I am sorry to hear. I understand it may be something out of your control but it seems you have clearly identified some "smells" that would be worth spending some time investigating.

For example, you can't have loops in deps, and therefore ~250 deps should not print a 6500 thousand entries long tree. At least, for this particular problem, you can isolate your project structure, without any code, and try to reproduce it externally. And, while you can override deps, the goal of an umbrella is to share dependencies, so overriding an umbrella sibling dependency is a smell too.

You said it's an enormous Jenga tower that's risky to breath around but it seems at the same time no one wants to invest on an air purifier. If it is of any help, you can look at the Remote case on the Elixir website (https://elixir-lang.org/blog/2025/01/21/remote-elixir-case/), they have a large codebase, around 15k files, 300 engineers (several dozens being Elixir ones), and while their codebase is healthy, you can see they had to invest on some "bottlenecks" that appeared along the way, such as CI times. And the need to invest in the code base itself will be true of any language as time passes. Best of luck!