Function detect_deviations 

pub fn detect_deviations(
    rules: &[Rule],
    files: &ExtractedFiles,
    threshold_override: Option<f64>,
) -> Result<Vec<Deviation>, PipelineError>

Run the deviation pipeline.

threshold_override (e.g. --threshold from CLI) wins over each rule’s threshold, which wins over the built-in default of 0.7.