refactor: refactor the analysis API.

[peterhuene]

This PR refactors the analysis API to assist in future engine work.

Primarily it exposes Task and Workflow from analyzed documents so that a task or workflow's inputs and outputs can be easily determined.

Additionally, this renames DocumentScope to simply Document to represent an analyzed document.

Scopes are now kept internally to a Task or Workflow, which allows for a scope method directly on those types.

As a result of the rename, scope.rs has been renamed to document.rs.

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