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I did investigate and found that it was still possible to manage dxa.properties in the /config folder of the content service for on-premise setup.
In case if you are using cloud and docker container setup, then it's possible to pass as environment variables for containers.
Interestingly also found that this config was embedded into this udp-content-dxa-...
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Issue was fixed when I changed the namespace to com.sdl.dxa.modules from com.example.dxa.modules.test in the module.
now able to load entities from custom module as well.
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