3 files changed, 98 insertions, 10 deletions
diff --git a/runners/cli/src/main/kotlin/cli/main.kt b/runners/cli/src/main/kotlin/cli/main.kt
index 739539a9..1dc32a45 100644
--- a/runners/cli/src/main/kotlin/cli/main.kt
+++ b/runners/cli/src/main/kotlin/cli/main.kt
@@ -2,10 +2,7 @@ package org.jetbrains.dokka
 
 import kotlinx.cli.*
 import org.jetbrains.dokka.DokkaConfiguration.ExternalDocumentationLink
-import org.jetbrains.dokka.utilities.DokkaConsoleLogger
-import org.jetbrains.dokka.utilities.DokkaLogger
-import org.jetbrains.dokka.utilities.LoggingLevel
-import org.jetbrains.dokka.utilities.cast
+import org.jetbrains.dokka.utilities.*
 import java.io.*
 import java.net.MalformedURLException
 import java.net.URL
@@ -80,6 +77,7 @@ class GlobalArguments(args: Array<String>) : DokkaConfiguration {
 
     private val _includes by parser.option(
         ArgTypeFile,
+        fullName = "includes",
         description = "Markdown files that would be displayed in multi-module page separated by the semicolon `;`)"
     ).delimiter(";")
 
@@ -406,14 +404,23 @@ fun parseLinks(links: List<String>): List<ExternalDocumentationLink> {
             }
 }
 
+fun initializeConfiguration(globalArguments: GlobalArguments): DokkaConfiguration = if (globalArguments.json != null) {
+        val jsonContent = Paths.get(checkNotNull(globalArguments.json)).toFile().readText()
+        val globals = GlobalDokkaConfiguration(jsonContent)
+        val dokkaConfigurationImpl = DokkaConfigurationImpl(jsonContent)
+
+        dokkaConfigurationImpl.apply(globals).apply {
+            sourceSets.forEach {
+                it.externalDocumentationLinks.cast<MutableSet<ExternalDocumentationLink>>().addAll(defaultLinks(it))
+            }
+        }
+    } else {
+        globalArguments
+    }
+
 fun main(args: Array<String>) {
     val globalArguments = GlobalArguments(args)
-    val configuration = if (globalArguments.json != null)
-        DokkaConfigurationImpl(
-            Paths.get(checkNotNull(globalArguments.json)).toFile().readText()
-        )
-    else
-        globalArguments
+    val configuration = initializeConfiguration(globalArguments)
     DokkaGenerator(configuration, globalArguments.logger).generate()
 }
 
diff --git a/runners/cli/src/test/kotlin/cli/CliTest.kt b/runners/cli/src/test/kotlin/cli/CliTest.kt
new file mode 100644
index 00000000..5910e938
--- /dev/null
+++ b/runners/cli/src/test/kotlin/cli/CliTest.kt
@@ -0,0 +1,30 @@
+package org.jetbrains.dokka
+
+import junit.framework.Assert.assertTrue
+import org.junit.Test
+import java.lang.IllegalStateException
+import java.nio.file.Paths
+import kotlin.test.assertEquals
+
+class CliIntegrationTest {
+
+    @Test
+    fun `should apply global settings to all source sets`() {
+        val jsonPath = Paths.get(javaClass.getResource("/my-file.json")?.toURI() ?: throw IllegalStateException("No JSON found!")).toFile().toString()
+        val globalArguments = GlobalArguments(arrayOf(jsonPath))
+
+        val configuration = initializeConfiguration(globalArguments)
+
+        configuration.sourceSets.forEach {
+            assertTrue(it.perPackageOptions.isNotEmpty())
+            assertTrue(it.sourceLinks.isNotEmpty())
+            assertTrue(it.externalDocumentationLinks.isNotEmpty())
+
+            assertTrue(it.externalDocumentationLinks.any { it.url.toString() == "https://docs.oracle.com/javase/8/docs/api/" })
+            assertEquals(it.sourceLinks.single().localDirectory, "/home/Vadim.Mishenev/dokka/examples/cli/src/main/kotlin")
+            assertEquals(it.perPackageOptions.single().matchingRegex, "my-custom-regex")
+        }
+
+    }
+
+}
diff --git a/runners/cli/src/test/resources/my-file.json b/runners/cli/src/test/resources/my-file.json
new file mode 100644
index 00000000..49dda814
--- /dev/null
+++ b/runners/cli/src/test/resources/my-file.json
@@ -0,0 +1,51 @@
+{
+  "moduleName": "Dokka Example",
+  "moduleVersion": null,
+  "outputDir": "$outputPath",
+  "pluginsClasspath": ["$pluginsClasspath"],
+  "cacheRoot": null,
+  "offlineMode": false,
+  "sourceLinks": [{
+    "localDirectory": "/home/Vadim.Mishenev/dokka/examples/cli/src/main/kotlin",
+    "remoteUrl": "https://github.com/Kotlin/dokka/tree/master/examples/gradle/dokka-gradle-example/src/main/kotlin",
+    "remoteLineSuffix": "#L"
+  }],
+  "externalDocumentationLinks": [{
+    "url": "https://docs.oracle.com/javase/8/docs/api/",
+    "packageListUrl": "https://docs.oracle.com/javase/8/docs/api/package-list"
+  }],
+  "perPackageOptions": [{
+    "matchingRegex": "my-custom-regex",
+    "skipDeprecated": "true",
+    "reportUndocumented": "true",
+    "includeNonPublic": "true",
+    "documentedVisibilities": ["PUBLIC", "PRIVATE", "PROTECTED", "INTERNAL", "PACKAGE"]
+  }],
+  "sourceSets": [
+    {
+      "displayName": "jvm",
+      "sourceSetID": {
+        "scopeId": ":dokkaHtml",
+        "sourceSetName": "main"
+      },
+      "sourceRoots": [
+        "$projectPath"
+      ],
+      "dependentSourceSets": [],
+      "samples": [],
+      "includes": [],
+      "includeNonPublic": false,
+      "reportUndocumented": false,
+      "skipEmptyPackages": true,
+      "skipDeprecated": false,
+      "jdkVersion": 8,
+      "sourceLinks": [],
+      "perPackageOptions": [],
+      "externalDocumentationLinks": [],
+      "noStdlibLink": false,
+      "noJdkLink": false,
+      "suppressedFiles": [],
+      "analysisPlatform": "jvm"
+    }
+  ]
+}