5.1 changes to fix serious nesting bug

This is a pretty large changeset, so I'll annotate here at the top after an explanation. During some integration testing at LinkedIn, we discovered that trying to "shim" a global variable using an AMD wrapper would be a clean way to support script tags (mixed environment) while beginning to roll out larger AMD support in the site. We discovered that when shimmed, globals were coming back as the empty object `{}` and debugging led to severe problems in `TreeDownloader`.

This refactor
* Replaces `TreeDownloader` with `TreeRunner` (a new file to signal the internal API has changed)
* Operates on the `module` object by reference whenever possible
* Removes unused library code and dead code paths from these refactors

And here's the file by file details (significant changes):
* **LICENSE** Removed no longer used library references, added new references
* **examples/** A new example that shows how to shim global variables AMD style
* **gruntfile.js** Removed no longer used library & file references, added new files & references
* **src/analyzer.js** No longer checks for empty files
* **src/communicator.js** Sets the contents to a new Error object on 404 errors (instead of flagging)
* **src/executor.js** Operates on references to the module instead of setting/unsetting properties all the time. New stack trace analysis powered by stacktrace.js (more performant for what we wanted)
* **src/treedownloader.js** Removed, replaced with `treerunner.js`
* **src/treerunner.js** Refactor of `treedownloader.js` designed to operate directly on the tree and manage the dependency execution and resolution process (formerly was in `RequireContext`
* **includes/common.js** Reduced lines of code by using references created by Executor