I did not know about GNU Stow. I want to try to use this for my dotfiles along with a simple Makefile to automate calling stow on all of the directories. This will also be a nice way to manage the differences between my home configuration and work configuration. One make rule per environment. Thanks for sharing.
edit: I use xstow for managing ~/opt -- putting stuff like ~/opt/xstow/golang-git, with symlinks to ~/opt/{bin,lib,man} -- making it easy to add the relevant folders to PATH, MANPATH etc in .bashrc.
