I uploaded the log that shows that I configured the github app as mentioned in the docs but the declarative checkout doesn't work, all other features work. I got it working by manually configuring GitSCM but it's a bad experience after doing so much setup work for the Github app. 

How I fixed it: 
options

{ skipDefaultCheckout true }

stages {
stage('Checkout') {
steps

{ checkout([ $class: 'GitSCM', branches: [[name: '*/main']], doGenerateSubmoduleConfigurations: false, extensions: [], submoduleCfg: [], userRemoteConfigs: [[ credentialsId: 'ssh-github', url: 'git@github.com:rootitnow/rootstrap.git' ]] ]) }

}