Sub sub-folders not working in controllers

[eluser]adamp1[/eluser]
How is this a maintenance nightmare? I would have thought real life directory's would have a better naming convention. It seems mad not to use folders since folders are only for us humans, the computer doesn't need them.

Code:

/admin
    /server
      logs.php
      settings.php
      stats.php
    /users
      search.php
      manage.php

Or would this be better?

Code:

/admin
    logs.php
    settings.php
    stats.php
    search.php
    manage.php

I don't know about some people but the first puts each controller in its related folder, while the second is a total mess. What's the stats.php controller for? Users or the server (Well I can't tell straight away).

Yes I could put a prefix before each but that makes the file names and url more messy.

EDIT:
Really all that is needed is one extra level of sub folders. So max 2 deep, that would then let us to achive everything.