STOW is great, it is simple and works well especially combined with git. That's what I do [0], and recently combined it with org-mode for literate programming, so each program has just a README.org that then generates all the files via org tangle [1] [2]. For example, here is my file that generates my Xorg configuration [3] over several files, nicely readable on GitHub, in Emacs, or just as plain text.
[0] https://github.com/podiki/dot.me/
[1] https://web.archive.org/web/20190924102437/https://expoundit...
[2] https://orgmode.org/manual/Working-with-Source-Code.html
[3] https://github.com/podiki/dot.me/tree/master/x11