Dependency fixes
List of changes:
- Update all dependencies in line with the "Debian stable/Ubuntu LTS from 6 months ago".
- Remove legacy code that was there fore backwards compatibility
- Fix a lot of deprecation warnings due to changes in python/scipy/numpy/mpl
- Update all links to use https, resolve several permanent redirects, update or remove a few broken links
- Remove unmaintained macports/homebrew installation instructions
Still TODO: squash/regroup commits.
Closes #386 (closed)