I have Eclipse and IntelliJ running side-by-side. I have installed and configured Google Cloud Tools on both of them.
IntelliJ gives me the options to deploy my application to Standard and Flexible App Engine environments. Instructions - https://cloud.google.com/tools/intellij/docs/deploy-flex
Eclipse, on the other hand, only allows me to build and deploy App engine apps to Standard App egnine environment. Instructions - https://cloud.google.com/eclipse/docs/deploying
Is there someway to build an App engine project in Eclipse and deploy it to Flexible App engine environment?