Using GNU Stow to manage your dotfiles
> but many/most dotfiles reside at the top-level of your home directory, where it wouldn't be a good idea to initialize a VCS repository.Right. Which is why I use git with a workspace detached from the git directory. The git directory is in ~/dotfiles/.git, with "git config core.worktree ~", and I set an alias "dgit=git --git-dir ~/dotfiles/.git". The advantage of this method is that there are no symlinks to maintain, however initial clone is a bit painful, since you have to move the files and set the config.It's not perfectly straightforward, but it's as close to it as I could get it.