Yes all of the above, plus the online documentation, which is marginally more up to date than the doc with the prog.
And there's some video's also.
http://pcgen.org/get-help/videos/
Here's the full step by step answer
Step 1
In the PCGen data folder, create a folder labeled mystuff in the Pathfinder Homebrew folder, you structure will look like this
\data\pathfinder\homebrew\mystuff
Step 2
Create a text file called "mystuff.pcc" in the step 1 folder
Step 3
Edit "mystuff.pcc" file with Notepad (or bbedit if mac) paste the following into it
CAMPAIGN:My stuff
GAMEMODE:Pathfinder
RANK:8
GENRE:Fantasy
BOOKTYPE:Homebrew
SETTING:My Homebrew Campaign
TYPE:Homebrew.PathfinderHomebrew
SOURCEDATE:2013-10
ABILITY:my_abilities.lst
Step 4
Create a text file called "my_abilities.lst" in the step 1 folder
Step 5
Edit "my_abilities.lst" file with Notepad (or bbedit if mac) paste the following into it
Pragmatic Activator
KEY:Pragmatic Activator ~ Trait
CATEGORY:Special Ability
TYPE:Trait.BasicTrait.MagicTrait
PREMULT:1,[PREABILITY:1,CATEGORY=Special Ability,Pragmatic Activator ~ Trait],[!PREABILITY:1,CATEGORY=Special Ability,TYPE.MagicTrait]
DESC:While some figure out how to use magical devices with stubborn resolve, your approach is more pragmatic. You may use your Intelligence modifier when making Use Magic Device checks instead of your Charisma modifier
BENEFIT:While some figure out how to use magical devices with stubborn resolve, your approach is more pragmatic. You may use your Intelligence modifier when making Use Magic Device checks instead of your Charisma modifier
BONUS:SKILL|Use Magic Device|max(CHA,INT)-CHA
Step 6
Load PCGen, you should see a "My Stuff" source on the left. Load that and create your character.
The latest stable version of PCGen (6.06.01) already has an implementation for Heirloom Weapon. You simply need to add the Adventurer's Armory (the source of the trait) to your Sources to make use of it. After you select Heirloom Weapon, another ability category is added to the Trait list, called Heirloom Weapon - you can select the specific benefit you want in here.
Best Answer
Disclaimer: There are probably multiple ways of defining abilities and templates in PCGen. The solution below is the one I implemented and tested.
First, define the Terror creature's special abilities. The ability descriptions below are based on the wording of the Terror Creature template. In PCGen definition syntax, each gets its own line. Also note the tab separation before each capitalized keyword - that is intentional.
I put these 3 lines in the default homebrew file
my_homebrew\my_abilities.lst.Second, define the template itself. Fortunately, Darkvision is already defined for us, as well as the alignment kit (1) that changes the alignment (rather than requiring a prerequisite alignment):
I put this line in the default homebrew file
my_homebrew\my_templates.lst.Finally, when you load your sources, include the source for your homebrew content. Then, when creating a new creature sheet, go to the Templates tab. Scroll down and select "Terror", then hit the "Add Template" button. And that's it! The changes should be visible on the Character Sheet tab.