http://paizo.com/threads/rzs2m2b8?Guidance-on-Paizo-Blog-on-Intelligent-Animals#18
"If an animal starts with an Int of 3 or higher, it's not an animal; it must be a magical beast or other creature type (as is the case with a 1st level wizard's familiar). If an animal advances to higher than 2 on its own, it doesn't change creature types. It's still an animal unless another effect changes its type (like being turned into a zombie or changing to a magical beast as a paladin's mount does at 11th level). So a semi-intelligent animal companion is still an animal, and thus falls within the set of creatures upon which Handle Animal is needed."
http://paizo.com/paizo/faq/v5748nruor1fq#v5748eaic9osa
"An animal with Intelligence of 3 or higher remains a creature of the animal type unless its type is specifically changed by another ability."
The Advanced Creature and Advanced Creature - Animal templates still contain wording to the effect of "INT bonuses should not be applied to animals, as increasing an animal's INT above 3 transforms it into a magical beast"
The method that HeroLab uses to determine the number of Tricks an Animal Companion may learn also needs to be updated to match this ruling. A 5HD Animal Companion with a 3 INT has 8 Tricks in HeroLab, but from the rules:
http://paizo.com/pathfinderRPG/prd/skills/handleAnimal.html#_handle-animal
"An animal with an Intelligence score of 1 can learn a maximum of three tricks, while an animal with an Intelligence score of 2 can learn a maximum of six tricks."
And;
http://paizo.com/paizo/faq/v5748nruor1fq#v5748eaic9osa
"An animal may learn 3 additional tricks per point of Intelligence above 2."
So a 5HD Druid/Ranger companion with INT of 3 should be able to learn 9 Tricks, plus the two "bonus" tricks for being a Companion (which don't count towards the limit of 9 the animal can be taught).
http://paizo.com/prd/classes/druid.html#animal-companions-184
"If an animal starts with an Int of 3 or higher, it's not an animal; it must be a magical beast or other creature type (as is the case with a 1st level wizard's familiar). If an animal advances to higher than 2 on its own, it doesn't change creature types. It's still an animal unless another effect changes its type (like being turned into a zombie or changing to a magical beast as a paladin's mount does at 11th level). So a semi-intelligent animal companion is still an animal, and thus falls within the set of creatures upon which Handle Animal is needed."
http://paizo.com/paizo/faq/v5748nruor1fq#v5748eaic9osa
"An animal with Intelligence of 3 or higher remains a creature of the animal type unless its type is specifically changed by another ability."
The Advanced Creature and Advanced Creature - Animal templates still contain wording to the effect of "INT bonuses should not be applied to animals, as increasing an animal's INT above 3 transforms it into a magical beast"
The method that HeroLab uses to determine the number of Tricks an Animal Companion may learn also needs to be updated to match this ruling. A 5HD Animal Companion with a 3 INT has 8 Tricks in HeroLab, but from the rules:
http://paizo.com/pathfinderRPG/prd/skills/handleAnimal.html#_handle-animal
"An animal with an Intelligence score of 1 can learn a maximum of three tricks, while an animal with an Intelligence score of 2 can learn a maximum of six tricks."
And;
http://paizo.com/paizo/faq/v5748nruor1fq#v5748eaic9osa
"An animal may learn 3 additional tricks per point of Intelligence above 2."
So a 5HD Druid/Ranger companion with INT of 3 should be able to learn 9 Tricks, plus the two "bonus" tricks for being a Companion (which don't count towards the limit of 9 the animal can be taught).
http://paizo.com/prd/classes/druid.html#animal-companions-184