The generated .classpath file contains an error if project.xml contains <build> <resources> <resource> <directory>${basedir}</directory> <includes> <include>plugin.jelly</include> <include>plugin.properties</include> <include>project.properties</include> <include>project.xml</include> </includes> </resource> </resources> </build> The classpathentry that should include the files contains a trailing pipe character in attribute 'including': <classpathentry excluding="" including="plugin.jelly|plugin.properties|project.properties|project.xml|" kind="src" path="."></classpathentry> That trailing pipe character confuses Eclipse 3.1. See Bug 105581 in Eclipse's Bugzilla: https://bugs.eclipse.org/bugs/show_bug.cgi?id=105581