Doc correction
Merge branch 'dev' of https://github.com/oaqa/bagpipes into dev
uimaFit 1.4.0 -> 2.0.0
Switched analysis engine creation to non-deprecated function
Merge branch 'dev' of https://github.com/oaqa/bagpipes into dev

Conflicts:
	pom.xml
	src/main/scala/edu/cmu/lti/oaqa/bagpipes/executor/uima/UimaAnnotator.scala
added some documentation and organized the code a bit. Still requires additional missing class documentation
added support for multiple inputs in collection reader, and also added a Root case class for the configuration tree to separate the collection reader descriptor from the annotators (i.e., a root node must contain a collection reader descriptor). Fixes issue #2