Help on document directories structure

Hi,
I have a perplexity about the right organization of project documents.
If I have well understood, the document directories structure in ProjeQtOr is the same for every project!!!
If so, in which way can I better consider the unavoidable differences about project organization needs (for scope, dimension, tipology, number and kind of files, ecc.)?

I know the possibility to define my own directory structure (and I already did so in a previous release), but it remains the same for all the projects. So, if I add some new dir for a project, I see it also for all the other projects,
It would be great, instead, that when I chose the project in the selector, in the document window I filter also the directory structure of the selected project, in this way reducing the big confusion for showing folders not used by the selected project.
But I understand also that the ProjeQtOr User needn't too much of the document window and its folders structure, because he can view, filter and search the project files directly in the List window.

Just as I was doing these tests, I noticed a problem in my current setup of version 5.3.1!!!

Even if I have created and uploaded some document (ie, now id# is 3), in the List window I don't see anything.
And also when I try to change directly the "document directories", the List Window is empty.
But the strange thing is that the SW has not given me any mistake ever...

HELP!!!
Making some tests I have understood that sw DB has corrupted, because the real folder tree present on the Host is different from that recorded in the SW. And I don't know why!!!
In reality, the folder structure that shows the "Document Window" is the same of that on the Host, meanwhile this one is different from that the SW shows in the combo box of the field "parent directory" in the Description section when I try to create a new directory...
How can I fix the problem, without lose all the other data already in the DB?
Thanks

The difference lay be linked to project selected for directories.
You can select as a parent only directories wthout project of with same project as the current directory.

Sorry, but I haven't well understood your explanation. Can you explain more?

You can define the structure you want...
For instance :
Project 1
Directory 1 of Project 1
Directory 2 of Project 1
Project 2
Directory 1 of Project 2
Directory 2 of Project 2

The same as above. Can you explain more?

In any case, now I can't do anything because I don't see any item in the List Window, nor in the Detail Window...
What can I do to fix the problem?