Support multiple cohort-method comparisons instead of only the first one

Title
Support multi-comparison cohort-method generation from cm_comparisons.json

Body

Problem

The cohort-method generator currently materializes only the first comparison in cm_comparisons.json.

Current behavior

Even when multiple valid comparisons are present, only the first is propagated into the generated cohort-method artifacts and script.

Risk

• silent under-generation of intended analyses
• confusing mismatch between comparison-selection artifacts and final execution script
• users may assume all selected comparisons are included when only one is executed

Requested change

Update the cohort-method shell and generator to support multiple comparisons end-to-end.

Acceptance criteria

• all selected comparisons in cm_comparisons.json are considered during generation
• generated output can represent multiple cohort-method analyses
• script generation remains compatible with supported HADES versions
• output/state clearly identifies which comparisons were included
• regression tests cover one-comparison and multi-comparison cases

Start with the cohort-method shell and generator that consume cm_comparisons.json, then trace how selected comparisons reach generated artifacts and the execution script. Compare one-comparison and multi-comparison behavior, and use regression tests to verify all selected comparisons are represented, supported HADES script generation remains compatible, and output/state identifies included comparisons.