Implement auxiliary-qubit separation from arXiv:2603.24717 §4.3 - #117

Node.js 20 is deprecated. The following actions target Node.js 20 but are being forced to run on Node.js 24: arduino/setup-protoc@v3. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/