Sounds like you want a "traditional filesystem hierarchy" and like I said before, your request will fall on deaf ears. This is the same request that mercurial-dev gets from people switching from subversion: "I only want to check out a subdirectory, not the whole project!" to which the common response is, "You should rethink your 'project' if you only want a subdirectory." Take a look at subrepos and subpaths:

and maybe projrc:

For what it's worth, I never liked petsc-dev being in a different folder than petsc-3.x. It is not confusing to have them all like so:

petsc/petsc-3.1

petsc/petsc-dev