Separate code and config files

It would help a lot if the code and the config files appeared in different directories. In general, when I do an update of the code to the running environment, I do _not_ want the config files to be updated - which prevents me from running a git update in situ.
If I put them elsewhere, then I have two versions of the same file which is fraught with risk, and I have to have a script to copy files around.