Folder structure after setting up file storage.

Why do you need to understand this, and what are you attempting to do. Generally it's not a good use of upstream time to explain the underpinnings of Phabricator unless you are another Phabricator developer.

What I would like to understand is why the directory for the local file storage is cluttered so fast with empty directories and especially why the empty folders are not removed.

In general, I prefer to keep directories as clean as possible.

You have basically two options:

1. Pay for upstream support under Consulting. With this we're happy to spend whatever time you need to more closely understand the underpinnings, security and storage models in Phabricator.

2. Examine the source code yourself (or via another 3rd party).

T9212 better explains why we're not able to handle very specific support needs (for free) on a day to day basis.

Thank you for your answer, this helps me understanding the issue better.