Ceej is right, and I realized it right after I posted. Git can't
version empty directories.  There is a long thread about it here, with
Linux weighing in.  http://kerneltrap.org/mailarchive/git/2007/7/17/251902.
I don't know if anything has been done in Git to change this behavior.

I'm not sure I would like to have the SVN (or BZR) repo
contain .gitignore files because that would imply it should also
have .whateverignore files for every other SCM that might hold web2py.

That would be a bad idea for a number of reasons, but the most
troubling would be that this would duplicate the "ignore" information
in a lot of places and would then be error prone and a pain to
maintain.

Of course one could put some file in each empty directory as a work-
around as Ceej suggests but that would only address the empty
directory problem and not the ignore problem.

Maybe there is a better way that kills two birds with one stone.  I
observe that the basic information about empty directories is in the
Makefile, as well as the info for which stuff should be ignored.
Maybe this could be generalized so one could have targets like
"gitconfig" that would create the required empty directories and also
put .gitignore files with the correct contents where they go.

Good or bad idea?
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