Add some missing mdev calls to JNI bindings.

The following functions were added:

- mdev_num_links_in
- mdev_num_links_out
- mdev_num_connections_in
- mdev_num_connections_out
- mdev_id
- mdev_start_queue
- mdev_send_queue

A rudimentary, non-functional TimeTag.java class has been added for
the last two functions, but needs work.
Include the other JNI-generated headers, and fix some detected function prototype problems.
Update documentation for msig_update() with regards to timetag value.
JNI: Add an initializer for TimeTag supporting sec/frac pair.
JNI: Add optional timetag support to Signal.update().
JNI: Add support for msig_value().

User must call Signal.value() with a valid array of the correct size,
and optionally a valid TimeTag object.  The function returns a boolean
indicating whether the signal has a value.
JNI: Add optional timetag argument to Signal.query_remotes().
JNI: Add Signal.set_rate() and Signal.rate().
Merge branch 'master' into jni

- Removes Signal.msig_get_rate() and replaces it with the signal
  properties interface.
JNI: Rename TimeTag.IMMEDIATE to TimeTag.NOW.
JNI: Keep a reference to a Signal object for each signal.

This is so that the Signal object can be passed to the InputListener
as an argument without creating a new one every time it is called.
Device.add_input() and add_output() are now completely native.
JNI: Provide a complete set of arguments to the input handler.

Still need to construct a valid TimeTag object however.
JNI: Remove obsolete msig_set_query_callback() stub.
JNI: Add Device.Signal.set_instance_event_callback().
JNI: Add Signal.set_callback().
JNI: Add several instances-related functions.

  - Device.Signal.start_new_instance
  - Device.Signal.release_instance
  - Device.Signal.num_active_instances
  - Device.Signal.num_reserved_instances
  - Device.Signal.active_instance_id
  - Device.Signal.set_instance_allocation_mode
JNI: Add Device.Signal.match_instances().
JNI: Fix TimeTag object reference in Device.Signal.release_instance().
JNI: Allow Device.Signal.release_instance() to be called with a default NOW timetag.
JNI: Add Device.Signal.update_instance() for all data types.

Note, as for Device.Signal.update(), we don't include `count'
parameter since it can be calculated from the array length and the
signal vector length.