feat(toolkit): ship macro_lactone_toolkit package

Unify macrolactone detection, numbering, fragmentation, and
splicing under the installable macro_lactone_toolkit package.

- replace legacy src.* modules with the new package layout
- add analyze/number/fragment CLI entrypoints and pixi tasks
- migrate tests, README, and scripts to the new package API

tests/test_fragmentation.py

@@ -0,0 +1,53 @@
+from rdkit import Chem
+
+from macro_lactone_toolkit import MacrolactoneFragmenter
+
+from .helpers import build_macrolactone
+
+
+def test_fragmentation_returns_empty_list_without_sidechains():
+    built = build_macrolactone(12)
+    result = MacrolactoneFragmenter().fragment_molecule(built.smiles, parent_id="plain")
+
+    assert result.fragments == []
+
+
+def test_fragmentation_emits_labeled_and_plain_smiles_round_trip():
+    built = build_macrolactone(16, {5: "ethyl", 8: "methyl"})
+    result = MacrolactoneFragmenter().fragment_molecule(built.smiles, parent_id="mol_001")
+
+    assert result.parent_id == "mol_001"
+    assert result.ring_size == 16
+    assert {fragment.cleavage_position for fragment in result.fragments} == {5, 8}
+
+    for fragment in result.fragments:
+        labeled = Chem.MolFromSmiles(fragment.fragment_smiles_labeled)
+        plain = Chem.MolFromSmiles(fragment.fragment_smiles_plain)
+
+        assert labeled is not None
+        assert plain is not None
+        assert Chem.MolToSmiles(labeled, isomericSmiles=True)
+        assert Chem.MolToSmiles(plain, isomericSmiles=True)
+        assert any(
+            atom.GetAtomicNum() == 0 and atom.GetIsotope() == fragment.cleavage_position
+            for atom in labeled.GetAtoms()
+        )
+        assert any(
+            atom.GetAtomicNum() == 0 and atom.GetIsotope() == 0
+            for atom in plain.GetAtoms()
+        )
+
+
+def test_fragmentation_preserves_attachment_bond_type():
+    built = build_macrolactone(16, {6: "exocyclic_alkene"})
+    result = MacrolactoneFragmenter().fragment_molecule(built.smiles, parent_id="bond_type")
+
+    fragment = next(fragment for fragment in result.fragments if fragment.cleavage_position == 6)
+    labeled = Chem.MolFromSmiles(fragment.fragment_smiles_labeled)
+    plain = Chem.MolFromSmiles(fragment.fragment_smiles_plain)
+
+    for mol in (labeled, plain):
+        dummy_atom = next(atom for atom in mol.GetAtoms() if atom.GetAtomicNum() == 0)
+        neighbor = dummy_atom.GetNeighbors()[0]
+        bond = mol.GetBondBetweenAtoms(dummy_atom.GetIdx(), neighbor.GetIdx())
+        assert bond.GetBondType() == Chem.BondType.DOUBLE