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Transforms needed by most or all documents:
- `Decorations`: Generate a document's header & footer.
- `Messages`: Placement of system messages stored in
`nodes.document.transform_messages`.
- `TestMessages`: Like `Messages`, used on test runs.
- `FinalReferences`: Resolve remaining references.
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Place any system messages generated after parsing into a dedicated section
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Append all post-parse system messages to the end of the document.
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Remove comment elements from the document tree (only if the
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