Fixes GRADLE-3150: Accept DOCTYPE declaration in pre-existing application descriptor

Groovy changed the behavior of `XmlParser` and `XmlSlurper` as of 2.0. In essence, a new constructor has been added that allows enabling or disabling support for `DOCTYPE` declarations. The problem, however, is that they made it so that the default constructor (which most of us were using) is set to not allowing it.

I added an integration test that reproduces the error and changed from the default constructor to the 3-arguments one, with enabled `DOCTYPE`, which reestablishes the pre-Groovy2 behavior.