New Deployment Strategy

Now that each of the three FLAGSHIP Miso projects implement JSDoc (and because
they implement a similar internal file structure), all of their API
documentation can be automatically generated from the source files themselves.
The documentation template itself lives in [a separate
repo](https://github.com/misoproject/miso-jsdoc-template), although I would be
open to including it here instead.

This changeset introduces two additional dependencies:

- GNU Make (for intelligent conditional building)
- Node.js (for JavaScript comment parsing via JSDoc)

In addition, it moves all source files to the `src/` directory and removes all
files that are generated programatically (this accounts for the vast majority
of the changeset). The `site/` directory is now blacklisted via the project's
top-level `.gitignore` file, simplifying the process of cleaning and
re-building the site.