Stage 2: run the cleaning pipeline

Usage

stage_clean(
  state,
  multi_analyte_resolutions = NULL,
  value_corrections = NULL,
  cleaning_steps = NULL
)

state: State list from stage_ingest().
multi_analyte_resolutions: Optional data frame/list with row_index (or row), action, and optional value/values columns. row_index is the original_row_id as written to pending.csv, so it stays valid after synonym or multi-analyte splits. Applied after cleaning and before curation.
value_corrections: Optional data frame with column, pattern, replacement, and optional match_mode columns. Applied to the detected data before cleaning, so before Unicode folding: match Unicode hyphens with \\p{Pd}, not -. See apply_value_corrections().
cleaning_steps: Optional named list of logicals switching cleaning steps on or off: unicode, whitespace, cas, names, synonyms, isotopes, multi, chiral, truncated, bare_formula, reference_flags. Omitted names keep their defaults.

The state with cleaning_result, merged_tags, and merged_chemical_tags added.