[Refactor] Move Model.prototype.method into Document.prototype.method

We currently have functions defined on `Model.prototype` which can be confusing to people looking at the docs, expecting a specific function to be on the `Document` section.

AFAICT there is virtually no benefit to defining methods on `Model.prototype` since `Model` returns a `Document` instance, we should define only statics on `Model`, and leave prototype methods to `Document`.

Am I missing something here? Let me know if those changes sound reasonable, and I'll put in a PR.

The issue names Model.prototype and Document.prototype as the main entry points; inspect where their methods are defined and how the API documentation presents them. Determine which prototype methods should move while keeping statics on Model, then verify the existing tests and documentation checks; done means document methods live on Document and Model exposes only statics.

Written by the indexing model from the issue text.