FS path changes arising from post-PR669 discussion with Josh

This is something of a mixed bag and requires https://github.com/openmicroscopy/bioformats/pull/374 to work. Major themes are:
- Josh's fix for adjusting permissions, enabling
  - change template path to have import set ID (actually timestamp) not at top level
- import through `ImportLibrary` fixes paths (so import from Windows to Unix is improved)
- the temp file manager is used by unit tests
- BioFormats is consulted on how many parent directories of a path to retain
- general cleanup of messy code.