diff --git a/dexlib/src/main/java/org/jf/dexlib/AnnotationDirectoryItem.java b/dexlib/src/main/java/org/jf/dexlib/AnnotationDirectoryItem.java
index b485930c..7605ecd6 100644
--- a/dexlib/src/main/java/org/jf/dexlib/AnnotationDirectoryItem.java
+++ b/dexlib/src/main/java/org/jf/dexlib/AnnotationDirectoryItem.java
@@ -109,9 +109,11 @@ public class AnnotationDirectoryItem extends OffsettedItem<AnnotationDirectoryIt
 
     public int place(int index, int offset)
     {
-        Collections.sort(fieldAnnotationList);
-        Collections.sort(methodAnnotationList);
-        Collections.sort(parameterAnnotationList);
+        if (!dexFile.getInplace()) {
+            Collections.sort(fieldAnnotationList);
+            Collections.sort(methodAnnotationList);
+            Collections.sort(parameterAnnotationList);
+        }
         return super.place(index, offset);
     }
 
diff --git a/dexlib/src/main/java/org/jf/dexlib/ClassDataItem.java b/dexlib/src/main/java/org/jf/dexlib/ClassDataItem.java
index f74b05c1..6a3e3f00 100644
--- a/dexlib/src/main/java/org/jf/dexlib/ClassDataItem.java
+++ b/dexlib/src/main/java/org/jf/dexlib/ClassDataItem.java
@@ -342,6 +342,15 @@ public class ClassDataItem extends OffsettedItem<ClassDataItem> {
             }
         }
 
+        public void copyTo(DexFile dexFile, EncodedMethod copy) {
+            super.copyTo(dexFile, copy);
+
+            CodeItem codeItem = copy.codeItemReferenceField.getReference();
+            if (codeItem != null) {
+                codeItem.setParent(copy.methodReferenceField.getReference());
+            }
+        }
+
         public int getAccessFlags() {
             return accessFlagsField.getCachedValue();
         }
diff --git a/dexlib/src/main/java/org/jf/dexlib/ClassDefItem.java b/dexlib/src/main/java/org/jf/dexlib/ClassDefItem.java
index 838cdd0c..897871da 100644
--- a/dexlib/src/main/java/org/jf/dexlib/ClassDefItem.java
+++ b/dexlib/src/main/java/org/jf/dexlib/ClassDefItem.java
@@ -171,6 +171,20 @@ public class ClassDefItem extends IndexedItem<ClassDefItem> {
         return ((Integer)this.offset).compareTo(o.offset);
     }
 
+    public void copyTo(DexFile dexFile, ClassDefItem copy) {
+        super.copyTo(dexFile, copy);
+
+        AnnotationDirectoryItem annotationDirectoryItem = copy.classAnnotationsReferenceField.getReference();
+        if (annotationDirectoryItem != null) {
+            annotationDirectoryItem.setParent(copy);
+        }
+
+        ClassDataItem classDataItem = copy.classDataReferenceField.getReference();
+        if (classDataItem != null) {
+            classDataItem.setParent(copy);
+        }
+    }
+
     public void addField(ClassDataItem.EncodedField encodedField, EncodedValue initialValue) {
         //fields are added in ClassDefItem instead of ClassDataItem because we need to grab
         //the static initializers for StaticFieldInitialValues