Dependency conflicts

Hi,
Recently I've run into some Bundler dependency conflicts with Machined's libraries.
This pull request updates the dependencies slightly to make sure Bundler can activate the correct versions of the Gems.

The issues I've run into are:
* machined 1.0.2: thor ~> 0.15.4
* padrino-core 0.10.6: thor ~> 0.14.3

Bundler sometimes fails to resolve Tilt because padrino-core has a more restrictive version range than the other libraries:
* sinatra: tilt >= 1.3.3, ~> 1.3
* padrino-core 0.10.7: tilt ~> 1.3.0

This one is intermittent, if Sinatra's dependencies are resolved first then tilt 1.4.1 is activated which causes padrino-core to fail activation because it's expecting something in the ~> 1.3.0 range.
So I've added an explicit dependency on tilt~> 1.3.3 to make sure it gets activated early.

I also updated some of the tests which were failing on my machine - some of the directories were being enumerated out of order I think.