diff --git a/dexlib/src/main/java/org/jf/dexlib/AnnotationDirectoryItem.java b/dexlib/src/main/java/org/jf/dexlib/AnnotationDirectoryItem.java
index 7647f564..f0790644 100644
--- a/dexlib/src/main/java/org/jf/dexlib/AnnotationDirectoryItem.java
+++ b/dexlib/src/main/java/org/jf/dexlib/AnnotationDirectoryItem.java
@@ -44,6 +44,14 @@ public class AnnotationDirectoryItem extends OffsettedItem<AnnotationDirectoryIt
     private final FieldListField<FieldAnnotation> fieldAnnotationListField;
     private final FieldListField<MethodAnnotation> methodAnnotationListField;
     private final FieldListField<ParameterAnnotation> parameterAnnotationListField;
+
+
+    //typically each AnnotationDirectoryItem will have a distinct parent. The only case that isn't true is when
+    //the AnnotationDirectoryItem *only* contains class annotations, with no other type of annotation. In that
+    //case, the same AnnotationDirectoryItem could be references from multiple classes.
+    //This isn't a problem though, because this field is only used in compareTo to determine the sort order,
+    //which handles it as a special case
+    private ClassDefItem parent = null;
                                              
     protected AnnotationDirectoryItem(final DexFile dexFile, int offset) {
         super(offset);
@@ -135,6 +143,48 @@ public class AnnotationDirectoryItem extends OffsettedItem<AnnotationDirectoryIt
         return Collections.unmodifiableList(parameterAnnotationList);
     }
 
+
+    private boolean isInternable() {
+        //an instance is only internable if it has only class annotations, but
+        //no other type of annotation
+        if (classAnnotationsReferenceField.getReference() == null ||
+            fieldAnnotationList.size() > 0 ||
+            methodAnnotationList.size() > 0 ||
+            parameterAnnotationList.size() > 0) {
+            return false;
+        }
+        return true;
+    }
+
+    public int hashCode() {
+        //an instance is only internable if it has only class annotations, but
+        //no other type of annotation
+        if (!isInternable()) {
+            return super.hashCode();
+        }
+        return classAnnotationsReferenceField.getReference().hashCode();
+    }
+
+    protected void setParent(ClassDefItem classDefItem) {
+        this.parent = classDefItem;
+    }
+
+    public int compareTo(AnnotationDirectoryItem annotationDirectoryItem) {
+        if (!isInternable()) {
+            if (!annotationDirectoryItem.isInternable()) {
+                return parent.compareTo(annotationDirectoryItem.parent);
+            }
+            return -1;
+        }
+
+        if (!annotationDirectoryItem.isInternable()) {
+            return 1;
+        }
+
+        return classAnnotationsReferenceField.getReference().compareTo(
+                annotationDirectoryItem.classAnnotationsReferenceField.getReference());
+    }
+
     public static class FieldAnnotation extends CompositeField<FieldAnnotation>
             implements Comparable<FieldAnnotation> {
         private final IndexedItemReference<FieldIdItem> fieldReferenceField;
diff --git a/dexlib/src/main/java/org/jf/dexlib/AnnotationItem.java b/dexlib/src/main/java/org/jf/dexlib/AnnotationItem.java
index 57451568..b7ab41dc 100644
--- a/dexlib/src/main/java/org/jf/dexlib/AnnotationItem.java
+++ b/dexlib/src/main/java/org/jf/dexlib/AnnotationItem.java
@@ -69,6 +69,14 @@ public class AnnotationItem extends OffsettedItem<AnnotationItem> {
         return annotationField;
     }
 
+    public int compareTo(AnnotationItem annotationItem) {
+        int comp = ((Integer)visibilityField.getCachedValue()).compareTo(annotationItem.visibilityField.getCachedValue());
+        if (comp == 0) {
+            comp = annotationField.compareTo(annotationItem.annotationField);
+        }
+        return comp;
+    }
+
     public enum Visibility {
         build(0x00),
         runtime(0x01),
diff --git a/dexlib/src/main/java/org/jf/dexlib/AnnotationSetItem.java b/dexlib/src/main/java/org/jf/dexlib/AnnotationSetItem.java
index 97db1abf..725411c1 100644
--- a/dexlib/src/main/java/org/jf/dexlib/AnnotationSetItem.java
+++ b/dexlib/src/main/java/org/jf/dexlib/AnnotationSetItem.java
@@ -83,4 +83,22 @@ public class AnnotationSetItem extends OffsettedItem<AnnotationSetItem> {
         }
         return annotationItems;
     }
+
+    public int compareTo(AnnotationSetItem annotationSetItem) {
+        if (annotationSetItem == null) {
+            return 1;
+        }
+
+        int comp = ((Integer)annotationReferences.size()).compareTo(annotationSetItem.annotationReferences.size());
+        if (comp == 0) {
+            for (int i=0; i<annotationReferences.size(); i++) {
+                comp = annotationReferences.get(i).getReference().compareTo(
+                        annotationSetItem.annotationReferences.get(i).getReference());
+                if (comp != 0) {
+                    break;
+                }
+            }
+        }
+        return comp;
+    }
 }
diff --git a/dexlib/src/main/java/org/jf/dexlib/AnnotationSetRefList.java b/dexlib/src/main/java/org/jf/dexlib/AnnotationSetRefList.java
index 98aed076..403f9a7c 100644
--- a/dexlib/src/main/java/org/jf/dexlib/AnnotationSetRefList.java
+++ b/dexlib/src/main/java/org/jf/dexlib/AnnotationSetRefList.java
@@ -88,4 +88,18 @@ public class AnnotationSetRefList extends OffsettedItem<AnnotationSetRefList> {
 
         return annotationSets;
     }
+
+    public int compareTo(AnnotationSetRefList annotationSetRefList) {
+        int comp = ((Integer)annotationSetReferences.size()).compareTo(annotationSetRefList.annotationSetReferences.size());
+        if (comp == 0) {
+            for (int i=0; i<annotationSetReferences.size(); i++) {
+                comp = annotationSetReferences.get(i).getReference().compareTo(
+                        annotationSetRefList.annotationSetReferences.get(i).getReference());
+                if (comp != 0) {
+                    break;
+                }
+            }
+        }
+        return comp;
+    }
 }
diff --git a/dexlib/src/main/java/org/jf/dexlib/ClassDataItem.java b/dexlib/src/main/java/org/jf/dexlib/ClassDataItem.java
index ac4bd505..9b43051d 100644
--- a/dexlib/src/main/java/org/jf/dexlib/ClassDataItem.java
+++ b/dexlib/src/main/java/org/jf/dexlib/ClassDataItem.java
@@ -49,6 +49,7 @@ public class ClassDataItem extends OffsettedItem<ClassDataItem> {
     private final EncodedMemberList<EncodedMethod> directMethodsListField;
     private final EncodedMemberList<EncodedMethod> virtualMethodsListField;
 
+    private ClassDefItem parent = null;
 
     public ClassDataItem(final DexFile dexFile, int offset) {
         super(offset);
@@ -310,6 +311,10 @@ public class ClassDataItem extends OffsettedItem<ClassDataItem> {
                     this.codeItemReferenceField = new OffsettedItemReference<CodeItem>(dexFile, codeItem,
                             new Leb128Field(null), "code_off")
             };
+
+            if (codeItem != null) {
+                codeItem.setParent(methodIdItem);
+            }
         }
 
         protected void setPreviousMember(EncodedMethod previousMethod) {
@@ -329,6 +334,14 @@ public class ClassDataItem extends OffsettedItem<ClassDataItem> {
                     AccessFlags.CONSTRUCTOR.getValue())) != 0);
         }
 
+        public void readFrom(Input in) {
+            super.readFrom(in);
+            CodeItem codeItem = codeItemReferenceField.getReference();
+            if (codeItem != null) {
+                codeItem.setParent(methodReferenceField.getReference());
+            }
+        }
+
         public int getAccessFlags() {
             return accessFlagsField.getCachedValue();
         }
@@ -396,4 +409,21 @@ public class ClassDataItem extends OffsettedItem<ClassDataItem> {
     public String getConciseIdentity() {
         return "class_data_item @0x" + Integer.toHexString(getOffset());
     }
+
+    protected void setParent(ClassDefItem classDefItem) {
+        this.parent = classDefItem;
+    }
+
+    public int compareTo(ClassDataItem other) {
+        if (parent == null) {
+            if (other.parent == null) {
+                return 0;
+            }
+            return -1;
+        }
+        if (other.parent == null) {
+            return 1;
+        }
+        return parent.compareTo(other.parent);
+    }
 }
diff --git a/dexlib/src/main/java/org/jf/dexlib/ClassDefItem.java b/dexlib/src/main/java/org/jf/dexlib/ClassDefItem.java
index 5cf98f2d..837297d3 100644
--- a/dexlib/src/main/java/org/jf/dexlib/ClassDefItem.java
+++ b/dexlib/src/main/java/org/jf/dexlib/ClassDefItem.java
@@ -31,10 +31,9 @@ package org.jf.dexlib;
 import org.jf.dexlib.EncodedValue.EncodedValue;
 import org.jf.dexlib.EncodedValue.EncodedValueSubField;
 import org.jf.dexlib.Util.TypeUtils;
+import org.jf.dexlib.Util.Input;
 
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
+import java.util.*;
 
 public class ClassDefItem extends IndexedItem<ClassDefItem> {
     private final IndexedItemReference<TypeIdItem> classTypeReferenceField;
@@ -90,6 +89,10 @@ public class ClassDefItem extends IndexedItem<ClassDefItem> {
         classInterfacesListReferenceField.setReference(implementsList);
         sourceFileReferenceField.setReference(source);        
         classDataReferenceField.setReference(classDataItem);
+
+        if (classDataItem != null) {
+            classDataItem.setParent(this);
+        }
     }
 
     public TypeIdItem getSuperclass() {
@@ -162,9 +165,10 @@ public class ClassDefItem extends IndexedItem<ClassDefItem> {
     }
 
     public int compareTo(ClassDefItem o) {
-        //sorting is implemented in SortClassDefItemSection, so this class doesn't
-        //need an implementation of compareTo
-        return 0;
+        //The actual sorting for this class is implemented in SortClassDefItemSection.
+        //This method is just used for sorting the associated ClassDataItem items, so
+        //we can just do the comparison based on the offsets of the items
+        return ((Integer)this.offset).compareTo(o.offset);
     }
 
     public void addField(ClassDataItem.EncodedField encodedField, EncodedValue initialValue) {
@@ -205,10 +209,28 @@ public class ClassDefItem extends IndexedItem<ClassDefItem> {
 
     public void setAnnotations(AnnotationDirectoryItem annotations) {
         this.classAnnotationsReferenceField.setReference(annotations);
+        annotations.setParent(this);
     }
 
     public void setClassDataItem(ClassDataItem classDataItem) {
         this.classDataReferenceField.setReference(classDataItem);
+        if (classDataItem != null) {
+            classDataItem.setParent(this);
+        }
+    }
+
+    public void readFrom(Input in, int index) {
+        super.readFrom(in, index);
+
+        ClassDataItem classDataItem = classDataReferenceField.getReference();
+        if (classDataItem != null) {
+            classDataItem.setParent(this);
+        }
+
+        AnnotationDirectoryItem annotationDirectoryItem = classAnnotationsReferenceField.getReference();
+        if (annotationDirectoryItem != null) {
+            annotationDirectoryItem.setParent(this);
+        }
     }
 
     public static int placeClassDefItems(IndexedSection<ClassDefItem> section, int offset) {
@@ -238,6 +260,18 @@ public class ClassDefItem extends IndexedItem<ClassDefItem> {
 
         public int placeSection(int offset) {
             currentOffset = offset;
+
+            //presort the list, to guarantee a unique ordering
+            Collections.sort(section.items, new Comparator<ClassDefItem>() {
+                public int compare(ClassDefItem classDefItem, ClassDefItem classDefItem1) {
+                    return classDefItem.getClassType().compareTo(classDefItem1.getClassType());
+                }
+            });
+
+            for (ClassDefItem classDefItem: section.items) {
+                classDefItem.offset = -1;
+            }
+
             for (ClassDefItem classDefItem: section.items) {
                 placeClass(classDefItem);
             }
diff --git a/dexlib/src/main/java/org/jf/dexlib/CodeItem.java b/dexlib/src/main/java/org/jf/dexlib/CodeItem.java
index 82d907e0..69035079 100644
--- a/dexlib/src/main/java/org/jf/dexlib/CodeItem.java
+++ b/dexlib/src/main/java/org/jf/dexlib/CodeItem.java
@@ -54,6 +54,8 @@ public class CodeItem extends OffsettedItem<CodeItem> {
     private final FieldListField<TryItem> triesListField;
     private final EncodedCatchHandlerList catchHandlersListField;
 
+    private MethodIdItem parent = null;
+
     public CodeItem(final DexFile dexFile, int offset) {
         super(offset);
 
@@ -105,6 +107,10 @@ public class CodeItem extends OffsettedItem<CodeItem> {
         inArgumentCountField.cacheValue(inArguments);
         outArgumentCountField.cacheValue(instructionListField.getOutArguments());
         debugInfoReferenceField.setReference(debugInfo);
+
+        if (debugInfo != null) {
+            debugInfo.setParent(this);
+        }
     }
 
     protected int getAlignment() {
@@ -131,6 +137,10 @@ public class CodeItem extends OffsettedItem<CodeItem> {
         return debugInfoReferenceField.getReference();
     }
 
+    protected void setParent(MethodIdItem methodIdItem) {
+        this.parent = methodIdItem;
+    }
+
     public void copyTo(DexFile dexFile, CodeItem copy)
     {
         for (int i = 0; i < fields.length-2; i++) {
@@ -140,6 +150,20 @@ public class CodeItem extends OffsettedItem<CodeItem> {
         //the catchHandler copies will already exist
         catchHandlersListField.copyTo(dexFile, copy.catchHandlersListField);
         triesListField.copyTo(dexFile, copy.triesListField);
+
+        DebugInfoItem copyDebugInfo = copy.getDebugInfo();
+        if (copy != null) {
+            copyDebugInfo.setParent(copy);
+        }
+    }
+
+    public void readFrom(Input in, int index) {
+        super.readFrom(in, index);
+
+        DebugInfoItem debugInfoItem = debugInfoReferenceField.getReference();
+        if (debugInfoItem != null) {
+            debugInfoItem.setParent(this);
+        }
     }
 
     public String getConciseIdentity() {
@@ -147,6 +171,19 @@ public class CodeItem extends OffsettedItem<CodeItem> {
         return "code_item @0x" + Integer.toHexString(getOffset());
     }
 
+    public int compareTo(CodeItem other) {
+        if (parent == null) {
+            if (other.parent == null) {
+                return 0;
+            }
+            return -1;
+        }
+        if (other.parent == null) {
+            return 1;
+        }
+        return parent.compareTo(other.parent);
+    }
+
     public static class TryItem extends CompositeField<TryItem> {
         private final IntegerField startAddr;
         private final ShortIntegerField insnCount;
diff --git a/dexlib/src/main/java/org/jf/dexlib/DebugInfoItem.java b/dexlib/src/main/java/org/jf/dexlib/DebugInfoItem.java
index 07fa5014..f8ac7411 100644
--- a/dexlib/src/main/java/org/jf/dexlib/DebugInfoItem.java
+++ b/dexlib/src/main/java/org/jf/dexlib/DebugInfoItem.java
@@ -49,6 +49,8 @@ public class DebugInfoItem extends OffsettedItem<DebugInfoItem> {
     private final FieldListField<IndexedItemReference<StringIdItem>> parameterNamesField;
     private final DebugInstructionList debugInstructionListField;
 
+    private CodeItem parent = null;
+
     public DebugInfoItem(final DexFile dexFile, int offset) {
         super(offset);
 
@@ -87,6 +89,10 @@ public class DebugInfoItem extends OffsettedItem<DebugInfoItem> {
         return ItemType.TYPE_DEBUG_INFO_ITEM;
     }
 
+    protected void setParent(CodeItem codeItem) {
+        this.parent = codeItem;
+    }
+
     public String getConciseIdentity() {
         return "debug_info_item @0x" + Integer.toHexString(getOffset());
     }
@@ -113,6 +119,18 @@ public class DebugInfoItem extends OffsettedItem<DebugInfoItem> {
         return parameterNamesList;
     }
 
+    public int compareTo(DebugInfoItem other) {
+        if (parent == null) {
+            if (other.parent == null) {
+                return 0;
+            }
+            return -1;
+        }
+        if (other.parent == null) {
+            return 1;
+        }
+        return parent.compareTo(other.parent);
+    }
 
 
     private class DebugInstructionList implements Field<DebugInstructionList> {
diff --git a/dexlib/src/main/java/org/jf/dexlib/DexFile.java b/dexlib/src/main/java/org/jf/dexlib/DexFile.java
index d50069f6..3a9e89a6 100644
--- a/dexlib/src/main/java/org/jf/dexlib/DexFile.java
+++ b/dexlib/src/main/java/org/jf/dexlib/DexFile.java
@@ -38,6 +38,7 @@ import java.security.DigestException;
 import java.security.MessageDigest;
 import java.security.NoSuchAlgorithmException;
 import java.util.HashMap;
+import java.util.List;
 import java.util.zip.Adler32;
 
 public class DexFile
@@ -90,10 +91,10 @@ public class DexFile
                 AnnotationDirectoriesSection,
                 TypeListsSection,
                 StringDataSection,
-                DebugInfoItemsSection,
                 AnnotationsSection,
                 EncodedArraysSection,
-                ClassDataSection
+                ClassDataSection,
+                DebugInfoItemsSection               
         };
     }
 
@@ -135,9 +136,9 @@ public class DexFile
             ItemType.TYPE_ANNOTATION_SET_REF_LIST.getMapValue(),
             ItemType.TYPE_ANNOTATIONS_DIRECTORY_ITEM.getMapValue(),
             ItemType.TYPE_TYPE_LIST.getMapValue(),
-            ItemType.TYPE_DEBUG_INFO_ITEM.getMapValue(),
             ItemType.TYPE_CODE_ITEM.getMapValue(),
             ItemType.TYPE_CLASS_DATA_ITEM.getMapValue(),
+            ItemType.TYPE_DEBUG_INFO_ITEM.getMapValue(),
             ItemType.TYPE_MAP_LIST.getMapValue()
         };
 
@@ -191,7 +192,7 @@ public class DexFile
         return forDumping;
     }
 
-    public void place() {
+    public void place(boolean sort) {
         int offset = 0;
 
         offset = HeaderItemSection.place(offset);
@@ -203,6 +204,9 @@ public class DexFile
         dataOffset = offset;
 
         for (OffsettedSection offsettedSection: offsettedSections) {
+            if (sort) {
+                offsettedSection.sortSection();
+            }
             offset = offsettedSection.place(offset);
         }
 
diff --git a/dexlib/src/main/java/org/jf/dexlib/EncodedArrayItem.java b/dexlib/src/main/java/org/jf/dexlib/EncodedArrayItem.java
index 9f819c34..19575dab 100644
--- a/dexlib/src/main/java/org/jf/dexlib/EncodedArrayItem.java
+++ b/dexlib/src/main/java/org/jf/dexlib/EncodedArrayItem.java
@@ -72,4 +72,8 @@ public class EncodedArrayItem extends OffsettedItem<EncodedArrayItem> {
     public ArrayEncodedValueSubField getEncodedArray() {
         return encodedArray;
     }
+
+    public int compareTo(EncodedArrayItem encodedArrayItem) {
+        return encodedArray.compareTo(encodedArrayItem.encodedArray);
+    }
 }
diff --git a/dexlib/src/main/java/org/jf/dexlib/EncodedValue/AnnotationElement.java b/dexlib/src/main/java/org/jf/dexlib/EncodedValue/AnnotationElement.java
index fa64f7ad..b12fa70f 100644
--- a/dexlib/src/main/java/org/jf/dexlib/EncodedValue/AnnotationElement.java
+++ b/dexlib/src/main/java/org/jf/dexlib/EncodedValue/AnnotationElement.java
@@ -54,7 +54,11 @@ public class AnnotationElement extends CompositeField<AnnotationElement>
     }
 
     public int compareTo(AnnotationElement annotationElement) {
-        return elementName.compareTo(annotationElement.elementName);
+        int comp = elementName.compareTo(annotationElement.elementName);
+        if (comp == 0) {
+            comp = encodedValue.compareTo(annotationElement.encodedValue);
+        }
+        return comp;
     }
 
     public StringIdItem getName() {
diff --git a/dexlib/src/main/java/org/jf/dexlib/EncodedValue/AnnotationEncodedValueSubField.java b/dexlib/src/main/java/org/jf/dexlib/EncodedValue/AnnotationEncodedValueSubField.java
index b8d94625..2f0db126 100644
--- a/dexlib/src/main/java/org/jf/dexlib/EncodedValue/AnnotationEncodedValueSubField.java
+++ b/dexlib/src/main/java/org/jf/dexlib/EncodedValue/AnnotationEncodedValueSubField.java
@@ -35,7 +35,7 @@ import java.util.Collections;
 import java.util.List;
 
 public class AnnotationEncodedValueSubField extends CompositeField<AnnotationEncodedValueSubField>
-    implements EncodedValueSubField<AnnotationEncodedValueSubField> {
+    implements EncodedValueSubField<AnnotationEncodedValueSubField>, Comparable<EncodedValueSubField> {
 
     private final ArrayList<AnnotationElement> annotationElementList = new ArrayList<AnnotationElement>();
 
@@ -88,4 +88,25 @@ public class AnnotationEncodedValueSubField extends CompositeField<AnnotationEnc
     public List<AnnotationElement> getAnnotationElements() {
         return Collections.unmodifiableList(annotationElementList);
     }
+
+    public int compareTo(EncodedValueSubField t) {
+        int comp = getValueType().compareTo(t.getValueType());
+        if (comp == 0) {
+            AnnotationEncodedValueSubField other = (AnnotationEncodedValueSubField)t;
+
+            comp = annotationType.compareTo(other.annotationType);
+            if (comp == 0) {
+                comp = ((Integer)annotationElementList.size()).compareTo(other.annotationElementList.size());
+                if (comp == 0) {
+                    for (int i=0; i<annotationElementList.size(); i++) {
+                        comp = annotationElementList.get(i).compareTo(other.annotationElementList.get(i));
+                        if (comp != 0) {
+                            break;
+                        }
+                    }
+                }
+            }
+        }
+        return comp;
+    }
 }
diff --git a/dexlib/src/main/java/org/jf/dexlib/EncodedValue/ArrayEncodedValueSubField.java b/dexlib/src/main/java/org/jf/dexlib/EncodedValue/ArrayEncodedValueSubField.java
index c9d26812..54e39ae6 100644
--- a/dexlib/src/main/java/org/jf/dexlib/EncodedValue/ArrayEncodedValueSubField.java
+++ b/dexlib/src/main/java/org/jf/dexlib/EncodedValue/ArrayEncodedValueSubField.java
@@ -35,7 +35,7 @@ import java.util.List;
 import java.util.Collections;
 
 public class ArrayEncodedValueSubField extends CompositeField<ArrayEncodedValueSubField>
-        implements  EncodedValueSubField<ArrayEncodedValueSubField>
+        implements  EncodedValueSubField<ArrayEncodedValueSubField>, Comparable<EncodedValueSubField>
 {
 
     private final ArrayList<EncodedValue> encodedValues;
@@ -88,4 +88,22 @@ public class ArrayEncodedValueSubField extends CompositeField<ArrayEncodedValueS
     public List<EncodedValue> getValues() {
         return Collections.unmodifiableList(encodedValues);
     }
+
+    public int compareTo(EncodedValueSubField t) {
+        int comp = getValueType().compareTo(t.getValueType());
+        if (comp == 0) {
+            ArrayEncodedValueSubField other = (ArrayEncodedValueSubField)t;
+
+            comp = ((Integer)encodedValues.size()).compareTo(other.encodedValues.size());
+            if (comp == 0) {
+                for (int i=0; i<encodedValues.size(); i++) {
+                    comp = encodedValues.get(i).compareTo(other.encodedValues.get(i));
+                    if (comp != 0) {
+                        break;
+                    }
+                }
+            }
+        }
+        return comp;
+    }
 }
diff --git a/dexlib/src/main/java/org/jf/dexlib/EncodedValue/EncodedIndexedItemReference.java b/dexlib/src/main/java/org/jf/dexlib/EncodedValue/EncodedIndexedItemReference.java
index cc4588f9..999bf8f7 100644
--- a/dexlib/src/main/java/org/jf/dexlib/EncodedValue/EncodedIndexedItemReference.java
+++ b/dexlib/src/main/java/org/jf/dexlib/EncodedValue/EncodedIndexedItemReference.java
@@ -34,7 +34,7 @@ import org.jf.dexlib.Util.EncodedValueUtils;
 import org.jf.dexlib.Util.Input;
 
 public class EncodedIndexedItemReference<T extends IndexedItem<T>>
-    implements EncodedValueSubField<EncodedIndexedItemReference<T>> {
+    implements EncodedValueSubField<EncodedIndexedItemReference<T>>, Comparable<EncodedValueSubField> {
     private int initialValueArg;
     private ValueType valueType;
 
@@ -140,4 +140,12 @@ public class EncodedIndexedItemReference<T extends IndexedItem<T>>
             return other.item == null;
         }
     }
+
+    public int compareTo(EncodedValueSubField t) {
+        int comp = getValueType().compareTo(t.getValueType());
+        if (comp == 0) {
+            return item.compareTo(((EncodedIndexedItemReference<T>)t).item);
+        }
+        return comp;
+    }
 }
diff --git a/dexlib/src/main/java/org/jf/dexlib/EncodedValue/EncodedValue.java b/dexlib/src/main/java/org/jf/dexlib/EncodedValue/EncodedValue.java
index badde4e3..4919fd67 100644
--- a/dexlib/src/main/java/org/jf/dexlib/EncodedValue/EncodedValue.java
+++ b/dexlib/src/main/java/org/jf/dexlib/EncodedValue/EncodedValue.java
@@ -34,7 +34,7 @@ import org.jf.dexlib.Field;
 import org.jf.dexlib.Util.AnnotatedOutput;
 import org.jf.dexlib.Util.Input;
 
-public class EncodedValue extends CompositeField<EncodedValue> {
+public class EncodedValue extends CompositeField<EncodedValue> implements Comparable<EncodedValue> {
     private class ValueTypeArgField implements Field<ValueTypeArgField> {
         private ValueType valueType;
         private byte valueArg;
@@ -89,7 +89,8 @@ public class EncodedValue extends CompositeField<EncodedValue> {
         }
     }
 
-    private class EncodedValueSubFieldWrapper implements Field<EncodedValueSubFieldWrapper> {
+    private class EncodedValueSubFieldWrapper
+            implements Field<EncodedValueSubFieldWrapper>, Comparable<EncodedValueSubFieldWrapper> {
         private final DexFile dexFile;
         private EncodedValueSubField subField;
 
@@ -141,6 +142,10 @@ public class EncodedValue extends CompositeField<EncodedValue> {
             EncodedValueSubFieldWrapper other = (EncodedValueSubFieldWrapper)o;
             return subField.equals(other.subField);
         }
+
+        public int compareTo(EncodedValueSubFieldWrapper encodedValueSubFieldWrapper) {
+            return subField.compareTo(encodedValueSubFieldWrapper.subField);
+        }
     }
 
     private final ValueTypeArgField valueTypeArg;
@@ -181,4 +186,8 @@ public class EncodedValue extends CompositeField<EncodedValue> {
     public EncodedValueSubField getValue() {
         return encodedValue.getEncodedValueSubField();
     }
+
+    public int compareTo(EncodedValue encodedValue) {
+        return this.encodedValue.compareTo(encodedValue.encodedValue);
+    }
 }
diff --git a/dexlib/src/main/java/org/jf/dexlib/EncodedValue/EncodedValueSubField.java b/dexlib/src/main/java/org/jf/dexlib/EncodedValue/EncodedValueSubField.java
index b8f7884a..78af5cb4 100644
--- a/dexlib/src/main/java/org/jf/dexlib/EncodedValue/EncodedValueSubField.java
+++ b/dexlib/src/main/java/org/jf/dexlib/EncodedValue/EncodedValueSubField.java
@@ -35,4 +35,5 @@ public interface EncodedValueSubField<T extends EncodedValueSubField> extends Fi
     public void setInitialValueArg(byte valueArg);
     public byte getValueArg();
     public ValueType getValueType();
+    public int compareTo(EncodedValueSubField encodedValueSubField);
 }
diff --git a/dexlib/src/main/java/org/jf/dexlib/EncodedValue/NullEncodedValueSubField.java b/dexlib/src/main/java/org/jf/dexlib/EncodedValue/NullEncodedValueSubField.java
index 559dad72..aafbf70d 100644
--- a/dexlib/src/main/java/org/jf/dexlib/EncodedValue/NullEncodedValueSubField.java
+++ b/dexlib/src/main/java/org/jf/dexlib/EncodedValue/NullEncodedValueSubField.java
@@ -32,7 +32,7 @@ import org.jf.dexlib.Util.AnnotatedOutput;
 import org.jf.dexlib.Util.Input;
 
 public class NullEncodedValueSubField
-    extends SimpleEncodedValueSubField<Object, NullEncodedValueSubField>
+    extends SimpleEncodedValueSubField<Integer, NullEncodedValueSubField>
 {
     public NullEncodedValueSubField() {
     }
@@ -55,4 +55,8 @@ public class NullEncodedValueSubField
     public ValueType getValueType() {
         return ValueType.VALUE_NULL;
     }
+
+    public int compareTo(EncodedValueSubField t) {
+        return getValueType().compareTo(t.getValueType());
+    }
 }
diff --git a/dexlib/src/main/java/org/jf/dexlib/EncodedValue/SimpleEncodedValueSubField.java b/dexlib/src/main/java/org/jf/dexlib/EncodedValue/SimpleEncodedValueSubField.java
index 09219279..45d366f3 100644
--- a/dexlib/src/main/java/org/jf/dexlib/EncodedValue/SimpleEncodedValueSubField.java
+++ b/dexlib/src/main/java/org/jf/dexlib/EncodedValue/SimpleEncodedValueSubField.java
@@ -30,7 +30,8 @@ package org.jf.dexlib.EncodedValue;
 
 import org.jf.dexlib.DexFile;
 
-public abstract class SimpleEncodedValueSubField<V, T extends SimpleEncodedValueSubField<V,T>> implements EncodedValueSubField<T>
+public abstract class SimpleEncodedValueSubField<V extends Comparable<V>, T extends SimpleEncodedValueSubField<V,T>>
+        implements EncodedValueSubField<T>, Comparable<EncodedValueSubField>
 {
     protected V value;
     protected byte valueArg = 0;
@@ -65,4 +66,12 @@ public abstract class SimpleEncodedValueSubField<V, T extends SimpleEncodedValue
         }
         return value.equals(other.value);
     }
+
+    public int compareTo(EncodedValueSubField t) {
+        int comp = getValueType().compareTo(t.getValueType());
+        if (comp == 0) {
+            return value.compareTo(((SimpleEncodedValueSubField<V, T>)t).value);
+        }
+        return comp;
+    }
 }
diff --git a/dexlib/src/main/java/org/jf/dexlib/IndexedItem.java b/dexlib/src/main/java/org/jf/dexlib/IndexedItem.java
index 0b8ff375..593766c0 100644
--- a/dexlib/src/main/java/org/jf/dexlib/IndexedItem.java
+++ b/dexlib/src/main/java/org/jf/dexlib/IndexedItem.java
@@ -28,7 +28,7 @@
 
 package org.jf.dexlib;
 
-public abstract class IndexedItem<T extends IndexedItem> extends Item<T> implements Comparable<T> {
+public abstract class IndexedItem<T extends IndexedItem> extends Item<T> {
     protected IndexedItem(int index) {
         this.index = index;
     }
diff --git a/dexlib/src/main/java/org/jf/dexlib/IndexedSection.java b/dexlib/src/main/java/org/jf/dexlib/IndexedSection.java
index db6cffdf..0cd01af1 100644
--- a/dexlib/src/main/java/org/jf/dexlib/IndexedSection.java
+++ b/dexlib/src/main/java/org/jf/dexlib/IndexedSection.java
@@ -77,10 +77,6 @@ public abstract class IndexedSection<T extends IndexedItem<T>> extends Section<T
         return itemToReturn;
     }
 
-    protected void sortSection() {
-        Collections.sort(items);
-    }
-
     public int place(int offset) {
         sortSection();
 
diff --git a/dexlib/src/main/java/org/jf/dexlib/Item.java b/dexlib/src/main/java/org/jf/dexlib/Item.java
index efb3f4f8..eddc919c 100644
--- a/dexlib/src/main/java/org/jf/dexlib/Item.java
+++ b/dexlib/src/main/java/org/jf/dexlib/Item.java
@@ -31,7 +31,7 @@ package org.jf.dexlib;
 import org.jf.dexlib.Util.AnnotatedOutput;
 import org.jf.dexlib.Util.Input;
 
-public abstract class Item<T extends Item> {
+public abstract class Item<T extends Item> implements Comparable<T> {
     protected int offset = -1;
     protected int index = -1;
     
diff --git a/dexlib/src/main/java/org/jf/dexlib/Section.java b/dexlib/src/main/java/org/jf/dexlib/Section.java
index e2fbbf19..07d216a7 100644
--- a/dexlib/src/main/java/org/jf/dexlib/Section.java
+++ b/dexlib/src/main/java/org/jf/dexlib/Section.java
@@ -33,6 +33,8 @@ import org.jf.dexlib.Util.Input;
 
 import java.util.ArrayList;
 import java.util.HashMap;
+import java.util.List;
+import java.util.Collections;
 
 public abstract class Section<T extends Item> {
     protected ArrayList<T> items;
@@ -112,6 +114,10 @@ public abstract class Section<T extends Item> {
         return offset;
     }
 
+    public List<T> getItems() {
+        return Collections.unmodifiableList(items);
+    }
+
     protected T getInternedItem(T item) {
         if (uniqueItems == null) {
             buildInternedItemMap();
@@ -126,5 +132,9 @@ public abstract class Section<T extends Item> {
         }
     }
 
+    protected void sortSection() {
+        Collections.sort(items);
+    }
+
     public abstract T intern(DexFile dexFile, T item);
 }
diff --git a/dexlib/src/main/java/org/jf/dexlib/StringDataItem.java b/dexlib/src/main/java/org/jf/dexlib/StringDataItem.java
index a060d728..0d3d7b77 100644
--- a/dexlib/src/main/java/org/jf/dexlib/StringDataItem.java
+++ b/dexlib/src/main/java/org/jf/dexlib/StringDataItem.java
@@ -69,11 +69,17 @@ public class StringDataItem extends OffsettedItem<StringDataItem> implements Com
         return value;
     }
 
+    public byte[] getStringBytes() {
+        return stringByteArray.value;
+    }
+
     public String getConciseIdentity() {
-        return "string_data_item: " + getStringValue();
+        return "string_data_item: " + Utf8Utils.escapeString(getStringValue());
     }
 
     public int compareTo(StringDataItem o) {
         return getStringValue().compareTo(o.getStringValue());
     }
+
+
 }
diff --git a/dexlib/src/main/java/org/jf/dexlib/StringIdItem.java b/dexlib/src/main/java/org/jf/dexlib/StringIdItem.java
index a2b709ef..95dd4055 100644
--- a/dexlib/src/main/java/org/jf/dexlib/StringIdItem.java
+++ b/dexlib/src/main/java/org/jf/dexlib/StringIdItem.java
@@ -28,6 +28,8 @@
 
 package org.jf.dexlib;
 
+import org.jf.dexlib.Util.Utf8Utils;
+
 public class StringIdItem extends IndexedItem<StringIdItem> {
     private final OffsettedItemReference<StringDataItem> stringDataReferenceField;
 
@@ -57,13 +59,17 @@ public class StringIdItem extends IndexedItem<StringIdItem> {
     }
 
     public String getConciseIdentity() {
-        return "string_id_item: " + getStringValue();
+        return "string_id_item: " + Utf8Utils.escapeString(getStringValue());
     }
 
     public String getStringValue() {
         return stringDataReferenceField.getReference().getStringValue();
     }
 
+    public StringDataItem getStringData() {
+        return stringDataReferenceField.getReference();
+    }
+
     public int compareTo(StringIdItem o) {
         //sort by the string value
         return getStringValue().compareTo(o.getStringValue());
diff --git a/dexlib/src/main/java/org/jf/dexlib/TypeListItem.java b/dexlib/src/main/java/org/jf/dexlib/TypeListItem.java
index cad9275b..eaa2ec16 100644
--- a/dexlib/src/main/java/org/jf/dexlib/TypeListItem.java
+++ b/dexlib/src/main/java/org/jf/dexlib/TypeListItem.java
@@ -31,7 +31,7 @@ package org.jf.dexlib;
 import java.util.ArrayList;
 import java.util.List;
 
-public class TypeListItem extends OffsettedItem<TypeListItem> implements Comparable<TypeListItem> {
+public class TypeListItem extends OffsettedItem<TypeListItem> {
     private final ArrayList<IndexedItemReference<TypeIdItem>> typeList = new ArrayList<IndexedItemReference<TypeIdItem>>();
 
     private final ListSizeField sizeField;
diff --git a/dexlib/src/main/java/org/jf/dexlib/Util/NumberUtils.java b/dexlib/src/main/java/org/jf/dexlib/Util/NumberUtils.java
index 11155136..644c8b1c 100644
--- a/dexlib/src/main/java/org/jf/dexlib/Util/NumberUtils.java
+++ b/dexlib/src/main/java/org/jf/dexlib/Util/NumberUtils.java
@@ -66,13 +66,13 @@ public class NumberUtils {
     }
 
     public static long decodeLong(byte[] array, int startIndex) {
-        return  array[startIndex++] |
-                (array[startIndex++] >> 8) |
-                (array[startIndex++] >> 16) |
-                (array[startIndex++] >> 24) |
-                ((long)array[startIndex++] >> 32) |
-                ((long)array[startIndex++] >> 40) |
-                ((long)array[startIndex++] >> 48) |
-                ((long)array[startIndex++] >> 56);
+        return  (array[startIndex++] & 0xffL) |
+                ((array[startIndex++] & 0xffL) << 8) |
+                ((array[startIndex++] & 0xffL) << 16) |
+                ((array[startIndex++] & 0xffL) << 24) |
+                ((array[startIndex++] & 0xffL) << 32) |
+                ((array[startIndex++] & 0xffL) << 40) |
+                ((array[startIndex++] & 0xffL) << 48) |
+                ((array[startIndex] & 0xffL) << 56);
     }
 }
diff --git a/smali/src/main/java/org/jf/smali/smali.java b/smali/src/main/java/org/jf/smali/smali.java
index 8df14865..1745c73b 100644
--- a/smali/src/main/java/org/jf/smali/smali.java
+++ b/smali/src/main/java/org/jf/smali/smali.java
@@ -33,11 +33,13 @@ import org.antlr.runtime.CommonTokenStream;
 import org.antlr.runtime.tree.CommonTree;
 import org.antlr.runtime.tree.CommonTreeNodeStream;
 import org.jf.dexlib.DexFile;
+import org.jf.dexlib.AnnotationItem;
 import org.jf.dexlib.Util.ByteArrayAnnotatedOutput;
 
 import java.io.*;
 import java.util.LinkedHashSet;
 import java.util.Set;
+import java.util.List;
 
 public class smali
 {
@@ -125,7 +127,7 @@ public class smali
             System.exit(1);
         }
 
-        dexFile.place();
+        dexFile.place(false);
         try
         {
             ByteArrayAnnotatedOutput out = new ByteArrayAnnotatedOutput();