Add the ability to include empty directories to the zip format.

Per http://lemmasoft.renai.us/forums/viewtopic.php?f=32&t=2023
Add build.exclude_empty_directories variable.
Make loads after rollback non-greedy.

A greedy load after rollback can roll-back through with statements,
which are turned into with None statements until the start of the
next interaction. (Which is sensible behavior for the rollback
case, but fails when an after_load transition is scheduled.)

Fixes #95.