[build] Fix gradle plugin shadowJar building and uploading

gradle/loadRootProperties.gradle

@@ -10,5 +10,7 @@ file("$rootDir/gradle.properties").withReader {
     rootProperties.load(it)
 }
 rootProperties.each { k, v ->
-    ext.set(k, v)
+    if (!project.hasProperty(k)) {
+        ext.set(k, v)
+    }
 }

tools/kotlin-native-gradle-plugin/build.gradle

@@ -67,12 +67,18 @@ task pluginMetadata {
     }
 }
 
+configurations {
+    bundleDependencies {
+        transitive = false
+    }
+}
+
 dependencies {
     compile 'org.jetbrains.kotlin:kotlin-native-shared'
     compile "org.jetbrains.kotlin:kotlin-stdlib:$buildKotlinVersion"
     compile gradleApi()
 
-    shadow "org.jetbrains.kotlin:kotlin-native-shared"
+    bundleDependencies 'org.jetbrains.kotlin:kotlin-native-shared'
 
     testCompile gradleTestKit()
     testCompile 'junit:junit:4.12'
@@ -82,6 +88,11 @@ dependencies {
     testRuntime files(pluginMetadata)
 }
 
+shadowJar {
+    configurations = [project.configurations.bundleDependencies]
+    classifier = null
+}
+
 test {
     if (project.hasProperty("konan.home")) {
         systemProperty("konan.home", project.property("konan.home"))