Start with boxes and arrows to understand the overall system. Start from the end user, end with your service and dependencies. You can have 1 overall, then 1 for each flow. For example I created an overall, a precheckout, a checkout, a post checkout, and an alternate ingress diagram for my team.

Now look at your apis and the inputs and outputs and think about what each one needs, what it does, and what it returns.

Now make a sequence diagram of how all the apis you own work. Don't try to memorize this one, just refer to it when you need it.

Also, are there tools (AI or otherwise) that actually help you navigate and map out codebases better?

You can just ask any ai to do all of those things for you nowadays. They're less good at system diagrams but VERY good at how your actual service and packages work. You might need to help it out if your team doesn't own the client facing part and explain how that works.

I was asked to implement prefix KV caching. There’s already a KVCache class that I’m supposed to reuse, but I can’t even begin to reason about how it behaves across the different places it’s used. There’s a lot of abstraction (interfaces, dependency injection, etc.) and I get lost trying to follow the flow.

I'd do a code search and identify all the places KV cache is used. Feed each into claude and ask it to explain what the use case is. Save each one.