Possible fix for issues #380 and #372

After fighting with the debugger for two full days, I think I might have found the problem behind these two issues.
In de.unistuttgart.ims.coref.annotator.document.CoreferenceModel, when a new FeatureStructure (e.g. a Mention or Entity) is created, it is explicitly passed the respective org.apache.uima.jcas.JCas instance for the document:

protected Entity createEntity(String l) {
	Entity e = new Entity(documentModel.getJcas());
	e.setColor(colorMap.getNextColor().getRGB());
	e.setLabel(l);
	e.setFlags(new EmptyFSList<Flag>(documentModel.getJcas()));
	e.setMembers(new FSArray<Entity>(documentModel.getJcas(), 0));
	e.addToIndexes();
	return e;
}

See the call to documentModel.getJcas() above (which could be replaced by just getJCas(), but that's another issue). Later in that code, e.addToIndexes() is called, a method of org.apache.uima.cas.impl.FeatureStructureImplC:

/** add the corresponding FeatureStructure to all Cas indexes in the view where this FS was created*/
public void addToIndexes() {
	_casView.addFsToIndexes(this);
}

Here, the instance variable _casView seems to be the correct object reference. Adding the FeatureStructure to the indices works as expected. This is not the case for when e.g. a Mention (or Entity or anything else) is deleted, renamed, moved, whatever!

Here is an example: When deleting a Mention, the respective event is passed around and eventually this happens (m is the object reference to the Mention that is to be deleted):

m.removeFromIndexes();

In FeatureStructureImplC, this method acts just like the addToIndexes() we saw above: It assumes that the instance variable _casView of m holds the correct JCas reference. I am very far from understanding UIMA and its internal workings, but for me, this looks like it should work. But it doesn't. In fact, the _casView object used inside m.removeFromIndexes() is not the same as the one that's used when saving the project or exporting to CSV. I double-checked.

Now if we replace every call to addToIndexes() and removeFromIndexes() inside CoreferenceModel by addToIndexes(getJCas()) and removeFromIndexes(getJCas()), respectively (so we explicitly pass the JCas object used for the document), it all starts to work as intended:

• deleting mentions/entities, saving/exporting the project, reopening the project --> correct state!
• using the "Clear" or "Delete all entities" feature , reopening the project --> correct state!

Important question

Is there any case where a project/document uses multiple JCas instances? My solution assumes that the one returned by documentModel.getJcas() is the one true instance. I don't understand the project well enough, so that'd be important to check. If it's okay to just use this reference and pass it around, this PR solves those problems.

closes #380
closes #372