docs(medcat): CU-869b2fcrc Update migration guide

[mart-r]

This PR makes a number of major changes to the migration guide:

• Fixes the links to working_with_cogstack for v2
  • I.e split between cogstack-es and medcat-scripts
  • As well as installation instructions
    • pip install for cogstack-es
    • python -m medcat download-scripts for the scripts
• Fixes links to v2-specific trainer
  • Just the one in this repo
• Add embed-linker to list of optional extras
• Fixes FAQ regarding a lot of the above
• Fixes installation instructions for cogstack-es
  • I.e quote the optional extras to avoid using these as options in regex (which would probably find nothing)
  • Somewhat unrelated, really. But I saw it while making these changes

[tomolopolis]

Task linked: CU-869b2fcrc Update migration guide