No problem with this part, just thinking about StubDirectories. I suspect it will be worthwhile to go ahead and make 
the Stub*Directory classes more complete, but all in memory. (aka, have the stubs implement all the i/o related
bits (.list is done, but also .create/.clean/.delete)

Other note: certdirectory.Directory.listdirs() doesn't seem to be used anywhere, it can probably go away.