The StopWords.txt file contains a list of words to exclude from the index words. It is used to filter out common words such as "and", "the", etc.
To remove words from the StopWords.txt file, click on this menu item. A dialog box will appear that contains all the stop words. Mark the ones you wish to remove (by clicking on the checkbox) and then click on the Remove button. Those words are now deleted from the StopWords.txt file and any search you now look at (including the current one) is processed to include those words. Of course, a word will only appear if it was in the search and it does not appear in the StopWords.txt file.
Since formation of clusters and the similarity calculations are very dependent on stop words, you may find that including or excluding certain stop words can help form better clusters or find similar results that otherwise would be hidden.
In general, it is NOT a good idea to add many words to this file, since the effect of removing words from the Index may be puzzling in later searches.