Recently set up a multi module project in IntelliJ with the following structure:
/module1
/module2
/web-module
/sql
/lib
/a few more folders
I set up module1+2 and web-module as modules in IntelliJ so those show up, but how do you make the sql and lib folder show up in the project panel? They should be included in VCS as well, but IntelliJ ignores them. How do you add folders outside modules to a project?
Screenshot of project and explorer view:

In Project view mode all directories (except the ignored ones from the settings) should show up. Of course the base folder for your multi-project has to be the folder above module1.
EDIT:
Your project should look like this (project view tree):
And in this case, you should definitely see the other folders. I got a sample project set up where this is working.
EDIT 2:
From your screenshot, I assume you are missing the root directory (the project root is not as you expected). I added another screenshot. There should be a single root folder for your 3 modules. This one is missing at your screenshot. You have 3 separate folders with no common root folder. On MacOs, the project root is displayed in the window title. In my case it points to
~/devel/sandbox.I guess you should try to create a new project in for that
trunkfolder. From the scratch. Then add the existing modules and you should be fine?!