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Using external conf folder as resource folder with sbt-native-packager

I'm pretty new to sbt-native-packager. What I want is using external conf folder like a resource folder and configure the files inside it differently on each environment such as production, dev and etc. Project has src/universal/conf and bunch of configuration files under this directory used by libraries at runtime.

I exclude src/universal/conf during build so final jar does not has these conf files as resources. I checked bin/start.sh and only lib/ folder set as classpath.

How can I accomplish it? What's the best practices? I don't think that JavaServerPackaging is more convenient because final jar has several main methods to be used as separate applications on same node. So one dameon application looks like doesn't fit.

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