What you describe is weird. If you have regular app with no portlet.xml
inside, GateIn Deployer should not touched and then they should work as
normal web app.
I would try to check if no portlet descriptor is forgotten on .war archives.
Also I would check to wrap .war archives into .ear archive in case some
isolation aspect can be involved.
GateIn 3.6.x is an old branch I would also check with newer one (master).
If you think is an issue feel free to open a JIRA about it to fix it in a
next iteration of the project.