Avoiding massive controller: where to put individual files

core is to extend or replace core libraries.
model is for your data model (database classes).
libraries is for your other classes.
helpers is for file containing functions.
third_party is for files from other project used by you application.

Perhaps you could be more specific? Like perhaps delineate where core libraries differ from non-core libraries? I've heard that model files may do more than just deal directly with a database. Do helpers contain ONLY functions? Might they not contain classes?