There are definitely many trade-offs with using a circle pack layout - I snuck a bit of the reasoning into the collapsed section halfway through the write-up! Overall, this layout worked best for me, with the nesting feeling very natural and the circles feeling very "atomic".
But big picture, this write-up isn't tied to the current visualization! It's more focused on exploring _how_ a visual representation could help our understanding of codebases. There are tons of jumping off points, including different vizes!