Made some changes because there was a lot of problems getting it to work with Sublime 3 on my Windows machine.

Bug fixed where settings were being loaded too early. Now settings will only be loaded when they actual need to be.
Bug fixed with stdout and stderror where it would cause an infinite loop and crash Sublime.
Bug fixed while in debug mode and checking if command is enabled would crash the package.
Improved the output from shell to be a string vs byte string. Also made it filter out empty lines.

Let me know what you think, I am trying to setup a good workflow for Sublime, Vagrant & Windows.