I use a similar construct for managing config files (mostly the stuff that goes to /etc/*): put all the config for a specific program (or problem) into a VCS-ha

I use a similar construct for managing config files (mostly the stuff that goes to /etc/*): put all the config for a specific program (or problem) into a VCS-handled directory, then add a Makefile with an "install" target that copies everything into its place. Using GNU install (instead of ln or cp) allows for copying files (and creating directories) with fine control about permissions and ownership. This can also be done recursively: toplevel Makefile for a machine's configuration files calls the sub-makefiles that install apache, asterisk, openvpn configurations etc.