fix(module): skip area version-only extract churn

internal/pipeline/extract.go

@@ -501,6 +501,9 @@ func writeManagedFile(path string, data []byte) (writeState, error) {
 		if bytes.Equal(existing, data) {
 			return writeSkipped, nil
 		}
+		if areaGFFJSONEqualIgnoringRootVersion(path, existing, data) {
+			return writeSkipped, nil
+		}
 		if err := os.WriteFile(path, data, 0o644); err != nil {
 			return writeSkipped, fmt.Errorf("overwrite %s: %w", path, err)
 		}
@@ -516,6 +519,38 @@ func writeManagedFile(path string, data []byte) (writeState, error) {
 	return writeNew, nil
 }
 
+func areaGFFJSONEqualIgnoringRootVersion(path string, existing, extracted []byte) bool {
+	if !strings.HasSuffix(strings.ToLower(filepath.Base(path)), ".are.json") {
+		return false
+	}
+
+	var left, right gff.Document
+	if err := json.Unmarshal(existing, &left); err != nil {
+		return false
+	}
+	if err := json.Unmarshal(extracted, &right); err != nil {
+		return false
+	}
+	removeRootField(&left.Root, "Version")
+	removeRootField(&right.Root, "Version")
+
+	leftRaw, err := json.Marshal(left)
+	if err != nil {
+		return false
+	}
+	rightRaw, err := json.Marshal(right)
+	if err != nil {
+		return false
+	}
+	return bytes.Equal(leftRaw, rightRaw)
+}
+
+func removeRootField(s *gff.Struct, label string) {
+	s.Fields = slices.DeleteFunc(s.Fields, func(field gff.Field) bool {
+		return field.Label == label
+	})
+}
+
 func cleanupStaleFiles(p *project.Project, desired map[string]struct{}, scope extractionScope) (int, []error) {
 	candidates := make([]string, 0, len(p.Inventory.SourceFiles)+len(p.Inventory.ScriptFiles)+len(p.Inventory.AssetFiles))
 	if scope.Source && safeCleanupRoot(p.SourceDir(), p.Root) {