More specifically, where git mostly looks at code as a collection of files and differences in individual lines, codeq breaks it down into code as a collection of semantic units (function definitions for clojure, possibly class definitions, methods, etc. if other languages are supported). Your version control system would actually understand if a particular method had been moved from a subclass into a parent class, instead of just considering it as lines being deleted here and added elsewhere.
I don't think this is an alternative to another product. Instead I think it's something fairly new and interesting: they built a tool which takes your tokenized source code (presumably only in Clojure) and your git log and makes a queryable database out of it. So you could query "who changed my kill_puppies function last year" or other semi-structured things, as opposed to a combination of git blame + ack + ctags.
Like they said in the article, this would be the underpinnings of a larger system; something to manage code deployments, or an IDE, or a code review tool.
A smarter and faster version of git-bisect - given an anonymous function, when does the answer returned change working backwards through the codebase?
Or perhaps time warp integration - request a build of project foo but with library bar from the last tagged release version and function baz from a year ago.