bunch prune is too aggressive

[tamird]

bunch prune seems not to handle sub-packages.

For instance, my project depends on github.com/cockroachdb/cockroach/util, but bunch prune only sees the top-level github.com/cockroachdb/cockroach, which is not used directly. bunch prune then removes github.com/cockroachdb/cockroach, which means I don't have github.com/cockroachdb/cockroach/util anymore, and that's Bad.

[dkulchenko]

Completely retooled the way bunch prune works in 404d8a4, this is now fixed.

[tamird]

Looks good, thanks!