Filter out non-existent java source roots in kapt tasks

#KT-24716 fixed

libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/kapt2/simple/build.gradle

@@ -22,4 +22,6 @@ dependencies {
     compile "org.jetbrains.kotlin:annotation-processor-example:$kotlin_version"
     kapt "org.jetbrains.kotlin:annotation-processor-example:$kotlin_version"
     testCompile 'junit:junit:4.12'
-}
+}
+
+compileKotlin.kotlinOptions.allWarningsAsErrors = true

libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/internal/kapt/KaptTask.kt

@@ -74,6 +74,7 @@ abstract class KaptTask : ConventionTask() {
             .filterTo(HashSet(), ::isRootAllowed)
 
     private fun isRootAllowed(file: File): Boolean =
-        !FileUtil.isAncestor(destinationDir, file, /* strict = */ false) &&
+        file.exists() &&
+                !FileUtil.isAncestor(destinationDir, file, /* strict = */ false) &&
                 !FileUtil.isAncestor(classesDir, file, /* strict = */ false)
 }