Yes. If you can't have that then it is a pretty crappy system. Sort of like IBM 360 where you only had a root directory with a truckload of files in it. In excusable in 2012 (or even 1972).

You're absolutely right. I mean, what's the point of even having files with code in them? I want to just draw my matrix block pattern in MS Paint and have this automatically be run in parallel. -or- Why can't I just clone petsc-dev/src/ts??? I don't want the whole goddamn source tree!