Added the File Ids for serialization

Added a unique id to each file that ColorRule filters can point to so
that files aren't duplicated during serialization.
The same thing needs to be done for attributes.
Refactoring ColorRule

Refactored several files related to variables on ColorRule
+ Renamed the ColorRuleColorMenu to ColorRuleOptionsMenu since its
purpose is more broad than setting colors
+ Renamed ColorRuleMenu to ColorRuleFilterMenu since that is what the
functionality evolved into
+ Gave options variables a consistent naming scheme.
+ rule_type = filter_method
+ sizing_type = sizing_method
+ method = coloring_method
~ Moved existing static names for these variables into ColorRule from
ColorController, and added the ones that didn't exist.
~ Refactored the FilterMenu so to break up the OnGUI method.
Small ClusterController Refactor

Basically just changed group_id to cluster_id on node and updated the
relevant places it was used.