Looking at the code for org.apache.solr.client.solrj.request.CoreAdminRequest.MergeIndexes it looks like it should use params.add instead of .set:

 if (indexDirs != null)  {
        for (String indexDir : indexDirs) {
          params.set(CoreAdminParams.INDEX_DIR, indexDir);
        }
      }

I haven't tested it out to see if the server actually does index all of the indexDir=... params sent in on one line so maybe this does already work.

Chris

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