I never tried a light configuration as you but shouldn't you put the oneJar settings in the root sbt file? You want to package the root and include guy right?
I tried something similar for the first time today and started with oneJar but when using a full sbt configuration the compiler complained that settings were a Seq(_) and sbt expected a single setting or something like that. I switched to sbt-assembly and it worked.
sbt-oneJar has not been updated for 2 years while sbt-assembly was recently updated. I'm not sure which one is preferred but I'd rather use an active tool.
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