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Yes, that's an option, but in my case sometimes I want to search in java files, sometimes in txt files and sometimes in both... Maybe I could index two times the same folder (one only with java files and another only with txt), but DocFetcher says "Overlaps between indexes are not allowed". Anyway it probably would have other problems such as duplicated results in *.doc.
I think that is good to have everything indexed, because you never know what you will need to find in the future...
I think that adding this filter (and maybe others such as modification date or creation date, path) may be very useful. Maybe an easier solution would be letting the user sort the results by extension (clicking on the header of the table of results).
I have created a ticket with this feature request: https://sourceforge.net/p/docfetcher/feature-requests/88/