Preserve dependencies when uninstalling from the CLI

Previously, the CLI did not keep track of a dependency's users. This
meant that installing two extensions with a common dependency and
then unistalling one extension would break the other extension as the
common dependency would be deleted:

 1. Install a that depends on c
 2. Install b that depends on c
 3. Uninstall b
 4. a is now broken as c has been deleted

This commit updates the CLI to maintain a count for each artifact
that's installed into /lib. An artifact is now only deleted when the
count reaches zero.

As part of this change the code has been
extensively refactored to bring the structure into line with other CLI
commands and to improve testability.

Closes gh-1410