Refactor documentation tree

[toddjonker]

As noted in #202, our (inherited) documentation layout is wonky, as it has the javadoc tree “inside” the Fusion module hierarchy, rather than as a sibling. This is largely because we want to render this index from Markdown using the magic fusion document command, and that currently requires everything to be under fusion/src alongside module code.

We should rework this so that the Fusion and Java references are sibling directories.

Getting this figured out well help us have stable URLs.