Incorporated Patrick's feedback comment on #211 and made maven build/dep-resolution atleast a bit faster.

* RDD, *RDDFunctions -> org.apache.spark.rdd
* Utils, ClosureCleaner, SizeEstimator -> org.apache.spark.util
* JavaSerializer, KryoSerializer -> org.apache.spark.serializer

This commit makes Spark invocation saner by using an assembly JAR to
find all of Spark's dependencies instead of adding all the JARs in
lib_managed. It also packages the examples into an assembly and uses
that as SPARK_EXAMPLES_JAR. Finally, it replaces the old "run" script
with two better-named scripts: "run-examples" for examples, and
"spark-class" for Spark internal classes (e.g. REPL, master, etc). This
is also designed to minimize the confusion people have in trying to use
"run" to run their own classes; it's not meant to do that, but now at
least if they look at it, they can modify run-examples to do a decent
job for them.

As part of this, Bagel's examples are also now properly moved to the
examples package instead of bagel.

superstep value upon recomputation, and set the default storage level in
Bagel to MEMORY_AND_DISK

Also rename parent project to spark-parent (otherwise it shows up as
"parent" in IntelliJ, which is very confusing).

to lack of memoization

See the discussion at https://github.com/mesos/spark/pull/355 for why
default profile activation is a problem.

by using -Dhadoop -Phadoop2.

This will make it easier to make the "run" script work with a Maven build