The Template tag ADDLEVEL tag is not being applied when the template is called from within a Race object.
1) Load Pathfinder Core Rules and Bestiary.
2) Create new character and apply any Ancient Dragon kit. -> An error pops up telling you there are not enough skill point/Feat slots available.
3) Abort kit. Note that the Summary tab show 4 Dragon HD.
4) Quit PCGen and edit pbf_templates_dragons.lst in the bestiary_core folder to make any Great Wyrm template VISIBLE:YES and save.
5) Relaunch PCGen and load the Pathfinder Core Rules and Bestiary
6) Create new character, select an alignment and add the the Great Wyrm race for which you modified the template. Note that Summary tab shows 4 Dragon HD.
7) Switch to the Template subtab and remove the Great Wyrm template and then reapply it. This may require the moving away from the Race/Template tab and then returning.
8) The Summary tab should now display a number of Dragon HD appropriate for the Great Wyrm desired.
I have verified this issue exist back to 5.17.3 but do not have any earlier dev versions to check. Note that 5.16.4 does not have this problem.
Confirmed with PFRPG black dragons of various ages. Weirdly I can see the class being added in the code but it doesn't seem to stick.
The issue is that the race assumes it is the only thing allocating monster classes. Thus as part of applying the race it erases the monster classes and readds those listed in the race. This does not work as the template has already been applied and thus its levels get removed/ignored.
I've added an interim fix. This adds the levels but they are in the wrong order and the total appears on the wrong line. I'll come back to this and sort out a more precise fix that gets the entries in the right order.
As of 5.17.9, it appears that everything except feats is working correctly. When addlevel is used in a template (from within a race object, at least), the number of feats is set to 1, regardless of how many hit dice the creature had, either before or after the template is applied. I'm assuming this is from STARTFEATS, rather than anything else. Dragons (any of them) are the easiest example to find of this.
We should get this resolved after the UI is put in place. Upping Priority.
Repots received that this has been fixed in trunk now.