The `Tool` and `Repository` classes are pretty fundamental to the
product, but are a bit of a mess. Some upcoming work will be changing
these classes some, and it felt like a good time to make sure we had
properly brought this up to modern standards.

This change adds and rewrites documentation for these classes, making
types, exceptions, and behaviors a lot more clear. The classes and
methods can now be better understood when viewing the generated
documentation.

The next change in this series will rearrange some methods in the
`Repository` class in order to better keep the class organized going
forward.

Testing Done:
Built the docs. Checked to make sure there weren't any build errors
or broken links.

Reviewed at https://reviews.reviewboard.org/r/10768/