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Update automatically using maven:
mvn -Dtycho.mode=maven org.eclipse.tycho:tycho-versions-plugin:set-version -DnewVersion=new_version-SNAPSHOT mvn -Dtycho.mode=maven org.eclipse.tycho:tycho-versions-plugin:update-eclipse-metadata -DnewVersion=new_version-SNAPSHOT
The first command seems to do the trick. Note that this only updates the versions and does not make release.