This kind of extra folder added to the published output occurs when there are references to resources outside of the folder where the main published DITA Map is located. If you open the main DITA Map in the Oxygen DITA Maps Manager view and use the "Validation and check for completeness" toolbar action, there is a checkbox there called "Report references to resources outside of the DITA Map folder" which you can enable in order to have all these links reported to you.
The Oxygen transformation scenario has a specific parameter called "fix.external.references" which when enabled will try to bring the external referenced topics inside the output folder when the publishing is done, thus resulting in this extra folder being added (as not adding this extra folder might mean there is a possibility to overwrite topics having the same name located in the base folder.
A possibility might be to move your main DITA Map so that all references are to resources in folder structures located underneath it:
Right now we do not have a parameter to control the name of the ""oxy_ex" folders, if you want I can add an internal issue to add such a parameter. If such a parameter existed, how would you name this extra folder in your case?
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