Thank you Sikret for the information, I appreciate having this clarified.
Short Version: The issues are mostly conceptual and not technical, several of the HLAs may cause suboptimal targeting by IA's scripts. If you are worried you can skip any HLAs that grant some form of immunity. This shouldn't be game-breaking either way.
Long VersionOk, so you are talking about a conceptual incompatibility and not a technical incompatiblity. I was curious because I went out of my way when coding up the kit to make sure I used all of my own resources and in the case of existing spells made a copy and renamed it for the kit's use (so it will inherit whatever changes were made prior to installing the kit).
As far as the first point you list:
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Basically, if you have a kit which has access to duplicates of certain standard wizard or divine spells, the kit will be incompatible with IA (unless certain measurements are considered during creating those spells).
That part is already accounted for by the installation procedure. If IA makes any changes to the following existing standard wizard or divine spells
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Level 1
Cure Light Wounds, Detect Evil, Entangle, Shillelagh
Level 2
Barkskin, Charm Person or Mammal, Flame Blade, Goodberries, Resist Fire/Cold, Slow Poison
Level 3
Call Lightning, Hold Animal, Protection from Fire, Cure Medium Wounds, Cure Disease, Zone of Sweet Air, Summon Insects
Level 4
Animal Summoning I, Free Action, Neutralize Poison, Protection from Lightning, Call Woodland Beings, Poison
Level 5
Cure Serious Wounds, Animal Summoning II, Iron Skins, Pixie Dust, Insect Plague
Level 6
Cure Critical Wounds, Animal Summoning III, Conjure Animals, Conjure Fire Elemental, Fire Seeds, Dolorous Decay
Level 7
Heal, Conjure Earth Elemental, Sunray, Creeping Doom, Earthquake
Level 8
Nature's Beauty, Fire Storm, Regeneration
* Level 1: Sanctuary
* Level 2: Silence, 15' Radius
* Level 3: Remove Paralysis
* Level 4: Defensive Harmony
* Level 5: Chaotic Commands
* Level 6: Greater Command
* Level 7: Physical Mirror
* Level 8: Shield of the Archons
* Level 9: Raise Dead
Then if the Geomantic Sorcerer kit is installed after IA, IA's changes will be inherited. Install the Geomantic Sorcerer kit prior to IA and you'll have whatever version of the spells were there before.
For the second point
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Also, if your kit has innate abilities which casting/using them will grant certain immunities, those innate abilities will have to be made with certain considerations in mind to make the kit compatible with IA.
There will be conceptual incompatibilities. There shouldn't be any game-breaking issues (you cannot continue the game due to a bug), but there may be occasional targeting issues with the IA AI depending on how Sikret has accounted for checking what the player is and isn't immune to. I know that the SCSII AI seemed to target things intelligently and not have any major issues with these, and I've been told that the IA AI is as good or better than SCSII's AI. Like I've mentioned before, at the worst this might cause some suboptimal targeting in a few battles.
Specifically,
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Clarity (TIER 1 ABILITY)
With this ability, the geomantic sorcerer becomes immune to deafness, silence, miscast magic, feeblemind, and charm.
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Union of Magic (TIER 4 ABILITY)
Requires: Spell Casting Mastery
(Quintessence Magic)
School: Any School
Duration: Instantaneous
Casting Time: 6
Area of Effect: 60-foot radius
Saving Throw: None
This powerful spell sends out a 360 degree shockwave, causing everyone within its radius to become vulnerable to magic in all its forms, whether it be weaponry or spellcraft. All magical defense spells are eradicated, magical damage resistance is made nonexistent, magic resistance is lowered to nothing for 20 rounds, and all dispellable magics are removed.
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Immunity to Level 1 Spells (TIER 1 ABILITY)
This ability confers upon the geomantic sorcerer complete invulnerability to all level 1 spells.
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Arcane Futility (TIER 4 ABILITY)
Requires: Blessing of Nature
(Quintessence Magic)
School: Any School
Duration: 5 rounds
Casting Time: 1
Area of Effect: Self
Saving Throw: None
With this spell, the caster encases himself within a shell that prevents all magical energy from entering for a short time, regardless of its form. For 5 rounds, the caster gains complete immunity to magical damage, direct magical effects, and magical weaponry. In addition, it grants the player 100% magic resistance and immunity to timestop. Because of the power of the spell, all magical effects on the caster are dispelled upon casting, but for the duration of the spell the player is free to cast spells both within and outside of the shell.
QUOTE
Druid Immunities (TIER 1 ABILITY)
As a high level druid, you are immune to all forms of poison, disease, and level drain. Non-magical weapons have no effect upon you, and you cannot be forcefully put to sleep. In addition, you gain an additional 25% resistance to fire, electricity, cold, and acid.
Are the abilities/innates/immunities that may cause issues. All are HLAs. Sure, they may be somewhat overpowered on paper, but I typically find them to be less so in my games in actual practice due to how the game actually works. Of course IA would likely change the balance with respect to that.
So, if you are concerned about them unbalancing IA or causing suboptimal targeting for the scripts then you can avoid choosing them when leveling up.