We used to have a big project that had SonarQube analysis run on it for every pull-request on GitHub. Everything worked fine.

Then we did some refactoring, and split the code into separate projects. Since the code is related, the repo is still the same. But, instead of running just one build+analysis we run multiple ones per pull-request.

Everything else works fine, except that the SonarQube GitHub plugin writes the problems found in the first build, then removes them in the second build and so on. So I get an email about problems in the first build, but when I go and look at the PR in GitHub, it's all green and no messages anywhere.

Optimally I would like to specify to SonarQube GH plugin that these builds should be handled as separate in the PR, but I haven't found a way to do that yet.