Before this fix, attempting to set a non top level environment
variable would fail with "Couldn't find flag".
This fixes it by passing in the flags that the env var is being set
from.
Fixes#3615
The purpose of this is to make it easier to maintain and eventually to
allow the rclone backends to be re-used in other projects without
having to use the rclone configuration system.
The new code layout is documented in CONTRIBUTING.