This one is more of a concern/question:
6.  When first creating a new module I noticed I was unable to deselect the "Shared" dependency.  Upon examination this dependency contains many of the D:OS system scripts you might want in a stand alone mod in the story editor.  So that's good.
But a huge problem I can see this being is what if you need to modify those story script files?  Because they are showing up as read only.
 
You can right-click these entries and select "Copy to my mod...". Afterwards you can edit these local copies.