I started getting it in #4205 and now it fails also for the merged #4095 in master.

If you pushed to those branches multiple times, the subsequent builds used cached objects; CodeQL was not built to cope with those:

Since CodeQL observes the activity of the compiler to understand the data flows in a repository, CodeQL requires a complete build to take place in order to perform analysis.

https://docs.github.com/en/code-security/code-scanning/troubleshooting-code-scanning/no-source-code-seen-during-build

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