Config load order different between runPlay vs stage

Using Gradle 5.5.1, Play 2.6 & play-plugin 0.6

I have a project with other play project dependencies & they had their own `reference.conf`. I also have `reference.conf` and `application.conf` files. When I stages. or create zip/tar distribution, using `bin/main` script, I can successfully start the application with correct config + log file (see #104 ).

But when running with `runPlay`, it seems order of loading conf files is not same, since it's not working, both config & log files loaded from other dependencies overrides my config, although it should be the opposite.

Is this a known issue?