As described here:
a Gnome Magus gets the following additional options for Favored Class bonus:
Gnome Add one of the following weapon special abilities to the list of weapon special abilities the magus may add to his weapon using his arcane pool: defending, ghost touch, merciful, mighty cleaving, vicious; allying, conductive, corrosive, corrosive burst, menacing. Once an ability has been selected with this reward, it cannot be changed.
This doesn't seem to be implemented at all. Create a gnome Magus character, add a Magus level, look at the list of Favored Class bonuses available, and note that "additional weapon abilities for arcane pool" aren't listed as options at all.
Is Advanced Race Guide in PCGen? I hadn't seen it when I loaded sources, but perhaps I missed it, or it's in the next version.
As to the pfsrd web site, my apologies. I thought it was run by Paizo, making it "official" and that they just happened to include 3rd party content (usually marked). It is a convenient way to link to the text under discussion. Do you have a preferred, official, online source of rules that is better to cite for PCGen discussions? I'll be happy to use that in the future.
Paizo's own rules website is called the PRD ("Pathfinder Reference Document") and is found at http://paizo.com/pathfinderRPG/prd/. However, it only includes the rules from the hardcovers of the Pathfinder RPG product line. The d20pfsrd.com site includes more books, such as all of Paizo's Golarion-specific books, as well as various 3rd party books. However, as they are a commercial site, they cannot use actual Golarion-based names and other intellectual properties of Paizo, so many of the Golarion-specific optioas are missing their context. Also, they tend to group rules together, as seen here with the favored class options, without correctly attributiung sources. It is peferctly fine to refer to that site, so there is no need to apologize, but one needs to be aware that it is not an official site and some things may not be perfectly clear or even be in error here or there.
The Advanced Race Guide is close to being finished and will soon be added to the sources included with PCGen.
Thanks for adding "Bonus Magus Special Ability" I can now select that for a favored class bonus in 6.01.07.
Is there any way to add a selector choice to it, for the specific weapon additional power, so that the chosen power can be specifically added in to the character sheet description under "Arcane Pool" (along with the basic augments), or at least as its own entry on the character sheet?
In other words, when I pick "Bonus Magus Special Ability" could you allow me to specify "ghost touch" and then that would be added to the list of abilities under the Arcane Pool on the character sheet?
Please open a new feature request, as that is a bit beyond the original tracker here.