Thanks for providing more insight on what remodeling mod support might look like from a developer's perspective. It really is a beast that requires careful thinking through several possible modes of approach (if it must be approached at all...!)
I currently use
Weathereye's Mod Loader for Windows to set the priority of my active mods and perform other simple mod management tasks.
This tool would surely be at risk of breaking if a major rewrite of game versus modding data should be undertaken, but the pain of its loss will be lessened if mod management were to be handled natively.
(The rest of this post is largely a testimonial about how I use the the mod loader.)
Graphic edits make up the bulk of my modlist in determining overwrite priority. Outside of my game directory, I maintain a spreadsheet that keeps track of which mod source should be overwriting what image file.
But once I have the modlist order sorted out, my method veers into micromanagement: whatever images not being used in my load order get moved to the mod's name-root folder to ensure these specific files never interact with truetile + truegfx subfolders. This step may seem redundant since overwrite priority is in place, but at least I can go browsing through fairly tidy subfolders.
One ardent wish I have on the graphics-side of modding is support for additional truetile variant indices. As much as I enjoy seeing the sprite artworks that members of the community were inspired to create for replacer mods, the impossibility of simultaneously using all these files feels unfortunate.
For instance, tree terrain tiles are limited to displaying 2-3 variants at most (including broadleaf trees in winter mode), but I would love to wander through woodlands populated with a mix of
Krutzel's Spirited Sprites having both its tall and standard-height trees alongside
kullervo's trees.
As for crafting, it's honestly a lot easier for me to dump a distribution of BAC (or other recipe-heavy mods) into a separate folder where it remains inactive but still available as reference material. With my active "BAC lite" folder, I'm at liberty to adapt excerpts from the parent mod and reorganize recipes according to my own idiosyncratic sense of order.
I give a similar treatment to new releases of URW: my Steam installation stays clean, previous versions are backed up in compressed folders, and the copy of my updated directory with the external mod loader will have as many or as few add-ons as I desire depending on which modlist is enabled.
In general, I consider mod-induced compatibility issues to be a natural consequence that players will inevitably struggle with. Building around the existing architecture is the furthest extent of what the majority of us are capable of; both the naive newcomer and the returning veteran will be in for a shock when they realize a particular modded setup happens to clash with the introduction of new standards in the metaphorical 'building regulations'.
I try to keep my own build flexible, but there's no pressure on me because I'm the primary beneficiary whom my modding endeavors are centred around. Brygun's passion for documenting and preserving the self-sufficiency tradition has an unfortunate side-effect of painting a target on his back since it's his username that people mainly associate with the modpack (and thus, there'll be someone available to blame when something goes wrong, however unfair that attitude is.)
Now, it certainly won't be detrimental for a person to learn how to read the modding syntax or do tests to figure out how to troubleshoot, but not everybody is equally motivated to invest in these skills 'just to play a game'. This subsection of players will definitely miss out on a lot of gems that are found in the game's primary source of documentation:
news.txtIt surely adds to one's enjoyment to find out how things work under the hood, but even without the external assets URW is super engaging on its own. (I personally spent 3 years completely ignorant of mods because reading forums seemed less interesting at the time...)
Streamlining mod integrations may sound nice in theory, but I'm worried that it will be a rocky road for a while before we reach a smooth grade. Rolling towards the destination might not feel worth the effort if the external tools I'm using now should cease to function before a replacement is ready - but a fear of future discomfort oughtn't impede me from enjoying what already exists in the present (especially since I exercised responsibility for preserving my current 'quality of life' through having a bunch of backups.)