I can imagine it's just how they have the build process set up. As they are developing it the structure is set up in a way that makes it easy to develop and it goes through a shipping build process and they probably just didn't take the time to write the scripts organize everything when it's built.

Just thought of another possible cause.

On later versions of visual studio, in the solution explorer you have "filters" instead of directories.

In earlier versions you would create a new folder, then add items to it nad it would end up in a new folder on the hard drive.

In the newer versions, filters are not directories. I have had a lot of cases where I have added a bunch of stuff in what I thought was a directory only to realise it's only a filter and all the files are actually in the applications root directory.

This might have to do something with development version data files, when a programmer does a change to some dll and exe, plus some data files, and testers, or someone else needing current version, did not want to recopy redundant files, what is what they might have to do if they were asked by windows to replace a folder, and the operation of "replace file" is already marked and commited for always "perform". But for that one would rather make a smarter application, so I am still surprised with this.