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Sync Nix shell files with qmk_firmware 0.14.2
Apply changes from qmk/qmk_firmware#13316 (update QMK CLI to 1.0.0, update other Python dependencies). The change that moved `nix` to `util/nix` (qmk/qmk_firmware#14132) is skipped to make using tools like `niv` easier.
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