Fix relative links in notebooks and documentation

[adrianjav]

Changes:

1. Fix all relative links in the notebooks to point to the documentation itself (and not the notebooks in the repo).
2. Remove the absolute links in index.md to relative links instead (mkdocs should address them properly).
3. The region graph notebook now has a table-of-content (indentation was wrong).
4. Add site_url to the configuration file of mkdocs.

I have tested them locally using mkdocs serve and everything works well in my machine.

Note: This will break the links on the notebooks themselves when seen from the repository/jupyter directly. (There are solutions exists to address this, but they are more involved.)