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