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1. All of the proficiencies are being redone to use less abstraction. Instead of Basic Science and Advanced science representing broad studies, there are different tiers of the various sciences starting with "fundamentals" on the topic. For example, fundamentals of chemistry, moving into organic/inorganic chemistry, etc.
Proficiencies have a more distinct line between "knowledge" such as chemistry and physics, and "practice" such as chemical synthesis and electronic assembly. What this will mean in practice is that proficiencies that are knowledge based will mostly be used for research and will be "discovered" via pioneering, while proficiencies that are ability based (knowing how to do something) are used for recipes and construction and will be learned on-the-job.
Almost all requirements will change to "soft requirements." Meaning, instead of tailoring being required to make this shirt, it will instead be required to make this shirt well.
Broadly speaking, learning by doing will mean that if you're not fully qualified but have all of the prerequisites to learn the required proficiencies, you will be allowed to perform the task with some penalties - workspeed, quality, failure chance, etc. This will make most proficiencies more accessible by nature of a requirement providing the experience itself.
2. Medical will be removed from the base mod in the next release and added to a new module for those that are interested. The medical tree will be expanded to specific capabilties such as suturing simple, complex, or even internal wounds, different specializations of surgery, etc. This will allow for a more complex system of tending requirements, and will also allow pre-industrial factions a more interesting set of proficiencies. Tending requirements will come in tiers, with each tier representing a level of effectiveness + a set of penalties for being unqualified. For example, repairing a stab to the heart will require heart surgery as a proficiency to be most effective, but may fall back to internal suturing and suffer a penalty.
Similar to the changes mentioned above, all doctors can learn medical proficiencies by doing. The "tend all" config is replaced with a "treatment strategy" config. Strategies determine if a doctor will always try to perform the most effective treatment possible even if they are unqualified (used to learn proficiencies) or if they should fallback to the most effective treatment plan that they are fully qualified to perform. Both options will suffer penalties, but fallback penalties will usually involve long term health impacts and treatment speed penalties, while unqualified tending will usually involve increased risk to the operation.
3. More at the end
4. I'm not entirely sure what the purpose of the proposed XP type is. Practical XP is itself intended to represent "applied" experience, hence it is mostly used for "applied" proficiencies. It's not represented as well in 1.x as in 2.0, however, since 1.x proficiencies don't have a lot of distinction between practical and theoretical to begin with.
Regarding the reference to "separate tracks:" Most likely a large portion of XP generated will follow a "a little and a lot" approach going forward. If you're trying to perform a surgery for the first time, the attempt will generate a little theoretical experience, and lot of practical experience. If you are only learning about the surgery in class, you will get a little practical experience, and a lot of theoretical experience. It's not quite what you're suggesting here, but I think it should alleviate some of what you're describing here. Essentially, almost any form of learning should allow the full proficiency to be unlocked, but there will be more optimal ways to learn if the player has the resources. This will also allow for "pioneering" of certain proficiencies by bruteforcing them.
5. Research is one of the few types of patch that cannot generate XP at all at the moment. Requirements are purely strict. It's not something that can't change, but I think generating XP for non-lead researchers would be a pretty low priority if only because the nature of the XP generation is limited. It's not something I've put much thought into yet.
Now, some more general notes:
The first iteration of the mod was designed with certain requirements, mainly focused on reducing the work that would have to go into development. For example, we opted to use "more abstract" proficiencies as key milestones, with "less abstract" proficiencies as specializations. Broadly speaking, Basic Science is a near-industrial level elementary school understanding of "science" topics. Advanced science is a broad college-level understanding. Biology is a specialization that could be considered what an industrial-level biology research/scientist would understand. There are some big limitations with this approach, some of which you've already pointed out. The biggest issue is that by defining an abstraction of a broad subject, we have to "roll in" a lot of different subcategories. Basic science is broad understanding of chemistry, biology, geology, physics, etc. Because of that, they apply to a lot of restrictions. It also makes assignment to backstories difficult, because we run into this situation where in order for the tribal healer (with a +8 to medical skill!) to have "medical" it has to assume that they are on par with an industrial surgeon - and also that they have all of the prerequisite anatomy and biology lessons of a modern surgeon.
In general, this has made pre-industrial recipes, buildings, research topics, and backstories substantially less interesting. Or, to summarize, the mod was not necessarily developed with "accurately simulating historical progression of human knowledge" as a core requirement. If I had to use a one liner, I'd say something like "Believably simulate personal knowledge as a requirement to perform certain activities."
The concept of "soft requirements" wasn't even part of the initial design, and was only added later. Combine that with the relatively low amount of recipes in vanilla, and you run into a situation where we are struggling to find ways to learn a proficiency because there are only X number of recipes that could feasibly use it, and we need Y of them to teach it as well. Inverting requirements such that ALL requirements also teach the proficiency allows us greater flexibiltiy both in how we use proficiencies (as requirements) and what proficiencies we have. Smithing a knife can both require Metalworking (understanding the basics of shaping metal) as well as teach Bladesmithing as a specialization.
All that to say, basically, "I know." Most of these are pain points that are being addressed in the next release in one form or another. Some may even be made worse, but change is on the way.
I do appreciate thorough feedback like this. It makes me happy to know that people are thinking through the mod and its features so carefully. We're working towards making the mod both more complex as well as more accessible in future versions. If you don't mind joining the Discord (linked in the description,) I basically use it as a forum for gathering detailed feedback and as a sort of development blog. I do check steam as well, but it is not a platform with development or community management in mind, so I prioritize discord.