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.