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By looking into the inner workings of PCGen, I have manage to cobble something together that seems to do the trick. However, this answer is in no way comprehensive, but meant to serve as a guide on how to patch your own homebrew stuff. For more information about working with Homebrew files, I suggest looking into the documentation (Help -> Documentation, F1), under the "List Files" heading (Sadly, I cannot link to specific pages of the documentation here).

Open up [PCGen]/data/pathfinder/homebrew/my_homebrew. This is the pre-installed Homebrew Campaign Thingy, which will do just fine for this purpose.

Traits are internally handled as "abilities". Using a good text editor (Notepad++ or similar), open up my_abilities.lst. Under #insert your data here, add the following line

Homebrew Trait      KEY:Trait ~ Homebrew Trait      CATEGORY:Special Ability    TYPE:Trait.BasicTrait.CombatTrait   PREMULT:1,[PREABILITY:1,CATEGORY=Special Ability,Trait ~ Homebrew Trait],[!PREABILITY:1,CATEGORY=Special Ability,TYPE.CombatTrait]      DESC:You have studied the workings of PCGen and managed to claw your way into creating a homebrew trait|PRERULE:1,DisplayFullAbility        NATURALATTACKS:Claw,Natural.Weapon.Melee.Finesseable.Piercing,*2,1d4


Let's look at this line more nicely formatted:

Homebrew Trait
KEY:Trait ~ Homebrew Trait
CATEGORY:Special Ability
TYPE:Trait.BasicTrait.CombatTrait
PREMULT:1,[PREABILITY:1,CATEGORY=Special Ability,Trait ~ Homebrew Trait],[!PREABILITY:1,CATEGORY=Special Ability,TYPE.CombatTrait]
DESC:You have studied the workings of PCGen and managed to claw your way into creating a homebrew trait.|PRERULE:1,DisplayFullAbility
NATURALATTACKS:Claw,Natural.Weapon.Melee.Finesseable.Piercing,*2,1d4

1. It starts off with the name of the ability, "Homebrew Trait"
2. Next up is the KEY keyword, followed by the internal name of the trait, allowing you to use this trait in other homebrew things, as a prerequisite for a feat, for example. I followed the naming convention I found in other *abilities.lst files.
3. The CATEGORY tag is there to list this under Special Abilities, nothing much to say here.
4. The TYPE tag is more involved. This is a dot-separated list of subcategories this Special Ability falls under. In this case, we have a trait which is a basic trait, and which is a combat trait. You can change the latter to what you like, but you'll have to change the prerequisites as well.
5. The line starting with PRExxx denotes prerequisites. PREMULT:1 states that only one of the following prerequisites need to be fulfilled. The prerequisites are given in square brackets.
• PREABILITY:1,CATEGORY=Special Ability,Trait ~ Homebrew Trait means that you qualify for this trait when you have this trait. In particular, it means 1 prerequisite ability from the Special Ability category, which is "Trait ~ Homebrew Trait". This is needed because of the second prerequisite.
• !PREABILITY:1,CATEGORY=Special Ability,TYPE.CombatTrait means "Not 1 Special Ability pf the CombatTrait type, as per the trait rules. Without the first prerequisite, this would make the trait disallow itself.
6. DESC is followed by the full description of the trait. Not sure what the PRERULE part does, just keep it there.
7. Finally, NATURALATTACKS adds the crunch. I copied this part from a Tiefling Alternate Racial Trait. It adds an attack called "Claw", lists the applicable types (see above), makes it 2 attacks, and sets the damage to 1d4.

Once you have written up your ability to your liking, save the file and open up PCGen. Go To Sources -> Select Sources (CtrlL), and go to the Advanced tab. In the dropdown list at the top, select Pathfinder RPG as your Game. On the right side, you should now see "Pathfinder RPG for Players", as well as "My Pathfinder Campaign". Click on Load. Your homebrew trait should now be available to choose from the list of traits.