19 days ago - ImpulZ - Direct link

To iterate on this one, modded servers currently may require mods to have mod.cpp file implemented (learn more about it at https://community.bistudio.com/wiki/DayZ:Modding_Structure). If the file is missing, folder names of mods need to be the same on both client and server side.

This is not intentional, and we are working to fix this as soon as possible in the upcoming days.

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DayZ:Modding Structure - Bohemia Interactive Community
The internal structure is largely up to the modders themselves, e.g. in case of script files, it doesn't matter where they are placed as long as they are in their respective script module and paths are set properly.