PackageManager: Store packages hierarchically, by version ...

As explained in the changelog, this hierarchy makes much more sense
than the current one, and will make it possible to read the version
from the directory name.

Add a "customCachePaths" configuration field. Fixes #838. ...

Allows defining additional paths that contain packages in sub folders with the pattern "(name)-(version)/(name)/" by defining a "customCachePaths" field in /etc/dub/settings.json or ~/.dub/settings.json.