The repository API defaults has a function, prepare_file, which is
responsible for creating a unique file to be used during the current
request.

This is usually used in the repository's get_file() function to store the
file before it is used elsewhere in the API to save the file to the
filestorage API.
It is also sometimes used to temporarily store credentials for the lifetime
of the session.

In all cases, this file is only expected to exist for the duration of the
session.

Switching to use of a per-request directory using make_request_directory()
ensures that the tempdir does not grow without control.

This commit also adds an upgrade step to remove all old temp directories
created by any repository currently installed.