Updated: Change start and stop mechanism for DynamicMySqlEntity to work on Linux

**Update** This is code that should have been part of #915 - the code that was merged was incorrect

Conflicts:
	software/base/src/test/java/brooklyn/entity/software/mysql/DynamicToyMySqlEntityBuilder.java
Fix BrooklynNode.HTTPS_PORT typo

- was previously using same key name as http_port
Fix BrooklynNodeIntegrationTest.testUsesLocation
Merge pull request #919 from aledsage/fix/BrooklynNodeIntegrationTest

Tests now pass - http://brooklyn.builds.cloudsoftcorp.com/job/Brooklyn-Branch-Test-Integration/10/
Fix NPE when BrooklynLauncher given ManagementContext

- caused by brooklynProperties being null
Merge pull request #920 from aledsage/fix/BrooklynLauncher-supplying-ManagementContext

Fix NPE when BrooklynLauncher given ManagementContext
clear up naming of RMI_REGISTRY, and fix bugs in JmxRmiAgent where it was binding to wrong registry port, plus javadoc for JmxRmiAgent
improve shared JMX support done by JavaSoftwareProcessSshDriver, leaning on new JmxSupport:
uses an agent by default so works with public IP addresses

ActiveMQ entity updated with new tests (also ActiveMQ now supports multiple instances);
not all other entities updated yet, however
fixes to JMX tests, including updating many of the JMX-based entities and integration tests to work with the new mechanism;
note Karaf reverses the jmx/rmi settings to be clearer (also it fixes the tests so that it cleanly shuts down, and checks for that);
to permit clean shutdown when jmxagent is set and a java-based tool is used to do the shutdown, we need a environmentVariablesReset() on the ScriptHelper;
this also gives us a way to make sure e.g. JBoss _install_ is not blocked on database coming up
(previously it would block trying to resolve a DB url set in java system properties, at the first shell used, now that is deferred until launch)
more fixes for specific JMX entities, tidying up installation of agent and disconnecting feeds
check if hostname is longer than 64 chars and attempt to repair the hostname on localhost (mapping to 127.0.0.1) if so
make java installation retry once on errors (due to ubuntu sometimes not fully ready on boot in AWS... blech)
tweak logging and error handling, deprecation, and bump up  timeouts in test in response to intermittent jenkins test failure
always publish SUBNET_HOSTNAME if it is available (and different to HOSTNAME), with convenience in Machines to find the best hostname
update cassandra to use subnet hostnames when available, so tests pass in HP cloud