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You need to add --lang pl-u-co-standard to the dgidx and dgraph components (in ./config/script/AppConfig.xml). By default Endeca sorts using endeca collation which "sorts text with lower case before upper case and does not account for character accents and punctuation." Standard collation sorts data "according to the International Components for Unicode (ICU) standard for the language you specify". See http://docs.oracle.com/cd/E35641_01/MDEX.621/pdf/AdvDevGuide.pdf , Chapter "Using Internationalized Data" for further details.
If by 6.1.3 you mean MDEX 6.1.3 (as opposed to Platform Services) I'm not sure this sorting was available then, you would need to check the chapter listed above in the MDEX 6.1.3 documentation.
Thanks a lot for providing the information. The changes are working fine with the version 6.2.2.
MDEX Advanced Development Guide for 6.1.3 is unavailable in internet. I made similar changes in the AppConfig file for 6.1.3 too, but the changes are not working.
Looks like this standard collation feature might have been introduced in the version 6.2.0.
I can confirm that locale-specific sorting was introduced in 6.2.0 and previous releases only supported unicode sorting. If you upgraded to 6.2, it's worth looking at bumping all the way to 6.4 - the upgrade steps are the same and 6.4 has a bunch of linguistic enhancements for language support in the mdex.