It seems we have some tied in a knot here, so let me see if I can help.
First, Harmony 3 does not have a download per se, at least in the Harmony 2 sense. Instead it has a clone that is made from Github. To help you along, we added a utility to do this for you in MPLAB X plugin. The framework downloader is now part of MHC, and is a plugin to the environment. You can find the Harmony 3 MHC tools in recent versions of MPLAB X.
Second, you do not actually ever have to go to Github, unless you want to. While the framework repos of your choice (they are all separate now) will be cloned via the installer, this is relatively seamless to you. You can upload and check version numbers from the MPLAB X environment.
There is a guide to all of this, which you should find here
. The guide will help you through the install of MHC, clone of the framework, and your first project or an outline of one. There are also several "getting started guides" in the Wiki on github if you want to follow that path. Once you have downloaded, each repo has its own documentation
that will walk you through libraries, application examples and some architecture items.
We are always looking to make this better. If you have specific questions or suggestions, please do let us know. Sorry about your confusion so far.