While it is correct that the Google Plugin for Eclipse has been removed from Google's documentation, it is still available.
To install it, in Eclipse Neon, click "Install new Software" and add in this URL.
http://dl.google.com/eclipse/plugin/4.6
Next, click through the dialogues to allow the installation, and restart Eclipse.
While Google has chosen to stop supporting this, I personally feel that the new Cloud Tools for Eclipse plugin is just not ready. Also, in the early days, JDO was what many people were using on top of the data layer, and since GAE has been around for 10+ years, many of us have a lot of infrastructure built on top of this that is costly to change. While it's still possible, in theory, to run the DataNucleus enhancer manually, it's a huge pain that requires in-depth knowledge of the inner workings of GAE and DataNucleus and knowledge of which dependencies go together. It may have been well-documented in the past, but today it is not.
But be warned, one of our engineers recently lost the ability to deploy the project to Google App Engine using the GPE and was forced to use the gcloud tool, which doesn't seem to have sensible defaults, like deploying to a non-default version and instead will deploy straight to default, well, by default. So we're writing a script around that command that will pass in --no-promote
so it doesn't immediately start migrating traffic... Visit the gcloud reference for app deploy for more details. Good luck!
For more information on the install process, please see How to install Google Plugin for Eclipse on mkyong.com.