Replace dummy covariate and negative-control placeholders in `06_cm_spec.R`

[rkboyce]

Title
Replace dummy covariate and negative-control concept-set placeholders in cohort-method generation

Body

Problem

06_cm_spec.R still relies on placeholder handling for covariate and negative-control concept sets instead of real backed selections.

The generated script can therefore leave:

• includedCovariateConceptIds empty
• excludedCovariateConceptIds empty
• negative control inputs effectively unbound

Current behavior

The generator is compatible with HADES version skew, but the concept-set plumbing for covariates and negative controls is still placeholder-level rather than real workflow-backed selection.

Risk

• errorOnHighCorrelation = TRUE can fail without a meaningful exclusion path
• users may think concept-set-driven covariate selection is active when it is not
• generated cohort-method specs may be structurally valid but analytically incomplete

Requested change

Implement real handling for covariate and negative-control concept-set inputs in cohort-method generation.

Acceptance criteria

• covariate concept-set ids can be sourced from real workflow artifacts rather than dummy placeholders
• negative-control concept-set inputs are backed by actual selected/generated artifacts
• generated 06_cm_spec.R reflects real ids when present
• failure modes are explicit when required concept-set inputs are missing
• regression tests cover populated and unpopulated concept-set cases