I know this is way old, but I got here via a search. Stop an app by deleting the <project>-anchor.txt file in the <AnypointStudio path>\plugins\org.mule.tooling.server.<your server version>\mule\apps folder.

First, thanks for that.

Second did you manage to do this?

"you can enable the mule run time in preferences tab of anypoint studio.

That is easiest way to stop specific applications on anypoint studio"?