Fix internal Links in Documentation

[MicahGale]

In #887 I noticed that a lot of the links in documentation to classes and functions are broken. This is probably my fault for changing namespaces and shifted around the API documentation. I'm just surprised this didn't show up in testing.

Tasks:

1. See if we can make this an error
2. Try auto-fixing everything.

[tjlaboss]

nitpicky mode might be what you're looking for