Restrict access to TopologyInstance constructor and compute() functions. Other public functions should also be changed to private or protected.

Create RoutingManager that is separate from TopologyManger. It hooks into TopologyManager via new ITopologyManagerBackend, butmakes it much more obvious that the TopologyManger and TopologyInstance is responsible for much of the routing. Before this change, the actual 'routing' and 'path-finding' implementation location wasn't very clear.

More REST API updates. Added JsonObjectWrapper class to wrap types that Jackson will serialize into arrays (illegal if outer type in JSON).

compute() has been optimized and all old code is gone. We no longer need to compute trees for each cluster. Furthermore, the computation of broadcast ports has been streamlined. Other routing/topology refactoring has been done as well.

Next round of refactoring. Attempting to normalize the terminology used. Fixed some bugs that have been around for a while too.

unit tests fixed by fixing an archipelago bug. A cluster is a *strongly connected* group of switches. A switch that is weakly connected to a cluster but not strongly connected to any other cluster will exist in its own cluster. This weak link, if not an external/BDDP-discovered link, will not be used to try and compute paths. Thus, while we compute clusters, any link that is not within a cluster and is not an external link is stored for reference when computing archipelagos. Essentially, the external links which typically are between clusters get merged into a new set with these weak links to allow for proper computation of archipelagos.

Changed ArrayList<> types to ImmutableList<> where applicable. OpenFlow messages are now cached in Forwarding.deleteFlowsByDescriptor().

Create wrapper class that takes an OFMessage and allows for direct use in other containers where we don't care about the XID of the message. For example, if we want to create a unit test with predictable results but the XIDs are different depending on unit test execution, we can use the wrapper class to guarantee consistency. In the main code, we can more easily compare OFMessages without care for the XID and create cool data structures like caches.

Put maximumRouteEntriesStored into floodlightdefault.properties. Topology manager and instance can now access it.

Added in the routecache. Similar to pathcache, routecache is computed by Yen's algorithm in the compute function. As the name implies, a routecache entry does not need to be built into a route, as it is already built. Future commits will involve replacing patchcache with the new routecache.

Transferred over all of the Yen's algorithm additions. This includes getRoutes(). Some additions may have been missed.

* Eliminated (new) warnings
* Fixed indentation
* Removed excess blank lines
* Improved some varable names
* Removed (unneeded) commented-out code
* Fixed up comments
* Added @Override annotations

ForwardingTest.testForwardDeleteFlowsByDescriptorMultiple() passed in Eclipse, but failed when run by "ant test".
Changed Forwarding.deleteFlowsByDescriptor() to use List<> instead of Set<> to simplify the unit test.
Tests now pass in every configuration I'm able to run them (eclipse single test, eclipse test class, eclipse all tests, ant all tests).

Also general code and comment cleanup.

Fix HA role REST API and add flag to allow us to toggle the controller's behavior when a transition to STANDBY occurs. For now, since we don't have much logic in other modules to handle STANDBY roles, we'll shutdown, but in the future, we should give the ability to stay running and await the next transition to ACTIVE.

Finally! Maven works a lot better. (1) create single jar with all dependencies. This is a much larger jar, but it is directly portable to another system... just use -cf and point to the floodlightdefault.properties file. (2) reduce unit test log verbosity... drastically. (3) include version and name in manifest for new version REST API. Note this also includes the web interface in the jar if the web interface submodule has been fetched prior to building the controller.