You can import the standalone "my cool app3" to the App Projects section with the following command:
$ iectl publisher app upload project \
--applicationname "my cool app3" \
--versionnumber "1.0.0" \
--webaddress "www.webaddress.com" \
--changelogs "Change logs" \
--projectid "unique id of Project(on IEM) in which you want to import this application" \
--categoryid "unique id of Catagory(on IEM) to which you want to assign your application" \
NOTICE
Direct .app file upload is not possible to IEM app-project.