Fix how Update command manages the upgrade-only attribute

Even with the attribute "upgrade-only", the Update command will add to the registry the entries corresponding to the plugins which were not copied into nxserver/bundles:

  <entry key="nxserver/bundles/nuxeo-importer-scan">
    <version name="5.6.0-HF01" path="nxserver/bundles/nuxeo-importer-scan-5.6.0-HF01.jar">
      <package>nuxeo-5.6.0-HF01-1.0.0</package>
    </version>
  </entry>

As a consequence, when uninstalling the package, there will be errors like:

Could not find jar with key: nxserver/bundles/nuxeo-importer-scan