As usual it took a mighty long time, but I finally managed to check in my changes and create a new snapshot.

Here is what's new:

• Support for @deprecated attribute in ikvmc. Compiled as System.ObsoleteAttribute (IsError = false).
• Support for declared exceptions. Reflection (Method.getExceptionTypes) will now return all declared exceptions that the method throws. C# (or VB.NET or whatever) code can use the OpenSystem.Java.ThrowsAttribute attribute to declare exceptions.
• Changed value type handling to treat null reference as default instance when unboxing (instead of throwing an unexpected NullPointerException). Added (experimental) support for customized boxing in map.xml.
• Remapped types can now have constant (non-blank static final) fields.
• java.lang.String and java.lang.Throwable now have the correct serialVersionUID.
• Fixed a bug (introduced with the ghost interfaces change) that caused virtual call to Object.clone() to fail with a CloneNotSupportedException.
• Changed static initializer support to use a special field (__<clinit>) in the base class to trigger the base class static initializer to run (instead of using RuntimeHelpers.RunClassConstructor). This should make static initialization a little faster.
• Changed "managed JNI" method lookup to support overloading.
• Made all introduced methods in ghost wrappers HideFromReflection.
• Re-enabled the warning for missing native methods on static compilation.
• Fixed reflection on .NET types to hide static methods on interfaces (Java doesn't allow them).
• Added dummy "native" methods for unused methods in java.lang.reflect.Proxy (to avoid warnings from ikvmc when compiling classpath.dll).
• Fixed InetAddress.getLocalHostname() method name typo.
• Added skeleton implementation of "native" methods for java.nio.channels.FileChannelImpl.
• Changed DupHelper in compiler to support "unitialized this" references.
• Changed compiler to emit ldc_i4_0 / conv_i8 instead of ldc_8 0 and various similar (small) optimizations.
• Added support for declaring exceptions on methods of remapped types and added appropriate declaration to map.xml.
• Added experimental remapping of gnu.classpath.RawData to System.IntPtr and custom boxing operator for gnu.classpath.RawData to box IntPtr.Zero to a null reference.
• Added support for ldnull and box opcodes to remapping instruction set.
• Added optional constant attribute to field element of remapping xml.
• Added ikvm\classpath\java\lang\ref\Reference.java (copied from GNU Classpath and modified to implement (most of) the required functionality).
• Added exclusion list to compilation of classpath.dll to remove unused classes (VMObject, VMString and VMThrowable).
• Fixed netexp to create classes for non-public base classes.
• Fixed netexp to export the interfaces a class implements.
• Fixed netexp to export declared exceptions.
• Some refactoring and a few small other changes.

I used Stuart's excellent japitools to test the remapping, reflection and round-tripping and found a lot of bugs this way. I ran japize on a  classpath.jar generated by netexp from classpath.dll. This way, the whole tool chain is tested (ikvmc -> reflection -> netexp).

Note that @deprecated doesn't round-trip, because Java reflection doesn't expose the fact that something is deprecated.

The full patch is here (excluding the new files, Reference.java and exclude.lst).

Updated binary and source snapshots are available.