diff --git a/core/src/main/kotlin/configuration.kt b/core/src/main/kotlin/configuration.kt
index f298a5d415..038a5bb777 100644
--- a/core/src/main/kotlin/configuration.kt
+++ b/core/src/main/kotlin/configuration.kt
@@ -3,6 +3,7 @@
 package org.jetbrains.dokka
 
 import org.jetbrains.dokka.plugability.ConfigurableBlock
+import org.jetbrains.dokka.utilities.cast
 import org.jetbrains.dokka.utilities.parseJson
 import org.jetbrains.dokka.utilities.toJsonString
 import java.io.File
@@ -100,6 +101,20 @@ data class GlobalDokkaConfiguration(
 
 fun GlobalDokkaConfiguration(json: String): GlobalDokkaConfiguration = parseJson(json)
 
+fun DokkaConfiguration.apply(globals: GlobalDokkaConfiguration): DokkaConfiguration = this.apply {
+    sourceSets.forEach {
+        it.perPackageOptions.cast<MutableList<DokkaConfiguration.PackageOptions>>().addAll(globals.perPackageOptions ?: emptyList())
+    }
+
+    sourceSets.forEach {
+        it.externalDocumentationLinks.cast<MutableSet<DokkaConfiguration.ExternalDocumentationLink>>().addAll(globals.externalDocumentationLinks ?: emptyList())
+    }
+
+    sourceSets.forEach {
+        it.sourceLinks.cast<MutableSet<SourceLinkDefinitionImpl>>().addAll(globals.sourceLinks ?: emptyList())
+    }
+}
+
 fun DokkaConfiguration.toJsonString(): String = toJsonString(this)
 fun <T : ConfigurableBlock> T.toJsonString(): String = toJsonString(this)
 
diff --git a/runners/cli/src/main/kotlin/cli/main.kt b/runners/cli/src/main/kotlin/cli/main.kt
index b5e1d2a3fd..1dc32a45a5 100644
--- a/runners/cli/src/main/kotlin/cli/main.kt
+++ b/runners/cli/src/main/kotlin/cli/main.kt
@@ -408,19 +408,8 @@ fun initializeConfiguration(globalArguments: GlobalArguments): DokkaConfiguratio
         val jsonContent = Paths.get(checkNotNull(globalArguments.json)).toFile().readText()
         val globals = GlobalDokkaConfiguration(jsonContent)
         val dokkaConfigurationImpl = DokkaConfigurationImpl(jsonContent)
-        dokkaConfigurationImpl.apply {
-            sourceSets.forEach {
-                it.perPackageOptions.cast<MutableList<DokkaConfiguration.PackageOptions>>().addAll(globals.perPackageOptions ?: emptyList())
-            }
-
-            sourceSets.forEach {
-                it.externalDocumentationLinks.cast<MutableSet<ExternalDocumentationLink>>().addAll(globals.externalDocumentationLinks ?: emptyList())
-            }
-
-            sourceSets.forEach {
-                it.sourceLinks.cast<MutableSet<SourceLinkDefinitionImpl>>().addAll(globals.sourceLinks ?: emptyList())
-            }
 
+        dokkaConfigurationImpl.apply(globals).apply {
             sourceSets.forEach {
                 it.externalDocumentationLinks.cast<MutableSet<ExternalDocumentationLink>>().addAll(defaultLinks(it))
             }