Began Work on JSDoc 3.0+ Compatibility

Used the rhino debugger to find areas in publish.js that no longer
worked with the new TaffyDB API. Fixed all of those and commented out
some parts of the template. Now it 'runs' under the latest version of
JSDoc (3.2) however it does not generate anything. I broke something
along the way that someone with more experience needs to take a look at
:)