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Yeah this is grim.
There is https://github.com/practicalli/clojure-deps-edn which solves this but it’s not linked to from any official docs which seems a miss to me. As well as the config and full documentation, it also comes with a video walking you through a demo of all the features.
Any large codebase can be broken up into small isolated components that can be reasoned about independently. This is how you structure Clojure projects if you want them to be maintainable. Clojure inherently encourages doing this by defaulting to immutability. The contract between components is the data being passed to the component and returned by it. Using Malli schemas at the edges of the components is a typical approach to documenting their APIs https://github.com/metosin/malli
I see the fact that people often end up creating large and tightly coupled monolithic codebases in static languages as a negative aspect of static typing. Such codebases are difficult to reason about even if you have guarantees that the types align. Ultimately, you need to understand the relationships in code, and how they relate to business logic. The more coupling an application has the harder it becomes to reason about it as a whole.
Ideally, I think applications should be structured as a bunch of Lego blocks that can be composed together. Each component should encapsulate some functionality, and then the flow of the business logic should bubble up to the top and expressed in how these components are chained together.