I had some trouble with this as well. In order to build successfully, I had to include more Eclipse plugin directories. In my installation, Eclipse Indigo has at least 3 "plugins" directories: /usr/lib/eclipse/plugins; /usr/lib/eclipse/dropins/jdt/plugins; /usr/lib/eclipse/dropins/sdk/plugins.
The Hadoop plugin configuration file only considers the first directory, so you have to add the following code to build.xml (change the eclipse-sdk-jars):
<path id="eclipse-sdk-jars">
<fileset dir="${eclipse.home}/plugins/">
<include name="org.eclipse.ui*.jar"/>
<include name="org.eclipse.jdt*.jar"/>
<include name="org.eclipse.core*.jar"/>
<include name="org.eclipse.equinox*.jar"/>
<include name="org.eclipse.debug*.jar"/>
<include name="org.eclipse.osgi*.jar"/>
<include name="org.eclipse.swt*.jar"/>
<include name="org.eclipse.jface*.jar"/>
<include name="org.eclipse.team.cvs.ssh2*.jar"/>
<include name="com.jcraft.jsch*.jar"/>
</fileset>
<fileset dir ="${eclipse.home}/dropins/jdt/plugins/">
<include name="org.eclipse.ui*.jar"/>
<include name="org.eclipse.jdt*.jar"/>
<include name="org.eclipse.core*.jar"/>
<include name="org.eclipse.equinox*.jar"/>
<include name="org.eclipse.debug*.jar"/>
<include name="org.eclipse.osgi*.jar"/>
<include name="org.eclipse.swt*.jar"/>
<include name="org.eclipse.jface*.jar"/>
<include name="org.eclipse.team.cvs.ssh2*.jar"/>
<include name="com.jcraft.jsch*.jar"/>
</fileset>
<fileset dir ="${eclipse.home}/dropins/sdk/plugins/">
<include name="org.eclipse.ui*.jar"/>
<include name="org.eclipse.jdt*.jar"/>
<include name="org.eclipse.core*.jar"/>
<include name="org.eclipse.equinox*.jar"/>
<include name="org.eclipse.debug*.jar"/>
<include name="org.eclipse.osgi*.jar"/>
<include name="org.eclipse.swt*.jar"/>
<include name="org.eclipse.jface*.jar"/>
<include name="org.eclipse.team.cvs.ssh2*.jar"/>
<include name="com.jcraft.jsch*.jar"/>
</fileset>
</path>
This allowed me to build successfully, and create the needed jar file. However, even after adding it to the Eclipse plugins directory, there is no MapReduce perspective or project. So, if you're able to overcome this last hurdle let me know.