Ensure `packages.zip` is cleaned up properly

* Previously, it wasn't being deleted, so files were only being added or
  updated, never removed
* Also, enable using non-zipped "packages" directory for experimenting
  with deployment efficiency (e.g., appcfg.py will precompile Python,
  but probably not inside zip files.)
Merge pull request #1285 from reciprocity/feature/deployment-fixes

Ensure `packages.zip` is cleaned up properly