well, I personally really like ipkg there.
it kindly asks you what to do, when a newer file is found, which should be overwritten. 😉
That makes sense for a packaging system but it would feel odd to me for “make install” to start asking questions.
Perhaps I’m missing the obvious having only just thought about this but how about
1. Copy the default configuration file to the correct directory but call it mt-daapd.conf.dist.
2. If mt-daapd.conf does not exist copy mt-daapd.conf.dist to mt-daapd.conf.
This means that if the user doesn’t have an existing configuration they will get something to start from. If they do then it won’t be overwritten but the latest configuration file will be conveniently available for reference.