HORNETQ-1419 Server doesn't deploy JMS Objects

When starting a standalone server using 'bin/hornetq run' the server
starts up but the jms objects such as Connection Factories and
Destinations configured in hornetq-jms.xml don't get deployed.

The reason behind this is that the "Run" command (Run.java) starts
the JMSServerManagerImpl without passing in a default config file and
we no longer put the default config dir into the server classpath
with the new startup method.

The fix is add a <jms> entry into hornetq.xml pointing to the default
hornetq-jms.xml file and in the "Run" command we pass the config
(if it configured) to JMSServerManagerImpl so that it will deploys
all the JMS stuff during start up.
Merge pull request #1876 from gaohoward/master_HORNETQ-1419

HORNETQ-1419 Server doesn't deploy JMS Objects
amqp work rebased after andy