What is the right way to maintain a “version for the server” – with only config files changed, in Git?

I sometimes work with Codeigniter, and after I’m done developing on the local site, I need to migrate the files to the server. All the files in the /config/ folder need to be changed to match the Server settings. It’s not right to make an entire commit for these changes, do I simply make Git ignore these files altogether, or is there a way to track these changes and apply them with Git at the right moment?