I find it annoying and surprising that "make clean" does not remove the PGO data.  If you change a source file, running "make clean" and "make" should result in a newly built executable, IMHO.  As it is now, you usually get a confusing build failure (PGO data is out of date).

The fix is fairly easy.  Make a new target that does what "clean" currently does.  Have the PGO build call that when it needs to preserve the PGO data.  Introduce a new "clean" target that does what the old clean did and also removes the PGO data.

Changing the build system is fraught with danger but I think this is a fairly safe change.  The current behavior is quite annoying, IMHO.