Using the sample code at http://erikpool.blogspot.com/2011/03/filtering-generated-entities-with.html I have altered this so that GenerateEntity and GenerateOptionSet to have the code:
return optionSetMetadata.Name.ToLowerInvariant().StartsWith("myprefix");
This generates the types including some enumerations for the optionsets. The actual implementation of the optionset in the entity doesn't use this however, but I get the following:
    [Microsoft.Xrm.Sdk.AttributeLogicalNameAttribute("myprefix_fieldname")]
    public Microsoft.Xrm.Sdk.OptionSetValue myprefix_FieldName
    {
        get
        {
            Microsoft.Xrm.Sdk.OptionSetValue optionSet = this.GetAttributeValue<Microsoft.Xrm.Sdk.OptionSetValue>("myprefix_fieldname");
            if ((optionSet != null))
            {
                return ((Microsoft.Xrm.Sdk.OptionSetValue)(System.Enum.ToObject(typeof(Microsoft.Xrm.Sdk.OptionSetValue), optionSet.Value)));
            }
            else
            {
                return null;
            }
        }
        set
        {
            this.OnPropertyChanging("myprefix_FieldName");
            if ((value == null))
            {
                this.SetAttributeValue("myprefix_fieldname", null);
            }
            else
            {
                this.SetAttributeValue("myprefix_fieldname", new Microsoft.Xrm.Sdk.OptionSetValue(((int)(value))));
            }
            this.OnPropertyChanged("myprefix_FieldName");
        }
    }
Obviously casting the OptionSetValue to an int in the setter does not compile, I assume that it should be generating the property with a type that matches the generated enum, but isn't. What do I need to do to correct this?