Bug-fixes and performance improvements for short-read Giraffe's supplementary identification algorithm - #5002

Node.js 20 is deprecated. The following actions target Node.js 20 but are being forced to run on Node.js 24: actions/cache@v4, actions/checkout@v2, actions/setup-node@v3. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/