There are two stages to add information about numbering and cross-referencing of content, specifically, enumerateTargetsPlugin and resolveReferencesPlugin these can be run at different times depending on if you are in a single-document or multi-document setup.
The enumeration transforms require state, and can instantiate a ReferenceState object or a MultiPageReferenceState for collections with multiple pages. The reference resolution is defined in those classes. To create your own reference management, use the IReferenceState interface to pass in.
The enumerateTargetsPlugin should be run early, and registers targets with the state through state.addTarget. This will also tick forward all of the counting in the document (e.g. "Section 3.2.4" or "Figure 5"). The numbering can be configured with a numbering option in the ReferenceState, or your own implementation of counting.
The resolveReferencesPlugin has a number of transformations for (1) links, which identify document level links to other md files; (2) crossReference transforms which link references in the state and replace children with, for example, "Figure 1"; and (3) inserting caption numbers into containers.
