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)