Complete Documention

@alexprescott_email.arizona.edu Here are a few tasks for completing the documentation. If you have others, consider adding them to the list and don't hesitate to assign any to @nfoks1 or @rmcd

- [ ] incorporate the 1000K particle run into the scaling results - after looking at this closer, I don't believe it's possible to incorporate them

• Use the index.rst file to lead the user through the documentation.
• @rmcd add example workflow of data prep from iRIC software and/or discuss how to get output from other models into required format.
• Fix image links in Readme to be URLs -- using a relative link won't work because ReadTheDocs uses ~/docs as the root, while the Gitlab landing page uses ~.
• Fix the API Reference autodoc
• Fix the API docstrings formatting errors (e.g. in LarvalParticles)