Could you confirm that both the build and sonar-scanner run in the same environment, and that there is no form of containerization or sandboxing that applies to one without the other?
If you confirm that, I would need to take a closer look at the sonar-cfamily-reproducer.tar.xz file that is generated by the scanner after the analysis. The full path to this file is printed later in the same warning. It would be nice if you could also share the full path of the header file that was missed by the analyzer as it exists on your machine.
I am starting a private thread with you in case you would prefer to share this information privately.
For now, they are running inside the same container, but we would like to separate them in the pipeline, meaning pass the buildwrapper output to the next container, produce the autogenerated source files and then run the scanner. If that’s possible.