* pom.xml: Use profiles to build with and without dependencies for a faster iterating cycle.
* src/main/java/jgreg/internship/nii/AE/XMIWriter.java: Clean the content of the outputDirectory instead of deleting it.

This avoids race conditions in case we run the program simultaneously with the same outputDirectory.
* src/main/java/jgreg/internship/nii/WF/AnnotatorWF.java: Retrieve the parameters from a configuration file and from the command line.
* src/main/java/jgreg/internship/nii/WF/AnnotatorWF.java: Formating style
* src/main/java/jgreg/internship/nii/WF/AnnotatorWF.java: Do not clear the directory
* src/main/java/jgreg/internship/nii/WF/StatisticsWF.java (StatisticsWF): Make it callable from command line