I think it's standard that nothing will be in the root of a WP installation besides WP itself. In fact, when I use XAMPP, I have multiple WP installs in the root of the htdocs folder, but nothing non-WP related within any of the installs.
However, I do agree that it's strange that this caused an issue. If you provide more information about what was in the "php" folder, we might be able to help prevent this in the future. As you might have noticed, the Edit Flow PHP classes are in a sub-folder of the main EF folder called simply "php", so I imagine the root cause was related to that conflict. But AFAIK, the search for the EF classes should only start at
wp-content/plugins/edit-flow/php/, so I'm surprised that something simply at
php/ would conflict.