Add a public numbering module and route fragmenting, validation,
and scaffold preparation through the canonical numbering entry.
Rewrite the repository entry docs around the fixed numbering
contract, add MkDocs landing pages, and document the mirror
mapping used for medicinal-chemistry comparisons.
Also refresh the validation analysis reports to explain the
canonical-versus-mirrored numbering relationship.
Implement the standard/non-standard/not-macrolactone classification layer
and integrate it into analyzer, fragmenter, and CLI outputs.
Port the remaining legacy package capabilities into new visualization and
workflow modules, restore batch/statistics/SDF scripts on top of the flat
CSV workflow, and update active docs to the new package API.
