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I've gone through The Art of Prolog, most of The Power of Prolog, and a good chunk of the P-99 problems, and I have to say I'm simultaneously fascinated by and sceptical of Prolog. For some problem domains, implicit search is a very desirable property, and I can definitely see Prolog shining in that case. There are also many desirable properties and possibilities that are often reiterated, but concrete examples of how they would work are often missing. It comes down to: how does "production Prolog" look? A talk on Strange Loop by Michael Hendricks on exactly that topic was really helpful (especially w.r.t. some useful tools and libraries: func and yall are really great, and I still need to check mavis), but it still leaves me wondering on a couple of things.
From a software engineering perspective, you may want to look into Logtalk. It answers several of your questions. For example, you ask "What tools make a larger codebase navigable and easier to work with?" Part of the answer is to use (automatically generated) diagrams that allow looking at the code from multiple abstraction levels, allowing navigating to both source code and its documentation. For example: