OOoUtils: fix `OOoBuilder.replace` creating duplicate entries in zipfile

This cleans up the API a bit:

• OOoBuilder.updateManifest is no longer a public API, OOoBuilder handles manifest by itself and it's not necessary to call this method.
• creating an OOoBuilder from an open file-like is no longer possible, it was not clear what the use case for this was.

Internally, this new implementation works by opening the zip file in the constructor and keeping the content of each file in a dict.