Change build and run instructions to use assemblies

This PR 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.

This is still a work in progress, but I'm putting it up for comments. It's not yet fully tested with Maven, and there's still a TODO to make Maven's examples build as an assembly. In addition, I'd like to make the examples assemblies not include spark-core and all its dependencies, by listing spark-core as "provided". This seems easy to do in Maven but tougher in SBT.