Fix logback.xml resource inclusion (#4392)

This was broken in the native image `dist/package.mill` refactor, which
made the `dist` and `dist.native` modules depend on the upstream
`build.runner` directly rather than using the `dist.assembly. This
resulted in things like Thymeleaf logging tons of verbose DEBUG-level
output when run in the `build.mill` file

Author: lihaoyi