Add stage-local reference config bindings

internal/core/config/file_config.go

@@ -99,6 +99,7 @@ type fileModuleBinding struct {
 	Module     string
 	LLMProfile string
 	Options    map[string]any
+	References map[string]string
 }
 
 func (b *fileModuleBinding) UnmarshalYAML(node *yaml.Node) error {
@@ -133,6 +134,12 @@ func (b *fileModuleBinding) UnmarshalYAML(node *yaml.Node) error {
 					return err
 				}
 				b.Options = normalizeOptions(options)
+			case "references":
+				var references map[string]string
+				if err := valueNode.Decode(&references); err != nil {
+					return err
+				}
+				b.References = references
 			default:
 				return fmt.Errorf("field %s not found in module binding", keyNode.Value)
 			}
@@ -148,6 +155,7 @@ func (b fileModuleBinding) toPipelineBinding() pipeline.ModuleBinding {
 		Module:     strings.TrimSpace(b.Module),
 		LLMProfile: strings.TrimSpace(b.LLMProfile),
 		Options:    cloneOptions(b.Options),
+		References: normalizedStringMap(b.References),
 	}
 }
 
@@ -217,6 +225,19 @@ func (c *Config) applyFileConfigWithLookup(fileCfg FileConfig, lookup func(strin
 		if _, _, err := normalizedMapKeys(filePipeline.References, fmt.Sprintf("pipeline %q reference slot", pipelineID)); err != nil {
 			return err
 		}
+		if filePipeline.Chunk != nil {
+			if _, _, err := normalizedMapKeys(filePipeline.Chunk.References, fmt.Sprintf("pipeline %q chunk reference slot", pipelineID)); err != nil {
+				return err
+			}
+		}
+		if _, _, err := normalizedMapKeys(filePipeline.Input.References, fmt.Sprintf("pipeline %q input reference slot", pipelineID)); err != nil {
+			return err
+		}
+		if filePipeline.Output != nil {
+			if _, _, err := normalizedMapKeys(filePipeline.Output.References, fmt.Sprintf("pipeline %q output reference slot", pipelineID)); err != nil {
+				return err
+			}
+		}
 		for rawLaneID, fileLane := range filePipeline.Artifacts {
 			laneID := strings.TrimSpace(rawLaneID)
 			if laneID == "" {
@@ -225,6 +246,24 @@ func (c *Config) applyFileConfigWithLookup(fileCfg FileConfig, lookup func(strin
 			if _, _, err := normalizedMapKeys(fileLane.References, fmt.Sprintf("pipeline %q lane %q reference slot", pipelineID, laneID)); err != nil {
 				return err
 			}
+			if _, _, err := normalizedMapKeys(fileLane.Extract.References, fmt.Sprintf("pipeline %q lane %q extract reference slot", pipelineID, laneID)); err != nil {
+				return err
+			}
+			if fileLane.Merge != nil {
+				if _, _, err := normalizedMapKeys(fileLane.Merge.References, fmt.Sprintf("pipeline %q lane %q merge reference slot", pipelineID, laneID)); err != nil {
+					return err
+				}
+			}
+			if fileLane.Normalize != nil {
+				if _, _, err := normalizedMapKeys(fileLane.Normalize.References, fmt.Sprintf("pipeline %q lane %q normalize reference slot", pipelineID, laneID)); err != nil {
+					return err
+				}
+			}
+			for i, validator := range fileLane.Validators {
+				if _, _, err := normalizedMapKeys(validator.References, fmt.Sprintf("pipeline %q lane %q validator[%d] reference slot", pipelineID, laneID, i)); err != nil {
+					return err
+				}
+			}
 		}
 	}
 
@@ -280,8 +319,10 @@ func (c *Config) applyFileConfigWithLookup(fileCfg FileConfig, lookup func(strin
 		}
 		for _, laneID := range laneIDs {
 			fileLane := filePipeline.Artifacts[rawLaneIDs[laneID]]
+			extract := fileLane.Extract.toPipelineBinding()
+			extract.References = mergeStringMaps(normalizedStringMap(fileLane.References), extract.References)
 			lane := pipeline.ArtifactLaneProfile{
-				Extract:    fileLane.Extract.toPipelineBinding(),
+				Extract:    extract,
 				References: normalizedStringMap(fileLane.References),
 			}
 			if fileLane.Merge != nil {
@@ -353,6 +394,20 @@ func normalizedStringMap(values map[string]string) map[string]string {
 	return out
 }
 
+func mergeStringMaps(base map[string]string, override map[string]string) map[string]string {
+	if len(base) == 0 && len(override) == 0 {
+		return nil
+	}
+	out := make(map[string]string, len(base)+len(override))
+	for key, value := range base {
+		out[key] = value
+	}
+	for key, value := range override {
+		out[key] = value
+	}
+	return out
+}
+
 func resolveAPIKeyEnv(envName string, lookup func(string) (string, bool)) (string, error) {
 	name := strings.TrimSpace(envName)
 	if name == "" {