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Why Generated Source Folders are not Added to the Classpath
Maven plugins used to generate source code from resources or other sources can register additional source folders to Maven project during the build. Usually such plugins are bound to process-resources (or process-test-resources) build phase (for example jaxb, modello or xdoclet plugins). This means that to get those source folders for generated sources, we have to run corresponding Maven build phase.
Not all projects using generated sources, so for performance reasons, M2Eclipse does not run any Maven goals by default on project import. This can be changed in the Maven settings in “Window / Preferences / Maven / Goals to run on project import” (e.g. you can specify “process-resources” build phase or specific plugins in that field).
Alternatively you can run “Maven / Update project configuration” action from the project popup menu, which is configured to run “process-resources” by default and it can be also changed on the same preference page.