Vagrantfile changes, again

Inspired by #41.

Recently I build another Vagrant environment for Node.js application and learn a lot from that. So then I fix some Vagrant issue mentioned in the previous request and send this one :D. It is tested and works like a charm on my Mac.

Requires >= 1.6.0 by default, but 1.3.0 and newer should be fine by changing the `Vagrantfile`.

* Vagrantfile:
Use `:privilege => false` to bypass npm issues.
Use `:run => always` to always run on `vagrant up`

* README:
Update Vagrant section.

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Contribution agreement: I, Hsiao-Ting Yu, agree to release my work under CC0, with or without attribution.