feat(toolkit): add classification and migration

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.

pixi.toml

@@ -18,6 +18,7 @@ pytest = ">=8.3,<9"
 rdkit = ">=2025.9.1,<2026"
 pandas = ">=2.3.3,<3"
 numpy = ">=2.3.4,<3"
+matplotlib = ">=3.10,<4"
 
 [pypi-dependencies]
 macro_lactone_toolkit = { path = ".", editable = true }