Flatten `myst.yml`

[rowanc1]

Right now we have a few high level keys in the myst.yml including project/site/version/extends. It is confusing to users where to put the keys (mostly always under project). Additionally, when writing a shared configuration, for example, abbreviations, authors, etc. that requires you to write it under the project key.

Instead, I suggest that we lean into the single project, and flatten all keys that are in the project. Moving from:

version: 1
project:
  open_access: true
  license:
    content: Apache-2.0
    code: CC-BY-4.0
  references:
    foundations: https://projectpythia-mystmd.github.io/pythia-foundations
site:
  template: book-theme

to

version: 1
open_access: true
license:
  content: Apache-2.0
  code: CC-BY-4.0
references:
  foundations: https://projectpythia-mystmd.github.io/pythia-foundations
site:
  template: book-theme

There are still potentially some site options to configure, but they will be obviously related to the theme (nav links, footer, etc.).

@jmunroe

[fwkoch]

Some additional thoughts around simplifying/flattening the myst.yml:

• Many of the project fields are also allowed on site, but it's ambiguous why they would be defined in one place or the other. Almost exclusively, they are only needed on project. I think we should move all "SiteFrontmatter" (https://github.com/executablebooks/mystmd/blob/main/packages/myst-frontmatter/src/site/types.ts#L58) to "ProjectFrontmatter" and remove them from the site config
• With the above change, site will have way fewer fields; this means we can remove the site.options key and just define those options directly on the site.

[rowanc1]

Thanks @fwkoch -- I am a big fan of these changes and think it would make the onboarding simpler, and the code a lot simpler to reason about. This also is closer to mimic-ing how the exports options work, which is helpful.