From what I understand (correct me if I'm wrong) is that your main window, the file is main.php.Tout builds within this view, other view files in the folder are pieces to be placed in the main window.
Right.
1 / I do not know if all actions are all the main.php or is every views that support his actions?
Actions are in the /tool : saveXxxx.php, deleteXxx.php, ...
2 / I read in a previous post what role each played folder and your architecture does not meet completely the MVC design pattern, which is why I want to know if you have some kind of pattern (such as drawings MVC existing on the internet) that shows how each of your parts to interract understand better now?
No, no specific pattern. Just "convention" rather than "description".
The MVC design pattern is not so far. The most difference is the definition of fields in the model that will help draw the screens.
(Because to me it looks like a reversed MVC without the C where all actions and commands are executed at views)
Not exactly. Each action can be considered as a controller. Some kind of MVC 1.
3 / Why did you choose Dojo?
Why not ?
Why not not using jQuery
Why not ?

(what are the advantages to face Dojo jQuery for this project?)?
What are your main use Dojo?
Dojo is almost everywhere : fields are dojo managed (automatic format control, auto extendable text area, calendar control, grid view for lists, tree wirdget, ...).
All the widgets in Dojo are the main reason why I choose Dojo. when I started Project'Or RIA, about 3 years ago, it was the most complete and reliable.
I hesitated between Dojo, JQuery and ExtJs.
I finaly choose Dojo because of powerfull Dojox.Grid : very reliable, and designed to display very long lists without having to set any pagination thanks to lazy loading. I just tried with 10.000 lines displayed : it's realy quick !!!
4/Je am not too comfortable with the persistence framework for php, what is its purpose?
Save and retreive Data to the Database...
All is in /model/persistence. Mostly in SqlElement.php (every persistant class extends this one).
5/Quels are your key files (not those who develop functionality but just those that establish the relationship between the parties for the proper functioning of your software as: projector.php and others that I do not necessarily know)? And what roles play?
Really most important are :
/tool/projector.php (loaded on every script, controling security)
/model/persistence/SqlElement.php : the core persistence class