Cloud Tools for Eclipse supports existing Java App Engine applications, whether built with Eclipse, ant, Maven, gradle, or some other system.
First, if you're not already using Eclipse, import the project into Eclipse as you would any other Java application. For example, if you have a Maven project, use the File > Import... > Existing Maven Projects wizard.
Once the project is open in Eclipse, select it in the Package Explorer or Project Explorer. Then open the context menu and select Configure > Convert to App Engine Project.
Cloud Tools for Eclipse applies an App Engine Standard facet to the project so that it can recognize the project as an App Engine project, and all relevant menu items appear. If not already present, a WEB-INF folder containing web.xml and appengine-web.xml files is created. Finally Cloud Tools for Eclipse adds the Servlet API 2.5 and JSP API 2.1, the versions supported in the App Engine standard environment, to the project classpath.
If the existing project was formerly a Google Plugin for Eclipse (GPE) project, Cloud Tools for Eclipse also removes the legacy GPE facets. This conversion is one way. You will not be as easily able to convert the project back to a GPE project.