Materialize extraction reference files

internal/framework/pipeline/runner.go

@@ -41,6 +41,7 @@ type RunInput struct {
 	StartedAt   time.Time
 	LLMProfiles []artifacts.LLMProfileManifest
 	Metadata    map[string]any
+	Warnings    []contracts.Warning
 }
 
 type RunOutput struct {
@@ -63,6 +64,7 @@ func (r *Runner) Run(ctx context.Context, input RunInput) (RunOutput, error) {
 		return output, err
 	}
 
+	output.Warnings = append(output.Warnings, cloneWarnings(input.Warnings)...)
 	output.Manifest = manifestFromPipeline(input)
 
 	adapter, err := r.registries.Inputs.Build(input.Pipeline.Input.Module)
@@ -184,6 +186,7 @@ func (r *Runner) runLane(ctx context.Context, input RunInput, doc *source.Source
 		result, err := extractor.Extract(ctx, contracts.ExtractionRequest{
 			Source:     doc,
 			Chunk:      &chunk,
+			References: CloneReferenceSet(lane.ReferenceSet),
 			LLMClient:  input.LLMClient,
 			LLMProfile: lane.Extract.LLMProfile,
 			Options:    cloneOptions(lane.Extract.Options),
@@ -500,6 +503,13 @@ func cloneLLMProfiles(profiles []artifacts.LLMProfileManifest) []artifacts.LLMPr
 	return append([]artifacts.LLMProfileManifest(nil), profiles...)
 }
 
+func cloneWarnings(warnings []contracts.Warning) []contracts.Warning {
+	if len(warnings) == 0 {
+		return nil
+	}
+	return append([]contracts.Warning(nil), warnings...)
+}
+
 func timePtr(t time.Time) *time.Time {
 	return &t
 }