Here is the link pointing to the source code of the graph >> clear() method:
https://github.com/DavidDurman/joint/blob/master/src/joint.dia.graph.js#L119. It actually does only a little, it removed all the cell models from the internal 'cells' collection. To understand this, I suggest to look at Backbone.Model and Backbone.Collection (
http://backbonejs.org/, JointJS uses Backbone internally). The batch:start and batch:stop events are not that important and don't affect anything. Those are used by Rappid plugins for batching up operations for, for example, later bulk undo/redo (in case of the CommandManager plugin).