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language codes are still duplicated. I think the easiest way to fix this is
is to change the lang_map configuration in your .tx/config file as follows
(using ja-JP as an example):

lang_map = ja_JP:ja-JP

Then tx pull the ja_JP translations available in Tx. 

Then change the lang_map to the correct value (as per
https://fedoraproject.org/wiki/Setting_up_a_document_with_Transifex):

lang_map = ja:ja-JP

tx push the ja translations.

Finally, tx delete the old ja_JP translations.


Feel free to contact me if you need more help with this.

Cheers,
Petr Kovar