Buildship assigns a separate classpath to the project because the Java tooling in Eclipse breaks when the class file disappears (the clean task is executed). You can assign the build/classes/java/main class to the classspath in the eclipse.classpath.file.whenMerged block. You’ll find examples for that too: Buildship 1.0.18 is now available
I’d also add the compileJava task to the `` to the synchronization tasks to keep the IDE up-to-date.