In https://github.com/gradle/gradle/blob/master/design-docs/dependency-management-bug-fixes.md#user-visible-changes-1, we stated (in summary):

For dependency with type: 'ext' (anything other than 'jar')
1. If pom.packaging in ['pom', 'jar', 'ejb', 'bundle', 'maven-plugin', 'eclipse-plugin'] will emit a deprecation warning before using 'module.jar'
2. If pom.packaging == 'foo' and 'module.foo' exists, then emit deprecation warning and use module.foo
3. If pom.packaging == 'foo' and 'module.foo' does NOT exist, use 'module.ext'

The problem is the case where pom.packaging == 'ext': In this case we should not be emitting a deprecation warning, I don't think. Otherwise, there's nothing a consumer can do to avoid the deprecation warning and consume a 'war' artifact from a module with pom.packaging == 'war'.