Seems to have problems with npm linked dependencies

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If I have in my my code say `require("immutable")` and in an `npm link`ed module elsewhere on my system the same require code it gets treated as two different libraries when factored and doesn't end up in the common bundle.

It's odd, and it works fine when not using `npm link`. I can only assume it's something to do with the paths of those files being quite different (ie, when linked it's not in the normal dep tree of the core code).

Frustrating though, especially when dealing with applications that are developed locally with private modules as abstracted parts of the core app. It very much bloats the code.

Start by reproducing the require("immutable") case with an npm-linked module and compare it with the non-linked dependency tree. Trace how factor-bundle identifies shared modules when their paths differ; done means the linked and local copies are recognized as one dependency and placed in the common bundle.

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