I suppose this is somewhat similar to your other question Sonar-scanner ignores input file generated by build-wrapper .
It may help to think that the files being analyzed are the intersection of what the build wrapper and the scanner find. This is especially useful for projects depending on external libraries: analyzing all the source files of the dependencies has a cost, takes time, and yet wouldn’t bring much value to your application.
Nonetheless, if you desire you can extend the set of files to be considered by the scanner by using the sonar.sources property. See its documentation:
I hope this helps.