This is a massive restructure to clean-up initialization

of bolt and its general api.

Importantly, this:
 - Converts internals of bolt to actual modules.
 - Lift ALL bolt implementation out of the global namepsace.
 - Only public api will be accessible.
 - Move public api from bolt.module.api to just bolt. This means
`bolt.require` and `bolt.define` are the qualified versions of the API.
 - Make bolt work out of the box on node.
 - Make the compiler a common js module that can just be pulled in.
 - Tidy up the hacky shit around the tests. A lot of it is tacked on
the outside when we rushed to get this done. Use a public API for
spinning up bolt in a more controlled fashion.
 - Consistency around naming. Prefer node to commonjs.
 - An actual api for test module.
 - Testing can work transparently on node and browser.
 - Add (conditional) karma scenario.
 - Use karma scenario for coverage.
 - Documentation notes.

Extra nice things.

 - There is now a scenario that runs karma to test the runtime. A
   side effect of this is that the scenario tests can provide a
   coverage report, see test/scenarios/karma/coverage after a run.
   Note that this only runs if you have karma set up, otherwise
   it just skips the test.
 - doc/api.markdown is a start at formalising the api for all the
   bits and pieces. It is a "where we are at", not really a "where
   we want to be". Longer term some of the apis will go away I
   hope.
 - doc/initialization.markdown is a description of the design used
   for this refactoring of the bolt start up process. It is not
   ideal, but it is in a lot better shape then when I started.

Fixes #26.

@marlimox For review. Good luck. There are probably a few sloppy bits left in there, I have attempted to tidy up as much as possible, but after 3 nights of this I need to tie it off, because I can't think about it clearly anymore. Yell at me where required. Also note that I have gone with bolt.runtime as top level namespace. I don't care that much, if you really want bolt.bolt I am ok with it. But you have to change it.