Figure out the story for onlySpecified in npm@3

[mgol]

npm 3 dedupes sub-dependencies by default which means node_modules contains many dependencies of dependencies directly, making the onlySpecified option to not work as it should.

We need to figure out what to do in such a case. Currently README contains a warning against using this option with npm@3. npm ls prints such info but it's very slow, way more than in npm@2 and one of the main goals of this module was to make this whole checking as fast as possible.

This option is still useful for bower so I don't think we want to depreciate it.

[treythomas123]

This would be nice to have. Basically a dry run of npm prune to see if there's any unnecessary packages hanging around.

[simlu]

I'd also very much love to have this option.