Fixed renaming nodes from xml file, removed lines in node constructor, changed how name is read from xml.

-> Fixed bug when renaming nodes that had arcs read from an pnml file.
  '-> Arc xml nodes were being deleted when renaming a node, so trying to update them was throwing an error.
-> Removed lines in node constructor
  '-> A couple of lines set defaults for _isRunningCondition and _isEffect, although they were already correctly set.
-> Changed how name is read from xml.
  '-> When reading a pnml file, place nodes' name might include whether it is a running condition or not.