Hello @hbigot ,
Thanks for the post, pretty exhaustive.
From the logs I suspect that there is something that you have not configured in terms of GitHub integration. Did you do the SonarQube server side configuration as described in GitHub Integration | SonarQube Docs (Setting up your GitHub App, and then importing your repository) ?
If you did, can you show me a screenshot of your GitHub integration in SonarQube (Menu Administration → ALM Integration → GitHub , and then click on “Check configuration”) like below
