ci: fix the linter (no Python 3.9 on ubuntu-latest) and cut duplicate runs - #386

Node.js 20 is deprecated. The following actions target Node.js 20 but are being forced to run on Node.js 24: actions/checkout@v4, actions/setup-python@v5, peter-evans/create-pull-request@v6, stefanzweifel/git-auto-commit-action@v5. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/