Generate dependency list as CSV + update secondary deps if needed

[infotroph]

Fixes #3250 by checking each newly-upgraded dependency for updates needed in its own dependencies to satisfy the declared requirements.

But also, does a larger rearrangement of generate_dependencies.R and pecan.depend.R to let us autogenerate simple dependency lists rather than splat out an entire R script:

• scripts/generate_dependencies.R now writes all parsed dependencies to docker/depends/pecan_package_dependencies.csv, and the list of GitHub remotes to docker/depends/pecan_deps_from_github.txt, and no longer touches pecan.depends.R.
• writing of Makefile.depends works as before with no changes in this PR.
• docker/depends/pecan.depends.R is now a static script that does not change when the dependency list does -- it now reads its deps from pecan_package_dependencies.csv.

Review Time Estimate

• [ ] Immediately
• [x] Within one week
• [ ] When possible

Types of changes

• [x] Bug fix (non-breaking change which fixes an issue)
• [ ] New feature (non-breaking change which adds functionality)
• [ ] Breaking change (fix or feature that would cause existing functionality to change)

Checklist:

• [ ] My change requires a change to the documentation.
• [ ] My name is in the list of CITATION.cff
• [ ] I have updated the CHANGELOG.md.
• [ ] I have updated the documentation accordingly.
• [ ] I have read the CONTRIBUTING document.
• [ ] I have added tests to cover my changes.
• [ ] All new and existing tests passed.