If the only issue is being able to get the BuildSystem revision associated with a pets-dev revision, How about adding a hook to BuildSystem that at each commit, writes the number of the revision into a file in the pets-dev repository and does a commit in the pets-dev repository? Then all that would be done is

cd $PETSC_DIR hg up -r <petsc revision> cd config/BuildSystem hg up -r `cat $PETSC_DIR/BuildSystemVersion.txt` Which I am sure can be done automatically with a hook.

It's not high tech, but it would work, right? Plus this could be done a posteriori for all past revisions of BuildSystem.

Actually, mercurial already implements this. They just call it 'subrepos'.