You know all of the transitive dependencies in the application stack of your company? Out of curiosity, what is the ballpark figure on the total number of transitive dependencies in your application?
I'm a few years out of the Java world these days, but you've vetted every line in every one of those Apache commons projects that gets pulled in? Because that's a lot of reading...
Over 10 years ago I went through every single Java RSS parsing library and all their forks (I think there were 5) to fix Xml eXternal Entity (XXE) attacks (eg[1]) and submitted fixes for them all.
That was a huge amount of work, because they all used random version of different XML parsers, all of which required external entity processing to be turned off in different ways.
None of the authors of the packages were aware of the issue, and as far I could determine at the time I was the only person in the entire Java ecosystem who knew all the different parsers arguments.
This was a critical, remotely exploitable vulnerability. I'd never claim to know about it now, and it was only for a few weeks back in 2006 that I really knew it then.
So when you say you "know" all the dependencies in your stack, what do you mean exactly?
So, the process would be something like: have a problem that a library might solve, find a library that could solve the problem, verify it can solve the problem, look through the implementation, look through it's dependencies, then actually include it in the build. If anything doesn't look nice at each step, rollback and find something else or start writing your own implementation.
Do this from beginning of the project and you'll always have a full understanding of the system.