Add version two LLM reports and safe execution diagnostics

internal/core/diagnostics/run_dir.go

@@ -54,6 +54,7 @@ type InvocationMetadata struct {
 	ReportJSONPath        string    `json:"report_json_path,omitempty"`
 	ConfigPath            string    `json:"config_path,omitempty"`
 	ConfigSource          string    `json:"config_source,omitempty"`
+	Overlay               string    `json:"overlay,omitempty"`
 	ConfigVersion         *int      `json:"config_version,omitempty"`
 	TranscriptDescription string    `json:"transcript_description,omitempty"`
 	Modules               []string  `json:"modules"`
@@ -222,6 +223,13 @@ func (r *RunDirectory) WriteJSONArtifact(name string, payload any) error {
 	return nil
 }
 
+func (r *RunDirectory) WriteArtifact(name string, payload []byte) error {
+	if err := os.WriteFile(filepath.Join(r.path, name), payload, 0o644); err != nil {
+		return fmt.Errorf("failed to write %s: %w", name, err)
+	}
+	return nil
+}
+
 func (r *RunDirectory) ApplyRetention(input RetentionDecisionInput) error {
 	decision := input
 	if decision.RetentionMode == "" {