Function refresh_index_for_changes_from_source_controlled 

fn refresh_index_for_changes_from_source_controlled(
    store: &mut AtlasStore,
    plan: &ScanRuntimePlan,
    changes: &WatchChangeSet,
    symbol_options: &SymbolBuildOptions,
    captured: Option<CapturedSourceState>,
    control: &IndexWorkControl,
) -> Result<IndexRefreshReport, CliError>

Consume optional exact discovery instead of inspecting affected paths again.