reference.conf is a file for library developers. All properties required by the library should be mentioned there and filled with reasonable default values when possible.

application.conf is a file for application developers. A developer can set values for properties used by libraries in case they are not the same as defaults. Also he/she can declare his own properties and refer them from the code.

When ConfigFactory.load is called all reference.conf and application.conf files are merged into one configuration and application.conf has higher precedence.

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