Clean up a few things

[IAlibay]

Cleaning up a few instructions:

First page:

• [x] Getting started instructions needs fixing Main public
• [x] removing alternate ligand "conformational" or protonation states
• [x] hide a few toc entries
• [x] Phase 2: make the cleanup script clearer
• [x] Phase 2: compute requirements need fixing
• [x] Phase 2: data storage - increase header
  • [x] add warning
  • [x] mention the script