Refactor internals / use common resources dir for local store (#35)

* Reorganize the code a bit into a LocalStore to manage the downloads area
  and remove unneeded classes, put some misc. stuff into util package
* Organize local filesystem cache space into contexts directory and
  a common resources directory
* Handle the local path being specified in configuration as a URL (so
  long as it uses the file: scheme) or as an absolute file path
* Parse locations in the JSON as URLs rather than Strings
* Store local copies of definition files, using pretty-printed JSON
* Replace Timer with Stopwatch
* Update README and javadocs

Also refactor to move things out of the main class and the main class'
package that are internal implementation details and shouldn't be
public-facing API.