refactor: decompose Methods.java into focused utility classes - #90

Node.js 20 is deprecated. The following actions target Node.js 20 but are being forced to run on Node.js 24: ./setup-nextflow/subaction, actions/cache@v4, actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683, actions/checkout@v4, actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b, actions/setup-python@v4. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/