Write support for Manifest#created_by.
Return duplicate lists from Manifest.

This is so that the lists cannot be changed directly, only by accessor methods.
This is important because, for example, adding a file aggregate to the manifest
should ensure that the corresponding file is present in the bundle.
Add an edited flag to Manifest to detect changes.
Add Manifest write access methods to the File class.
Add File#add and File#add_aggregate.

Also adds write access to the manifest aggregates list.