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Taken from this comment:
Before I start, let me express that I am grateful this extension was done in the first place. It is something needed and I hope it is added to the core as it will accelerate the development proccess. That being said..
I have a behavior that is called categorizable. Basically I add the behavior to any model that I want to be able to receive categories. In the behavior, I add the relationship with categories through the metaData of the Active Record.
This extension takes the relations from the Active Record from the relations() method which is an array containing a configuration. However, this configuration does not refresh when the metadata of relations is updated.
Therefore this plugin does not work if you add a relationship via the metadata of the active record.
There are two possible solutions for this.
Fix for issue #36
This fix adds ability to deal with relations defined in metadata of ActiveRecord