that you hope are bug free!