I agree we could do better in terms of re-structuring.
I also think “Modules” may be ok to have as a top level entity – although in reality these aren’t really pluggable “modules” as the name sometimes suggest to users. The idea was that in Bahmni Login Dashboard, one sees “modules” [Square Icons] and there needed to be a page dedicated to each icon at the top level.
Sub-system is too technical a jargon, and I would look recommend thinking of a more simpler scheme for naive users to be able to find.
BTW I also think that not everyone browses the WIKI using the left navigation, but instead use Google search to find documentation. But a more intuitive flow that allows for easier finding of appropriate pages will be welcomed.
You can make other changes @janux that you suggested to the wiki – besides the Module & Sub-System Changes. I feel good with those.