Optimize indexRepository methods getIndexedFS and flush
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                 Key: UIMA-1212
                 URL: https://issues.apache.org/jira/browse/UIMA-1212
             Project: UIMA
          Issue Type: Improvement
          Components: Core Java Framework
            Reporter: Eddie Epstein
            Assignee: Eddie Epstein


The getIndexedFS and flush methods currently iterate over all defined indexes. 
When the number of indexes is large, for example when there are many annotation 
types defined, this overhead becomes significant relative to lightweight 
annotator processing. By marking which indexes are actually used, it is 
possible to eliminate most of the overhead.

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