OK, I got it. After doing the following changes in the buildpaths of the 
projects 'cms' and 'core':
1. cms: Right-click-> Properties, Libraries tab, click on "Add jars..." and add 
the following:
- thirdparty/jboss-cluster/lib/jbossha.jar
- thirdparty/apache-jackrabbit/lib/jackrabbit-core.jar
- thirdparty/day-jcr/lib/jcr.jar
- thirdparty/jboss-hibernate/lib/hibernate.jar
- thirdparty/jboss-hibernate/lib/commons-collections.jar
- thirdparty/jboss-hibernate/lib/commons-logging.jar
- thirdparty/jakarta-io/lib/commons-io.jar
2. core: Right-click-> Properties, Libraries tab
2.1. Add jars:
- tools/lib/xalan.jar
- thirdparty/apache-myfaces/lib/myfaces-api.jar
- thirdparty/apache-myfaces/lib/tomahawk.jar
2.2. Add External jars. These should be created after building the sources.
- security/output/lib/portal-security-lib.jar
- faces/output/lib/portal-faces-lib.jar

Eclipse stops complaining after that. Hope it helps someone,

Pedro.


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