You've asked, I listened. You can now set up the tool NOT to configure Hammer for you. Some people wanted to enjoy the features of the tool, but wanted to configure the Map Editor by themselves. Now they can.
Also, I've noticed some binaries were missing in the last few updates. They have been added back in this minor update. If you have just downloaded the tool, and created a Mapbase Expanded, or Source SDK 2013 SP mod, some files may be missing. I suggest you copy the files manually, or recreate the mod.
In other news, Patreon now offers a free 7-day trial. This will allow newcomers to check out and try all the features the tool has to offer before subscribing. Just beware: once you start using it, there is no going back. I don't even know how to launch Hammer manually anymore.