Refactor docs table of contents

[bruno-f-cruz]

This pull request refactors the current docs by:

• Changing the toc structure to separate modules by page, attempting to improve readability
• Favor automodule instead of explicit calls to methods and classes for less future maintenance costs
• Adds guidelines for Metrics calculation
• Adds an example on how to cross reference modules/classes in the conceptual documentation (also see #24)
• Adds automatic generation of links to source code