> The trouble is that symlinks cut both ways. Every edit on every machine writes straight through the link into that machine’s clone of the repo

I have stow too in my micro DE, use it across a few machines and it's holding up really well. I designed my dotfiles so that changes would happens exclusively to files not tracked by stow. I have .zshrc tracked, but environment goes to .zshenv and general local customisation goes to .local/lib/zsh/overrides.zsh (https://gitlab.com/gabriel.chamon/archie/-/blob/main/deploym...). Hyprland config is tracked but device specific configs live in .config/hype/config/device.conf (https://gitlab.com/gabriel.chamon/archie/-/blob/main/deploym...). Deployment instructions/automation is to just copy dist folders in place, which aren't tracked by stow.

It depends on everyone's style. For me personally changes I don't remember having made to files I track in the repo are symptoms that I might need to review how I organize my files. Maybe those changes were something that broke and I forgot to commit after fixing. In any case for me this bidirectional nature of symlinks are a feature, not a bug in this management system.