Fix CI

[gl-eb]

This is a draft PR to test possible fixes to the manybuild_linux jobs.

[gl-eb]

The ci workflow does not work on pull requests because GITHUB_REPO points to htseq/htseq but the PR branch is on a fork, e.g. gl-eb/htseq.
actions/checkout should take care of this, but v4 does not work because it depends on node20. Thus v3 should be the way to go. Currently the next issue are the file system paths for the build

[gl-eb]

Using the actions/checkout@v3 with path: htseq turns out to be a drop-in replacement for the previous cloning steps. All subsequent steps can remain the same.

[gl-eb]

Sorry to ping you gain @iosonofabio. The changes to CI in this PR should hopefully put an end to the failed checks seen in other PRs. Should you be happy with them and merge the PR, I can rebase #72 to include the changes.

Also sorry for the messy history of force pushing. The commit history is clean at least.

[iosonofabio]

Thanks for pinging. I'll review hopefully before EoW