Retain inhertited dependencies in the resolution logic

[sschuberth]

@sschuberth Looking at the kotlin plugin, it checks in the allDependencies if inherited,

https://github.com/JetBrains/kotlin/blob/07aee8831eb45690053028f39f3312e1c8e90f69/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/internal/KotlinDependenciesManagement.kt#L131-L136

It appears that if I change our resolution logic from clearing them as,

gradle-versions-plugin/src/main/groovy/com/github/benmanes/gradle/versions/updates/Resolver.groovy

Lines 127 to 134 in 9effd94

	Configuration copy = configuration.copyRecursive().setTransitive(false)
	// https://github.com/ben-manes/gradle-versions-plugin/issues/127
	if (copy.metaClass.respondsTo(copy, "setCanBeResolved", Boolean)) {
	copy.setCanBeResolved(true)
	}
	copy.dependencies.clear()
	copy.dependencies.addAll(latest)

to retaining those inherited as,

def all = new ArrayList(configuration.getAllDependencies())
all.removeAll(configuration.dependencies)

copy.dependencies.clear()
copy.dependencies.addAll(all)
copy.dependencies.addAll(latest)

Then the failure messages to resolve those configurations goes away,

> Task :dependencyUpdates
Failed to resolve :cli:implementation
Failed to resolve :model:implementation
Failed to resolve :utils:implementation

Originally posted by @ben-manes in #334 (comment)