Function run 

pub fn run<C: GroupingCache, A: ArtefactStore>(
    doc: &PlanDocument,
    backend: &dyn LlmBackend,
    cache: &C,
    artefacts: &A,
    fetch: &str,
    lang_fingerprint: &str,
    symbols_fingerprint: &str,
    progress: Option<&(dyn Fn(Progress) + Send + Sync)>,
) -> Result<PlanDocument, EngineError>

Run the grouping stage over a core-only document. Returns the same document with groups, reading_plan and the grouping audit fields filled, and "group" appended to generator.stages.