Function run_rules 

pub fn run_rules(
    rules: &[Rule],
    root: &Path,
    project_root: &Path,
    loader: &GrammarLoader,
    filter_rule: Option<&str>,
    filter_tag: Option<&str>,
    filter_ids: Option<&HashSet<String>>,
    debug: &DebugFlags,
    files: Option<&[PathBuf]>,
    path_filter: &PathFilter,
    walk_config: &WalkConfig,
) -> Vec<Finding>

Run rules against files in a directory. Optimized: combines all rules into single query per grammar for single-traversal matching.