chore(docs): check formatting of docs in ci and do initial formatting

[corneliusroemer]

TODO: still fails due to some ignore file thing

Closes #2419

• It works, it fails when it's not formatted:

• The biggest diff here is that we need to format to pass things

[fhennig]

I found this indent with 3 spaces a bit odd:

4. Send a POST request:
   - The API path to use is: `<Backend URL>/<organism>/submit`
   - Add your group ID to the query parameters: `?groupId=<group id>`

But I checked and it looks fine:

Probably it was done like that so it lines up with the text after "4. "

[fhennig]

@corneliusroemer you mentioned you have a lot of stuff to do, so I took the liberty to pick up your work here.

I have added the .gitignore file to the prettier check-format command to fix the issue you had initially.

I have also changed the formatting for md and mdx files to 2 space indent, as it's what we always use for YAML, so the YAML examples look right.

I hope that was fine!

[corneliusroemer]

Thanks @fhennig thanks for picking it up! I just have one comment re making format and check-format consistent. Feel free to approve (and merge if you like).

[fhennig]

yes good point about the formatting!

Since Chaoran created the issue initially, I'll let him also have a look at do the final approval.

@chaoran-chen

[chaoran-chen]

This looks great to me, thank you!