Object model changes to support 64bit.

Modify mirror objects so that references between them use an ObjectReference
value type rather than an Object* so that functionality to compress larger
references can be captured in the ObjectRefererence implementation.
ObjectReferences are 32bit and all other aspects of object layout remain as
they are currently.

Expand fields in objects holding pointers so they can hold 64bit pointers. Its
expected the size of these will come down by improving where we hold compiler
meta-data.
Stub out x86_64 architecture specific runtime implementation.
Modify OutputStream so that reads and writes are of unsigned quantities.
Make the use of portable or quick code more explicit.
Templatize AtomicInteger to support more than just int32_t as a type.
Add missing, and fix issues relating to, missing annotalysis information on the
mutator lock.
Refactor and share implementations for array copy between System and uses
elsewhere in the runtime.
Fix numerous 64bit build issues.

Change-Id: I1a5694c251a42c9eff71084dfdd4b51fff716822
diff --git a/runtime/thread.h b/runtime/thread.h
index 4a37ca0..b7f8bb0 100644
--- a/runtime/thread.h
+++ b/runtime/thread.h
@@ -487,23 +487,23 @@
                         ManagedStack::TopShadowFrameOffset());
   }
 
-  // Number of references allocated in JNI ShadowFrames on this thread
-  size_t NumJniShadowFrameReferences() const {
+  // Number of references allocated in JNI ShadowFrames on this thread.
+  size_t NumJniShadowFrameReferences() const SHARED_LOCKS_REQUIRED(Locks::mutator_lock_) {
     return managed_stack_.NumJniShadowFrameReferences();
   }
 
-  // Number of references in SIRTs on this thread
+  // Number of references in SIRTs on this thread.
   size_t NumSirtReferences();
 
-  // Number of references allocated in SIRTs & JNI shadow frames on this thread
-  size_t NumStackReferences() {
+  // Number of references allocated in SIRTs & JNI shadow frames on this thread.
+  size_t NumStackReferences() SHARED_LOCKS_REQUIRED(Locks::mutator_lock_) {
     return NumSirtReferences() + NumJniShadowFrameReferences();
   };
 
   // Is the given obj in this thread's stack indirect reference table?
   bool SirtContains(jobject obj) const;
 
-  void SirtVisitRoots(RootVisitor* visitor, void* arg);
+  void SirtVisitRoots(RootVisitor* visitor, void* arg) SHARED_LOCKS_REQUIRED(Locks::mutator_lock_);
 
   void PushSirt(StackIndirectReferenceTable* sirt) {
     sirt->SetLink(top_sirt_);
@@ -788,7 +788,7 @@
   // A positive value implies we're in a region where thread suspension isn't expected.
   uint32_t no_thread_suspension_;
 
-  // Cause for last suspension.
+  // If no_thread_suspension_ is > 0, what is causing that assertion.
   const char* last_no_thread_suspension_cause_;
 
   // Maximum number of checkpoint functions.