Reorganize docs

The main TOC now only displays top-level subpackages. Each subpackage describes and links to its functions, classes, etc. and any subpackages within it. This makes the main TOC much shorter and allows our docs to reflect the correct directory structure of the code.

For example, we used to have `skbio.stats.distance`, `skbio.stats.ordination`, `skbio.stats.gradient`, etc. all listed in the main TOC, all at the same level. We now simply list `skbio.stats` from the main TOC, and `skbio.stats` has its own page with links to its subpackages (`distance`, `ordination`, `gradient`, etc.).

Fixes #566. @ebolyen can you please review?