Update PROTEUS documentation

[stuitje]

Feature description

PROTEUS needs a documentation update that:

• Implements Diataxis structure to current docs;
• Implements Zensical (instead of mkdocs);
• Adds some tutorials;
• Adds a code architecture flowchart;
• Adds a detailed API reference;
• Other things (comments welcome).

Related to Issue #421. I have decided to create one issue for this so that it can be tackled in one PR.

Relevant people

@nichollsh @timlichtenberg

[timlichtenberg]

While you're at it; could you please address these (installation instruction) suggestions? :-)
openjournals/joss-reviews#9917 (comment)

[stuitje]

While you're at it; could you please address these (installation instruction) suggestions? :-)
openjournals/joss-reviews#9917 (comment)

Yes, will do 👍

[stuitje]

PROTEUS has been updated with Zensical and a Diataxis structure since PR #654 . A tutorial, API reference and flowchart still needs to be added.