The -cofactors flag and dataset cofactors column accept LigandDefinition
specifiers ("FAD", "FAD[atom_id:N]", "FAD[contact_res_ids:A_T259,A_D246]").
Matched HET groups merge into the protein surface (proteinAtoms) and are
excluded from ligand listings; per-item resolution lets a dataset column
override the global Params.cofactors.
New: analyze cofactors subcommand (HETATM survey + specifier dry-run),
PyMOL teal-stick visualization (vis_highlight_cofactors), distant-cofactor
and chain-excluded WARN diagnostics, aa_mapping collision WARN (R19),
drop-in safety benchmark with byte-equality on a never-present specifier.
Documentation in documentation/cofactors.md (user-facing) and
documentation/dev/cofactors.md (engineering record with R1-R24 design choices
and post-merge audit fixes). Tests in CofactorHandlerTest,
CofactorIntegrationTest, CofactorPipelineTest, CofactorAnalyzeTest,
DataTableCsvTest plus a Log4jCapture test helper.
