It appears (again) Linux already has something I wanted.
I manage dotfiles in git and wrote a script that checks recursively if file exists at $HOME and creates a symlink.
Turns out, stow already solves this.
My dotfile repo layout looks like this where dotfiles are encapsulated in root/:
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Command to stimulate setup. Remove --simulate to apply.
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Stow solves another problem for me – the undo.
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