I am not sure if anyone has experienced this, but ever since I downloaded Gitbox from the Mac App Store and I click on "Clone in Mac" from github.com. It launches Gitbox instead of GitHub for Mac. Sure enough when I uninstall Gitbox, clicking on "Clone in Mac" launched GitHub for Mac. What could be causing this? How/where is the association being made and is there a way to change it?
Screenshots to refer to them in my comments to Marvin:


The reason the Gitbox app is launched when you click on the Clone in Mac link is because the Clone in Mac link (on GitHub) uses the
github-mac://URL type. In your case, the Gitbox app registered itself to handle thegithub-mac://URL type presumably because you installed it after you installed GitHub for Mac.You can verify the URL type that each application uses by opening their respective
Info.plistfiles and searching for theCFBundleURLTypeskey. The locations for both the.plistfiles are:Please note that the file paths may be off for Gitbox as I don't actually have it installed and thus can't verify. Also note that if you encounter either
.plistfile in binary format, use the following commands to convert them as needed:From binary to XML:
From XML to binary: