Dotfiles in my home directory go in a repo that gets cloned and "installed" (I use a shell script that I wrote to make all the symlinks, but GNU Stow is probably better better). System level configuration and package installation is handled by ansible, with a certain amount of stuff controlled by conditional statements based on the distro and host name of the machine to allow arbitrarily local overrides.

All that said, if I was starting today I would strongly consider just putting everything into nix with home manager and carry that config around in a git repo that installed my packages and their configuration and encapsulated my entire environment.