After you have installed ConfigZilla and started to use it to generate your config files you will want to stop Git (or TFS) from tracking the config files because they are now build products rather than source files. Furthermore, their contents will be changing every time you do a build because the current time is included in the document comment. So you should add web.config, app.config or whatever.config to your .gitignore file.
[Aa]pp.config
[Aa]ppSettings.config
[Cc]onnectionStrings.config
[Ll]og4net.config
[Rr]eportingSettings.config
[Ss]omething.config
# Care! MVC has nested web.configs int its views folder.
# Only ignore the one in the root
/MyWebApp/[Ww]eb.config
Care needed! As the comment in the file shows, there can be web.configs in folders other than the root. If you aren't generating them from templates then you should continue to track them. Web applications are the only ones I know of where this happens : a newly created MVC 4 app has a Web.config under its Views folder and the application won't run without it. After setting up your .gitignore it is a good idea to commit everything and clone your repo to a new location and check that everything is still working.
If your config files have already gotten into your git repository then you will need to add them .gitignore as above and stop tracking them. Issue the following command:
git rm --cached <filename>