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.

scripts/batch_process_multi_rings.py

@@ -2,9 +2,8 @@ from __future__ import annotations
 
 import sys
 
-from macro_lactone_toolkit.cli import main
+from scripts.batch_process import main
 
 
 if __name__ == "__main__":
-    sys.argv = ["macro-lactone-toolkit", "fragment", *sys.argv[1:]]
-    main()
+    main(sys.argv[1:])