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.
Yes, the wording does mean that a cleric of the Light Domain gains 'Fireball' as part of the Cleric Spell List; and here's why the wording is different. I hope the following helps explain why
"The following spells are added to the warlock spell list for you," which shows that Fiend patron warlocks have Fireball in their spell lists, and so should be able to use Spell Scrolls of fireball.
The above Warlock phrasing, just as it's phrased for Wizards and other spell casting classes that gain extra spells through means of specialization, is phrased that way because each of those classes have a spell list that they must choose spells from as they level up. They do not inherently know all spells available to a Warlock. So the phrasing in this case means the fireball spell is added to the list of spells he can POTENTIALLY add to his 'Spells Known' list. For intents and purposes, those are now on his Warlock Spell List
Now enter Cleric, and the Paladin; which have very different methods of spell learning.
If you have a domain spell that doesn't appear on the cleric spell list, the spell is nonetheless a cleric spell for you."
It must phrase it like this because Clerics and Paladins do not have to choose what spells they learn as they level. Clerics and Paladins inherently have the knowledge of every spell on their list....because we're awesome like that....and can prepare spells as needed in between long rests. If I wanted to go with cure wounds one day and then give up cure wounds to take Inflict Wounds after a long rest? I can do that freely. I have direct access to every spell available to Clerics. So when I choose Light Domain and it says the Fireball spell that isn't on my class list nonetheless becomes a cleric spell? It's now part of my knowledge of cleric spells (On my list of spells), and thus able to be utilized in scroll form since I now have the knowledge of how 'Fireball' works magically.
The only reason it doesn't say these spells are added to your spell list for you, is because it wouldn't matter in a Cleric or Paladin's case. Any spell that's on our spell list is a spell we can cast should we choose to. Any spell that's on a Warlock/Wizard/Sorcerer spell list, is a spell they can cast only if they chose it from their spell list when gaining levels.
Best Answer
Non-SRD content needs to be added manually
I can't really prove this as a lot of the information found on the FAQ and pcgen website is outdated. However, it is clear that they only provide SRD content for 5e. A few examples of this idea from their FAQ/Page:
From The FAQ:
Clearly the fact that they are still referring to the future release of 5e this is very old but I would guess the situation of only being allowed to release SRD content is unlikely to have changed. You can also check their page on Publishers and Source Information but again, the information is probably quite outdated (5e is never mentioned).
Regardless, your best bet to include the source materials that you want is probably to add them yourself:
Adding content manually
Adding content to pcgen can be a lot of work. I suggest you take a look at the numerous tutorials and videos you can find online and even their discord channel1 for advanced help on how to to this. This is a complex enough matter that I think a full explanation of all the features of PCGen needed to master adding is a bit beyond the scope of what I can provide here.
I did fiddle with some Pathfinder content before (minor fixes to abilities mostly) so I thought I'd give this adding domains for 5e thing a try. Here is what I have learned (mostly from online searches and experimenting):
First, in order to not mess with the base SRD content, you probably want to create a separate folder for your content which we will call "homebrew". In your pcgen installation folder, you should be able to find a "data" folder that includes a "5e" folder. I'm using windows so this is what the path is for me:
You can find a "wizards_of_the_coast" folder which contains all the information from the SRD (hint: use what you find here to both understand the syntax of things and/or copy content to be changed). We are going to ignore that for now and create our own "homebrew\my_homebrew" folders:
Inside this, we create a file called "_my_campaign.pcc". Files with the .pcc extension are what pcgen uses to know what content to load. This is the main file that is going to list the files with content that you will want to load. The contents of this file should be (note that anything that comes after a # is a comment, text that is ignored by the program and that I am using to explain some things):
Next, we create the file with the actual content that you want to add in the same folder. Because the life domain that is already included in the SRD content can be found in a "srd5_abilities_class.lst" file, for organizational purposes it is probably a good idea to keep the names similar so I chose "homebrew_abilities_class.lst" (.lst files contain the actual classes/abilities, etc to be loaded). The contents of this file are:
Now as you can probably all I did was change some ability names and descriptions. A couple of note on what I learned in the process of fiddling with this:
After you have saved everything and have both these files:
You need to restart pcgen for it to load these. If everything works as expected, when loading advanced 5e sources you should now see the following, which allows you to include your homebrew along with the SRD content:
Then, when creating a cleric character, the Test Domain will show up as an option and add the associated abilities to the character:
The domain will now also add all the abilities it references, domain spells, etc (as set in the .lst file)
Conclusion
I have to say, this is a lot of work. One of the biggest issues I found is scrolling around to see all the content in the .lst files while trying to understand how they work. If one is to make a serious attempt at adding a large amount of content to pcgen I strongly recommend getting some sort of editor program appropriate to .lst files, which you can probably ask about in the discord group (at least something better than the notepad++ I used for this).
I know this isn't all that much but do I hope it at least helps you go in the right direction or at least gives you an idea on the kind of work involved in adding things to pcgen, and whether you find it worth it to invest some time into it (so you have an idea, between searching and experimenting, this probably took me around 4 hours to accomplish, I imagine it'd be faster moving forward, half of it was spent on figuring out the .pcc file). Good luck!
1.Taken from Theik's comment