What are some best practices for organizing Rust projects – modules, files, and workspace structure?

This is a HUGE question, so I'll only touch on it. I'm also very aware that any answer I give will upset someone! So I'm going to focus on how I like to do things!

Put similar things together. Say you have a Widget repository (data storage of some type). Create a widget module. mod.rs (or widget.rs) is just the public interface with very little code in it. Inside the directory, I define the types and operations - and then offer a public API. That forces anyone using my widget module to use my accessor code; and now it doesn't matter how I've implemented it. I can even break it off into its own crate (replace mod.rs with lib.rs) later.

This applies at the next level up, so you typically end up with a data or repository section - containing the various data repositories.

If I have to then break that off into a separate service for some reason, I keep the API in lib.rs and move the logic to a main.rs (you can have both!) - and the lib.rs will handle calling the service. That keeps the cognitive load of breaking out into more and more services low.

So, traits. This is where the pitchforks come out. I personally almost never say "oh, my widget repo needs an abstract trait and should be instantiated in case I decide to build a mock or change database completely" when I start. You can do that, but you're adding quite a bit of cognitive load and ceremony to your task. And for me, the task is usually: make the darned thing work!

That's not to say you can't later insert a trait, basing the trait interface off of the functions you've discovered that you need - and use that to define a mock. I personally won't do that until I actually want one!