Deprecated biolink:ChemicalSubstance still used in custom_curies.yaml and merged graph

[turbomam]

biolink:ChemicalSubstance was renamed to biolink:ChemicalEntity in the BioLink v2 chemical refactor (May 2021). KG-Microbe has two remaining uses of the deprecated term:

1. Live bug in kg_microbe/transform_utils/custom_curies.yaml (line 14):

chemical_production: &chemical_production_block
  category: "biolink:ChemicalSubstance"  # deprecated
  predicate: "METPO:2000202"  # produces

Any new transform run will emit ChemicalSubstance for chemical production outputs.

2. ~224k stale nodes in data/merged/merged-kg_nodes.tsv

Nodes sourced from ChEBI and BacDive carry biolink:ChemicalSubstance either alone or alongside biolink:ChemicalEntity. Example: CHEBI:30769 (Citric acid) has category biolink:ChemicalEntity|biolink:ChemicalSubstance.

Note: ontology_utils.py already has a replace_deprecated_categories() function mapping ChemicalSubstance → SmallMolecule, but it is not applied to the custom-curies path.

Before fixing, worth confirming the right replacement category for chemical production outputs — SmallMolecule may not always be appropriate for complex metabolites or mixtures.