Suppose I'm playing a character with Craft as a class skill. I put 1 rank in it, select Weaponsmith to fit my background and end up with Craft (Weapons) +4. Now, if I later decide I want to be able to make bows and arrows, do I also get another +3 bonus on Craft (Bows) when I invest a new rank? There are different kinds of craft, just like there are different kinds of knowledge, but the class skill bonus for craft is completely unspecified.
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Craft is actually a number of separate skills. So if you have the class bonus for craft you have it for all the skills in the craft "family".
If you only had 1 rank in weapons and not another in bows, it only affects that specific craft skill. If you are spending 2 ranks in them, 1 in both, then they are both receiving the bonus for being a class skill.