Are the feat parameters in protos.tab only for storing bonus feats? Or, are they also for intrinsic feats that are gained automatically upon level-up? I.e. does the game track the automatic feats separately and internally from bonus feats instead of listing them in protos.tab? What about skills/spells/whatever? Thanks.
Protos is for npc's, monsters, etc and is preset for the mod. It can be edited to some degree. It has no bearing/effect on pc's and does not change unless manually edited.
Not entirely sure what you're asking here ... any proto that is able to levelup is so done by the player, so the data is ad-hoc, stored in the charcter file (whatever it's called). Automatic feats like ranger abilities at levelup et al are I believe hardcoded - they are not listed in protos.tab as 'you will get this later' feats. Same with spells that are automatic, e.g. cleric spell availability. The spells lsited in protos.tab for any proto are the spells that that proto has memorized, not those which are available to it. Skill increases at levelup are I believe only applied by the player. Any skill listed for any given proto is a skill that that proto has in situ, not what it might attain later. When the game handled leveling for NPCs, there was a file that assigned levelup particulars according to each NPCs entry. It was very limited and didn't work well, though.