The loop occurred when numEdges < numVertices. This commit fixes it by
allowing generateRandomEdges to generate a multigraph.

Conflicts:
	graphx/src/main/scala/org/apache/spark/graphx/Pregel.scala

Improvements in example code for the programming guide as well as adding serialization support for GraphImpl to address issues with failed closure capture.

The bug was due to a misunderstanding of the activeSetOpt parameter to
Graph.mapReduceTriplets. Passing EdgeDirection.Both causes
mapReduceTriplets to run only on edges with *both* vertices in the
active set. This commit adds EdgeDirection.Either, which causes
mapReduceTriplets to run on edges with *either* vertex in the active
set. This is what connected components needed.

`sbt/sbt doc` used to fail. This fixed it.

Improving documentation and identifying potential bug in CC calculation.

Moved DStream and PairDSream to org.apache.spark.streaming.dstream

Similar to the package location of `org.apache.spark.rdd.RDD`, `DStream` has been moved from `org.apache.spark.streaming.DStream` to `org.apache.spark.streaming.dstream.DStream`. I know that the package name is a little long, but I think its better to keep it consistent with Spark's structure.

Also fixed persistence of windowed DStream. The RDDs generated generated by windowed DStream are essentially unions of underlying RDDs, and persistent these union RDDs would store numerous copies of the underlying data. Instead setting the persistence level on the windowed DStream is made to set the persistence level of the underlying DStream.

Remove now un-needed hostPort option

I noticed this was logging some scary error messages in various places. After I looked into it, this is no longer really used. I removed the option and re-wrote the one remaining use case (it was unnecessary there anyways).