Exception reported for hibernate3.jar entry:

!ENTRY org.jboss.tools.common.model 4 0 2012-08-10 09:51:13.338
!MESSAGE JarAccess: cannot obtain entry for path 'hibernate-distribution-3.5.6-Final.pom' from jar '/home/eskimo/Projects/jbds-build/jbosstools-src/hibernatetools/plugins/org.hibernate.eclipse.libs/lib/hibernate/hibernate3.jar'.

it happens because real name for hibernate-distribution-3.5.6-Final.pom entry is "/hibernate-distribution-3.5.6-Final.pom" (see list of entry names printed below)
lis ov entry names for hibernatetools/plugins/org.hibernate.eclipse.libs/lib/hibernate/hibernate3.jar:
...
META-INF/maven/org.hibernate/hibernate-envers/
META-INF/maven/org.hibernate/hibernate-envers/pom.xml
META-INF/maven/org.hibernate/hibernate-envers/pom.properties
/
/hibernate-distribution-3.5.6-Final.pom