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Opening this as a PR, and removing the link to the fish shell completions gist (the link was broken anyways after I renamed my account). If you don't want the completions merged, I can remove the completions script and just update the docs for the correct link.
The fish shell completions now respect SD_ROOT and should work fine. I've used this daily since I wrote it 1.5 years ago, and have never needed to fix anything. Note that this also works for completing the special commands
cat edit help new which
, which the zsh completions don't handle.I will update home-manager, and the docs for that, myself if you want to merge this.