After discuss this functionality on IRC, here is what we thinks about :

* Right-click on a folder into "All files" module will display the contextmenu. In this menu, we will see 2 new entries : "Add folder" & "Add new file"

=> A click on "Add folder" will display a basic window allow him to put the name of this new folder. A button "valid" will add it locally & in pendingCommit.
On next commit, it will be added to the repository. We could delete it via the pendingCommit module, with the standard "Remove this change" entry.

=> A click on "Add new file" will display a complex window. In it, we could specify the name of the file and the default content for it. We could propose some default content, taken from /doc-base/RFC/skeletons folders for php project (the folder to search for skeletons will be an entry into the project config file to allow others projects to specify one). On "valid", a new file will be created locally, and an editor will be open with the default content chosen. If the user decide to close the window without save the file, the file will be remove locally. If the user decide to save the file, a new entry will be added into pendingCommit module and we can decide to remove it via the default option as suggested below.

Ok. This is what we have thinking about. Please, feel free to modify it, as I haven't start this development ! ;)

Sounds good. 

And the context window may want to ask for a few basic bits of information like 
"Function Name" because OE can then insert it where it's needed (it's used in 
several places, like for ids).

And somewhere we could mention scripts/docgen because it offers customization, 
and is especially useful when documenting an entire extension. People should be 
well aware of that, instead of adding every single file through OE.