Feature/refactor

Significant refactoring of the codebase.
Fixes issues #1 and #2. Addresses #3 in a roundabout way.

Usually I wouldn't lump so many commits together, but switching to a settings-based configuration proved to be rather involved.

* Added new default behavior to update markers on file save.
* Added new default behavior to run code coverage report on save. Addresses #3, but may be a stopgap.
* Settings files now utilized instead of hard coded values. Fixes #1.
* Settings may be overridden by a .sublime-project file. Fixes #1.
* Added menu option and keyboard shortcut to toggle off markers. Fixes #2.
* Added menu options for updating markers and generating coverage reports.
* Debug messages are now toggled on and off in settings.
* Debug messages are now handled by a common function.
* Only handles extensions defined in the settings file, .php only by default.