Fix underlay provenance and resource path handling

internal/engine/load_metadata.go

@@ -125,9 +125,6 @@ func applyOverlayMetadata(metadata *Metadata, records []overlayRecord) {
 		if err != nil {
 			continue
 		}
-		if history := events[pointer]; len(history) != 0 && history[len(history)-1].Origin.Layer == info.Origin.Layer && history[len(history)-1].Origin.Operation == info.Origin.Operation {
-			continue
-		}
 		appendInputOriginEvent(events, baseline, pointer, path, info.Origin)
 	}
 	metadata.history = make(map[string][]Change, len(baseline)+len(events))
@@ -144,12 +141,37 @@ func appendInputOriginEvent(events map[string][]Change, baseline map[string][]Ch
 		return
 	}
 	history := events[pointer]
-	if len(history) != 0 && originContainedBy(history[len(history)-1].Origin, origin) {
+	if len(history) != 0 && originRepresentedByChange(path, origin, history[len(history)-1]) {
 		return
 	}
 	appendInputChangeEvent(events, baseline, pointer, Change{Path: path.clone(), Origin: cloneOrigin(origin)})
 }
 
+func originRepresentedByChange(path Path, origin Origin, change Change) bool {
+	if change.Path.String() == path.String() {
+		return originContainedBy(origin, change.Origin)
+	}
+	if !pathContains(change.Path, path) || origin.Layer != change.Origin.Layer || origin.Operation != change.Origin.Operation {
+		return false
+	}
+	// A subtree replacement already records its descendants' contributions.
+	// Their coordinates differ from the container's, but their sources must be
+	// covered by the operation; matching only the precedence role is insufficient.
+	for _, location := range origin.Locations {
+		found := false
+		for _, recorded := range change.Origin.Locations {
+			if location.SourceID == recorded.SourceID {
+				found = true
+				break
+			}
+		}
+		if !found {
+			return false
+		}
+	}
+	return true
+}
+
 func appendInputChangeEvent(events map[string][]Change, baseline map[string][]Change, pointer string, value Change) {
 	change := cloneChange(value)
 	history := events[pointer]