I believe the idea is that it makes it very explicit to track provenance of code between environments, eg merge staging->master is a branch merge operation. And all the changes are explicitly tracked in CI as a diff.
With directories you need to resort to diffing to spot any changes between files in folders.
That said there are some merge conflict scenarios that make it a little annoying to do in practice. The author doesn’t seem to mention this one, but if you have a workflow where hotfixes can get promoted from older versions (eg prod runs 1.0.0, staging is running 1.1.0, and you need to cut 1.0.1) then you can hit merge conflicts and the dream of a simple “click to release” workflow evaporates.
With directories you need to resort to diffing to spot any changes between files in folders.
That said there are some merge conflict scenarios that make it a little annoying to do in practice. The author doesn’t seem to mention this one, but if you have a workflow where hotfixes can get promoted from older versions (eg prod runs 1.0.0, staging is running 1.1.0, and you need to cut 1.0.1) then you can hit merge conflicts and the dream of a simple “click to release” workflow evaporates.