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.

Built the docs. Checked to make sure there weren't any build errors

or broken links.