Cleanse-like refactorings

 * https://github.com/joshmoore/openmicroscopy/commit/e6e4ab1d5eb3325fdd1a79e8d2bd43b21eef14fe makes initial changes to require the directory to be passed (e.g. `...fixpyramids /OMERO`) and adds a `--dry-run` for testing.
 * https://github.com/joshmoore/openmicroscopy/commit/34bbbc6b2918f86bc66596ee2337bfb9e5b019eb uses `os.walk` to pick up subdirectories.

With these, I think that `fixpyramids` command is probably generally useful. Conversation on the balance between this and the OOM fix on your PR, @melissalinkert.