Move bin/run-tests-from-scracth to bin/dev
Refactor organize script into well labeled sections, bring the
configuration options to the top and make the -h usage() function
print a much more helpful explanation of how to use the script
and also how to customize via env var configuration options.
Adds variables for configuration-defaults to the very top of the
file which makes it easy to change them in the future.
Also "sbt/sbt test" -> "sbt/sbt clean test" to blow away old
Shark build remnants that might get in the way of a clean build.