Anymore, if you want to generate documentation, you're using Sandcastle along with, most likely, some community-generated wrapper for it so you're not manually executing the bajillion steps Sandcastle requires to get things done. (Wow, that didn't sound bitter at all.) I use Sandcastle Help File Builder for several projects and like it a lot.
When Sandcastle generates its reflection information (so it can properly resolve links in your docs), you need to tell it where it can find third-party dependencies so it can generate the information it needs. All of this has to happen on the command line (no, there's not...