bin/setup in payaus is idempotent and does the whole install side (Homebrew, Xcode CLT, Brewfile, mise, Ruby, Node, Yarn). The only thing it won't do is rip rbenv and nvm out of your shell. Both of those prepend shims to PATH after .zshrc runs, so if they stay, which ruby / which node keeps resolving to rbenv / nvm even with mise activated. Corepack shims in nvm's node bin dir shadow mise's yarn too. So: unwind first, then run bin/setup.
Open ~/.zshrc and delete any lines like:
export PATH="$HOME/.rbenv/bin:$PATH"