Fix tests and auto-inline plugins

This pull requests does several things:

- First, it removes the mechanism related to the out-of-tree BuildConfig.groovy. This was not a very popular option anyway.
- Second, it adds several out-of-tree configuration strategies based of repo/transmart-dev. If transmart-dev is checked out on `../transmart-dev`, then this is used to:
    - configure repositories;
    - configure internal dependencies;
    - inline internal dependencies.
  
  The names of the directories of the internal dependencies (plugins) match those used in the repo layout. See [this](https://wiki.transmartfoundation.org/display/TSMTGPL/Developing+tranSMART%3A+repositories%2C+versions%2C+and+inline+plugins) for more info about repo. It should also explain the way [`DependencyManagement`](https://github.com/thehyve/transmart-dev/blob/master/DependencyManagement.groovy) works, but I haven't gotten around to write that part.
- Third, it fixes the transmartApp tests.
- Fourth, it enables travis.