I set up my Visual Studio Team Service account to clone my private GitHub repo and build the Windows UWP application anytime I queue a build. The cloning works without any issue
I solved this with the "secure files" feature: https://docs.microsoft.com/en-us/azure/devops/pipelines/library/secure-files?view=vsts
move %DOWNLOADSECUREFILE_SECUREFILEPATH% FolderOfMyProject
Now it behaves as though the certificate were checked in.