...someone playing this thing first time around, they aint going to put this together.
And if your answer is tech blurbs mention this. There are boat loads of tech tree info on transformations. Can't expect to remember all of them...
A first-time player who cannot figure it out and
does not look at the (at most
two) Pedia articles that say some sort of pre-existing modification is required before installing a
specific cybernetic implant is doing it to themselves. No amount of extra explanation is going to help people who refuse to take a hint in the first place. ¯\_(ツ)_/¯
Commendations are applied last. Flat stat changes first. Bonuses before that.
Akshully...
There is no real order. What happens is this: there are basically two caps: the total stat cap and the training cap, which is usually but not always lower (basic agents and reactions, for example). You can no longer get stats from training when you hit the training cap, but combat gains and 'flat' bonuses from transformations work up to the total cap.
And then there are essentialy two types of bonuses to your basic, capped stat value: soldier bonuses, which come from commendations and transformations, and armour bonuses. Neither is really limited, they are independent of each other and the basic, capped stat value, so there is no particular order. The only thing that might lower your theoretical end value is having different commendations/transformations with the same exact bonus. Which I think only happens with the "Master of..." and "Bane of..." commendations right now. Having the exact same level of mastery in two or more weapons gives you the bonus for only one of them. However, different
levels of bonuses still stack.
So you essentially have three values that are added together, and it doesn't matter in which order. The only thing you can sorta game and that isn't 100% deterministic is getting your very last combat stat gain that goes over the cap. This is not reduced to the cap after the fact, and since it can range from 1 to 6, your agents can end up at 0-5 points beyond their nominal maximal stat value. Transformations that provide a 'fill-up' stop exactly at the cap, so are a bit less efficient than combat training.
You can see your total
bonus stats in the '+' menu when looking an agent's info screen back at the base, and pressing a trigger button.
The problem is that it's not entirely clear if I can apply transforms to eligible rookies immediately with no net loss of stat gains produced by them or not.
As long as you don't care about the potential 5-point extra gain from combat, yes. Do note that getting the full 5 points does require you to do some moderately intensive training in the field, and it only applies to 'primary' stats like firing/throwing/melee/psi.
On the flipside, 'flat' transformation boosts are not subject to diminishing gains, so are a quick way to 'top up' an agent.
...this requires me to actually send them out to missions like manors or something...
After some time, certain missions essentially become training missions where you can just let your troops blast away at the enemy and gain stats. Zombies after you get good shotguns and more than two guys in a car, and also many of the melee-only cryptids, for example. Manors and the like a certainly
not training missions.
But, as psavola said, this degree of gym training is really nor very efficient. It's better to combine it with field training by sending rookies out on milk runs. Unless you have
massive amounts of newbies in training, and just pull replacements from them, as I've seen some people do. Training 200 agents by hand is a real pain. :'(
...the agent will need to get wounded or panic a couple of times in missions to be able to progress.
Or use pepper spray on relatively harmless or unconscious enemies. Protip: you can stack snoozing baddies on top of each other for massive gains from AoE weapons. Surfboards have even better gains, but are more risky and you can't use sleeping enemies.
Low initial reactions are also really hard to train, so they make a good filtering candidate.
Pepper spray works for reactions, too.
And reactions is a stat that doesn't have a lower training cap.
Just let them run out of sanity.
Isn't sanity kinda slow to recover and lack of sanity a pain to deal with during actual missions? I definitely remember it being that way before.
Naturally this involves rushing Gun Kata...
I assume Psiclones are more plentiful now? I used to hoard them, since there are several things you need them for (Gun Kata x number of soldiers and Skulljacks, mainly) and Solarius was stingier with the rewards a while ago.
With TNI, we're getting 90 FA, the regular stat cap.
Veterans can also get TNI, probably other enhancements as well, and have commendations coming out of their ears, so they're usually still quite a bit better than that. But 90 is indeed passable enough for everyone who's not a sniper.
The greatest manors have 10 % chance to upgrade to hybrid embassies after 6 months.
Not only, depends on who owns the manor. Hybrid embassies are the most common, yes.
At this point of the game, most of your funding comes from the council and its gradual upgrades keep you afloat. The second main source of income are the money briefcases and money bags...
Selling some random stuff that accumulates can earn not totally irrelevant amounts of money, too. Alien communicators, dead zombie parasites, some corpses, secret files, etc.
It's definitely not irrelevant. The -3 and -5 are applied daily, so manors actually incur -90 for tier 1, -120 for tier 2, -150 for tier 3 monthly each.
This accumulates quickly if you have many of them, which is the case eventually. My last run died to essentially manor overrun, I had 11 by October 1998. They also produce many cult infiltration missions, which are just annoying to respond to because they are produced very often and yet have considerable ignore penalty as well (-150).
They're largely irrelevant as long as you manage to regularly prune the manors, and are generally doing well with score. But if it starts to spiral out of control, it can get pretty bad, as you say. I think there have been people with 20+ before.
15 bug manors at once
Bug manors? Are the antmen finally invading now?