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.