Expose chunk plan provenance and safe diagnostics

internal/framework/pipeline/runner.go

@@ -63,6 +63,7 @@ type RunInput struct {
 
 type RunOutput struct {
 	Manifest         artifacts.RunManifest        `json:"manifest"`
+	ChunkPlan        *artifacts.ChunkPlanSummary  `json:"chunk_plan,omitempty"`
 	NormalizeOutputs []contracts.SerializedOutput `json:"normalize_outputs,omitempty"`
 	Rejected         []contracts.RejectedOutput   `json:"rejected,omitempty"`
 	Warnings         []contracts.Warning          `json:"warnings,omitempty"`
@@ -81,6 +82,11 @@ func (r *Runner) Run(ctx context.Context, input RunInput) (output RunOutput, err
 	input.llmClient = input.Prepared.dependencies.LLM
 
 	output.Manifest = manifestFromPipeline(input)
+	output.ChunkPlan = &artifacts.ChunkPlanSummary{
+		Mode: string(effectiveChunkCacheMode(input.ChunkCacheMode)), RequestedModule: input.pipeline.Chunk.Module,
+		LookupStatus: "skipped", LookupReason: "chunk plan lookup skipped",
+		ValidationStatus: "not_run", PublicationStatus: "not_requested",
+	}
 	checkpoints := input.Checkpoints
 	if checkpoints == nil {
 		checkpoints = NoopCheckpointRecorder()
@@ -193,6 +199,7 @@ func (r *Runner) Run(ctx context.Context, input RunInput) (output RunOutput, err
 		return failOutput(output), fmt.Errorf("write chunk debug artifact: %w", err)
 	}
 	chunkResult, err := r.runChunkPlan(ctx, input, doc, sourceInput, sessionID)
+	applyChunkPlanExecution(&output, chunkResult)
 	if err != nil {
 		return failOutput(output), err
 	}
@@ -481,10 +488,14 @@ func manifestFromPipeline(input RunInput) artifacts.RunManifest {
 
 	pipeline := input.pipeline
 	manifest := artifacts.RunManifest{
-		PipelineID:      pipeline.ID,
-		PipelineDigest:  pipeline.Digest,
-		InputModule:     pipeline.Input.Module,
-		Chunker:         pipeline.Chunk.Module,
+		PipelineID:     pipeline.ID,
+		PipelineDigest: pipeline.Digest,
+		InputModule:    pipeline.Input.Module,
+		Chunker:        pipeline.Chunk.Module,
+		ChunkPlan: &artifacts.ChunkPlanManifest{
+			Mode:            string(effectiveChunkCacheMode(input.ChunkCacheMode)),
+			RequestedModule: pipeline.Chunk.Module,
+		},
 		OutputEncoder:   pipeline.Output.Module,
 		ArtifactLanes:   make([]artifacts.ArtifactLaneManifest, 0, len(pipeline.ArtifactLanes)),
 		ValidatorChains: validatorChainManifests(pipeline.ValidatorChains),
@@ -673,11 +684,38 @@ func cloneMetadata(metadata map[string]any) map[string]any {
 	}
 	out := make(map[string]any, len(metadata))
 	for key, value := range metadata {
-		out[key] = value
+		out[key] = cloneMetadataValue(value)
 	}
 	return out
 }
 
+func cloneMetadataValue(value any) any {
+	switch typed := value.(type) {
+	case map[string]any:
+		return cloneMetadata(typed)
+	case []any:
+		out := make([]any, len(typed))
+		for i := range typed {
+			out[i] = cloneMetadataValue(typed[i])
+		}
+		return out
+	case json.RawMessage:
+		return append(json.RawMessage(nil), typed...)
+	case []byte:
+		return append([]byte(nil), typed...)
+	case []string:
+		return append([]string(nil), typed...)
+	case map[string]string:
+		out := make(map[string]string, len(typed))
+		for key, item := range typed {
+			out[key] = item
+		}
+		return out
+	default:
+		return value
+	}
+}
+
 func cloneLLMProfiles(profiles []artifacts.LLMProfileManifest) []artifacts.LLMProfileManifest {
 	if len(profiles) == 0 {
 		return nil