> Scattering the implementation in various files all over the source tree

If you treat the source tree seriously, you can communicate a lot with how it is structured

Well you can communicate organisation structure but not logic or intent. The directory is a tree and the Code is a graph.

You can communicate some information by looking at the org chart of a company but it does not really tell you much how it works.

Arguably a coding agent is less concerned about where the files are at then the code itself.