Update documentation

[abought]

Purpose

The user facing documentation is severely out of date, and many API examples do not run as written. To support upcoming external pentesting (as well as, you know, everyday users), this contains a number of updates.

Preview: https://topmedimpute.readthedocs.io/en/fix-2023-doc-updates/getting-started/

Changes to docs

• Add FAQs for common user questions such as sample size, security questions, etc
  • Explicitly mention the new US Govt ATO
• Add more guidance for data preparation
• Aim all contact questions at helpdesk and update staff list
• Fix available API params and include missing options
  • Update API examples to run as written (both curl and python versions) + update example payloads to reflect current structure
• Hide information that does not apply to TIS
• Hide docker and "create reference panels" documentation, to reflect that TIS is a more focused service
• Remove reference panels not supported on TIS; replace with link to MIS docs
• Remove references to HLA imputation. It's pretty cool, but only present in MIS. Documenting it for our service is confusing.
• Add readthedocs config files (mandatory as of Sept 2023)
  • Fix mkdocs syntax to reflect feature changes/ drift.

Other notes

I have reinstalled a missing RTD webhook that has prevented new doc builds from being published for 2 yr. Once this PR is approved, we should also update the branch that RTD uses for the public docs --> release. (the previous branch no longer exists)

Future additions

• Some jobs fail due to a missing GT field, but this error is shown only in admin logs (users don't receive an error message). Perhaps the "data preparation" section can clarify what fields are required?
• Is this section relevant for TOPMed imputation? Should it be edited? Or removed? https://topmedimpute.readthedocs.io/en/fix-2023-doc-updates/prepare-your-data/#quality-control-for-hrc-1000g-and-caapa-imputation

[abought]

Reminder to self: Albert (may??) have edits in flight on this branch.

Once the branch is stable, we should update our user instructions link to point to the TIS documentation. Presently the UI is sending people to the wrong place.
https://github.com/statgen/imputationserver/blob/release/files/minimac4.yaml#L5

[abought]

Added Jonathon's notes about GT field, since we've seen the error in the wild.

It's been two months since this PR was first created. Pinging for status: ok to merge and make additions later?

Signoff: build error is a known issue with an upstream vendor that removed access to dependencies. This PR only edits text files, so it doesn't break mergeability for this PR.

(honestly, it only ran CI because I forgot to add [ci skip] in the commit message)