DokkaConfiguration: Use `Set` instead of `List` when collections are expected to be distinct

28 files changed, 133 insertions, 194 deletions

diff --git a/core/src/main/kotlin/configuration.kt b/core/src/main/kotlin/configuration.kt
index 67c55861..b26b93a4 100644
--- a/core/src/main/kotlin/configuration.kt
+++ b/core/src/main/kotlin/configuration.kt
@@ -79,39 +79,35 @@ interface DokkaConfiguration : Serializable {
     val failOnWarning: Boolean
     val sourceSets: List<DokkaSourceSet>
     val modules: List<DokkaModuleDescription>
-    val pluginsClasspath: List<File>
+    val pluginsClasspath: Set<File>
     val pluginsConfiguration: Map<String, String>
 
     interface DokkaSourceSet : Serializable {
         val sourceSetID: DokkaSourceSetID
         val displayName: String
         val moduleDisplayName: String
-        val classpath: List<File>
-        val sourceRoots: List<SourceRoot>
+        val classpath: Set<File>
+        val sourceRoots: Set<File>
         val dependentSourceSets: Set<DokkaSourceSetID>
-        val samples: List<File>
-        val includes: List<File>
+        val samples: Set<File>
+        val includes: Set<File>
         val includeNonPublic: Boolean
         val includeRootPackage: Boolean
         val reportUndocumented: Boolean
         val skipEmptyPackages: Boolean
         val skipDeprecated: Boolean
         val jdkVersion: Int
-        val sourceLinks: List<SourceLinkDefinition>
+        val sourceLinks: Set<SourceLinkDefinition>
         val perPackageOptions: List<PackageOptions>
-        val externalDocumentationLinks: List<ExternalDocumentationLink>
+        val externalDocumentationLinks: Set<ExternalDocumentationLink>
         val languageVersion: String?
         val apiVersion: String?
         val noStdlibLink: Boolean
         val noJdkLink: Boolean
-        val suppressedFiles: List<File>
+        val suppressedFiles: Set<File>
         val analysisPlatform: Platform
     }
 
-    interface SourceRoot : Serializable {
-        val directory: File
-    }
-
     interface SourceLinkDefinition : Serializable {
         val path: String
         val url: String
diff --git a/core/src/main/kotlin/defaultConfiguration.kt b/core/src/main/kotlin/defaultConfiguration.kt
index 384ce392..1b79ec61 100644
--- a/core/src/main/kotlin/defaultConfiguration.kt
+++ b/core/src/main/kotlin/defaultConfiguration.kt
@@ -3,15 +3,13 @@ package org.jetbrains.dokka
 import org.jetbrains.dokka.DokkaConfiguration.DokkaSourceSet
 import java.io.File
 import java.net.URL
-import kotlin.reflect.full.memberProperties
-import kotlin.reflect.full.primaryConstructor
 
 data class DokkaConfigurationImpl(
     override val outputDir: File = DokkaDefaults.outputDir,
     override val cacheRoot: File? = DokkaDefaults.cacheRoot,
     override val offlineMode: Boolean = DokkaDefaults.offlineMode,
     override val sourceSets: List<DokkaSourceSetImpl> = emptyList(),
-    override val pluginsClasspath: List<File> = emptyList(),
+    override val pluginsClasspath: Set<File> = emptySet(),
     override val pluginsConfiguration: Map<String, String> = emptyMap(),
     override val modules: List<DokkaModuleDescriptionImpl> = emptyList(),
     override val failOnWarning: Boolean = DokkaDefaults.failOnWarning
@@ -22,25 +20,25 @@ data class DokkaSourceSetImpl(
     override val moduleDisplayName: String,
     override val displayName: String = DokkaDefaults.sourceSetDisplayName,
     override val sourceSetID: DokkaSourceSetID,
-    override val classpath: List<File> = emptyList(),
-    override val sourceRoots: List<SourceRootImpl>,
+    override val classpath: Set<File> = emptySet(),
+    override val sourceRoots: Set<File> = emptySet(),
     override val dependentSourceSets: Set<DokkaSourceSetID> = emptySet(),
-    override val samples: List<File> = emptyList(),
-    override val includes: List<File> = emptyList(),
+    override val samples: Set<File> = emptySet(),
+    override val includes: Set<File> = emptySet(),
     override val includeNonPublic: Boolean = DokkaDefaults.includeNonPublic,
     override val includeRootPackage: Boolean = DokkaDefaults.includeRootPackage,
     override val reportUndocumented: Boolean = DokkaDefaults.reportUndocumented,
     override val skipEmptyPackages: Boolean = DokkaDefaults.skipEmptyPackages,
     override val skipDeprecated: Boolean = DokkaDefaults.skipDeprecated,
     override val jdkVersion: Int = DokkaDefaults.jdkVersion,
-    override val sourceLinks: List<SourceLinkDefinitionImpl> = emptyList(),
+    override val sourceLinks: Set<SourceLinkDefinitionImpl> = emptySet(),
     override val perPackageOptions: List<PackageOptionsImpl> = emptyList(),
-    override var externalDocumentationLinks: List<ExternalDocumentationLinkImpl> = emptyList(),
+    override var externalDocumentationLinks: Set<ExternalDocumentationLinkImpl> = emptySet(),
     override val languageVersion: String? = null,
     override val apiVersion: String? = null,
     override val noStdlibLink: Boolean = DokkaDefaults.noStdlibLink,
     override val noJdkLink: Boolean = DokkaDefaults.noJdkLink,
-    override val suppressedFiles: List<File> = emptyList(),
+    override val suppressedFiles: Set<File> = emptySet(),
     override val analysisPlatform: Platform = DokkaDefaults.analysisPlatform
 ) : DokkaSourceSet
 
@@ -50,12 +48,6 @@ data class DokkaModuleDescriptionImpl(
     override val docFile: File
 ) : DokkaConfiguration.DokkaModuleDescription
 
-data class SourceRootImpl(
-    override val directory: File
-) : DokkaConfiguration.SourceRoot {
-    constructor(directoryPath: String) : this(File(directoryPath))
-}
-
 data class SourceLinkDefinitionImpl(
     override val path: String,
     override val url: String,
diff --git a/core/src/main/kotlin/utilities/json.kt b/core/src/main/kotlin/utilities/json.kt
index feac2b23..211037d6 100644
--- a/core/src/main/kotlin/utilities/json.kt
+++ b/core/src/main/kotlin/utilities/json.kt
@@ -1,26 +1,18 @@
 package org.jetbrains.dokka.utilities
 
 import com.fasterxml.jackson.core.JsonGenerator
-import com.fasterxml.jackson.core.JsonParser
-import com.fasterxml.jackson.databind.DeserializationContext
 import com.fasterxml.jackson.databind.DeserializationFeature
 import com.fasterxml.jackson.databind.SerializerProvider
-import com.fasterxml.jackson.databind.deser.std.StdScalarDeserializer
 import com.fasterxml.jackson.databind.module.SimpleModule
 import com.fasterxml.jackson.databind.ser.std.StdScalarSerializer
 import com.fasterxml.jackson.module.kotlin.jacksonObjectMapper
 import com.fasterxml.jackson.module.kotlin.jacksonTypeRef
-import org.jetbrains.dokka.DokkaConfiguration.SourceRoot
-import org.jetbrains.dokka.SourceRootImpl
 import java.io.File
 import com.fasterxml.jackson.core.type.TypeReference as JacksonTypeReference
 
 private val objectMapper = run {
     val module = SimpleModule().apply {
         addSerializer(FileSerializer)
-        addSerializer(SourceRoot::class.java, SourceRootSerializer)
-        addDeserializer(SourceRootImpl::class.java, SourceRootImplDeserializer)
-        addDeserializer(SourceRoot::class.java, SourceRootImplDeserializer)
     }
     jacksonObjectMapper()
         .registerModule(module)
@@ -53,13 +45,3 @@ private object FileSerializer : StdScalarSerializer<File>(File::class.java) {
         g.writeString(value.path)
     }
 }
-
-private object SourceRootSerializer : StdScalarSerializer<SourceRoot>(SourceRoot::class.java) {
-    override fun serialize(value: SourceRoot, g: JsonGenerator, provider: SerializerProvider) {
-        g.writeString(value.directory.path)
-    }
-}
-
-private object SourceRootImplDeserializer : StdScalarDeserializer<SourceRootImpl>(SourceRootImpl::class.java) {
-    override fun deserialize(p: JsonParser, ctxt: DeserializationContext): SourceRootImpl = SourceRootImpl(File(p.text))
-}
diff --git a/core/src/test/kotlin/utilities/DokkaConfigurationJsonTest.kt b/core/src/test/kotlin/utilities/DokkaConfigurationJsonTest.kt
index 35755f50..e8135f96 100644
--- a/core/src/test/kotlin/utilities/DokkaConfigurationJsonTest.kt
+++ b/core/src/test/kotlin/utilities/DokkaConfigurationJsonTest.kt
@@ -10,11 +10,11 @@ class DokkaConfigurationJsonTest {
     fun `simple configuration toJsonString then parseJson`() {
         val configuration = DokkaConfigurationImpl(
             outputDir = File("customOutputDir"),
-            pluginsClasspath = listOf(File("plugins/customPlugin.jar")),
+            pluginsClasspath = setOf(File("plugins/customPlugin.jar")),
             sourceSets = listOf(
                 DokkaSourceSetImpl(
                     moduleDisplayName = "customModuleDisplayName",
-                    sourceRoots = listOf(SourceRootImpl(File("customSourceRoot"))),
+                    sourceRoots = setOf(File("customSourceRoot")),
                     sourceSetID = DokkaSourceSetID("customModuleName", "customSourceSetName")
                 )
             )
@@ -49,13 +49,13 @@ class DokkaConfigurationJsonTest {
         assertEquals(
             DokkaConfigurationImpl(
                 outputDir = File("customOutputDir"),
-                pluginsClasspath = listOf(File("plugins/customPlugin.jar")),
+                pluginsClasspath = setOf(File("plugins/customPlugin.jar")),
                 sourceSets = listOf(
                     DokkaSourceSetImpl(
                         moduleDisplayName = "customModuleDisplayName",
-                        sourceRoots = listOf(SourceRootImpl(File("customSourceRoot"))),
+                        sourceRoots = setOf(File("customSourceRoot")),
                         sourceSetID = DokkaSourceSetID("customModuleName", "customSourceSetName"),
-                        classpath = listOf(File("classpath/custom1.jar"), File("classpath/custom2.jar"))
+                        classpath = setOf(File("classpath/custom1.jar"), File("classpath/custom2.jar"))
                     )
                 )
             ),
diff --git a/integration-tests/gradle/projects/it-basic-groovy/build.gradle b/integration-tests/gradle/projects/it-basic-groovy/build.gradle
index 405b55ed..fadf4287 100644
--- a/integration-tests/gradle/projects/it-basic-groovy/build.gradle
+++ b/integration-tests/gradle/projects/it-basic-groovy/build.gradle
@@ -15,8 +15,8 @@ dokkaHtml {
     failOnWarning = false
     dokkaSourceSets {
         customSourceSet {
-            sourceRoot { directory = file("src/main/java") }
-            sourceRoot { directory = file("src/main/kotlin") }
+            sourceRoot(file("src/main/java"))
+            sourceRoot(file("src/main/kotlin"))
             displayName = "custom"
             reportUndocumented = true
         }
diff --git a/kotlin-analysis/src/main/kotlin/org/jetbrains/dokka/analysis/AnalysisEnvironment.kt b/kotlin-analysis/src/main/kotlin/org/jetbrains/dokka/analysis/AnalysisEnvironment.kt
index 14067f43..cb65b168 100644
--- a/kotlin-analysis/src/main/kotlin/org/jetbrains/dokka/analysis/AnalysisEnvironment.kt
+++ b/kotlin-analysis/src/main/kotlin/org/jetbrains/dokka/analysis/AnalysisEnvironment.kt
@@ -540,7 +540,7 @@ class AnalysisEnvironment(val messageCollector: MessageCollector, val analysisPl
      * Adds list of paths to source roots.
      * $list: collection of files to add
      */
-    fun addSources(sourceDirectories: List<File>) {
+    fun addSources(sourceDirectories: Iterable<File>) {
         sourceDirectories.forEach { directory ->
             configuration.addKotlinSourceRoot(directory.path)
             if (directory.isDirectory || directory.extension == ".java") {
diff --git a/kotlin-analysis/src/main/kotlin/org/jetbrains/dokka/analysis/EnvironmentAndFacade.kt b/kotlin-analysis/src/main/kotlin/org/jetbrains/dokka/analysis/EnvironmentAndFacade.kt
index 009bc66c..38b0b69b 100644
--- a/kotlin-analysis/src/main/kotlin/org/jetbrains/dokka/analysis/EnvironmentAndFacade.kt
+++ b/kotlin-analysis/src/main/kotlin/org/jetbrains/dokka/analysis/EnvironmentAndFacade.kt
@@ -22,7 +22,6 @@ internal fun createEnvironmentAndFacade(
         addSources(
             (sourceSet.sourceRoots + configuration.sourceSets.filter { it.sourceSetID in sourceSet.dependentSourceSets }
                 .flatMap { it.sourceRoots })
-                .map { it.directory }
         )
 
         loadLanguageVersionSettings(sourceSet.languageVersion, sourceSet.apiVersion)
diff --git a/plugins/base/src/main/kotlin/translators/descriptors/DefaultDescriptorToDocumentableTranslator.kt b/plugins/base/src/main/kotlin/translators/descriptors/DefaultDescriptorToDocumentableTranslator.kt
index 1ac4edf7..383a3715 100644
--- a/plugins/base/src/main/kotlin/translators/descriptors/DefaultDescriptorToDocumentableTranslator.kt
+++ b/plugins/base/src/main/kotlin/translators/descriptors/DefaultDescriptorToDocumentableTranslator.kt
@@ -95,7 +95,7 @@ private class DokkaDescriptorVisitor(
     private fun Collection<DeclarationDescriptor>.filterDescriptorsInSourceSet() = filter {
         it.toSourceElement.containingFile.toString().let { path ->
             path.isNotBlank() && sourceSet.sourceRoots.any { root ->
-                Paths.get(path).startsWith(root.directory.toPath())
+                Paths.get(path).startsWith(root.toPath())
             }
         }
     }
diff --git a/plugins/base/src/main/kotlin/translators/psi/DefaultPsiToDocumentableTranslator.kt b/plugins/base/src/main/kotlin/translators/psi/DefaultPsiToDocumentableTranslator.kt
index cd43e635..71c19bbe 100644
--- a/plugins/base/src/main/kotlin/translators/psi/DefaultPsiToDocumentableTranslator.kt
+++ b/plugins/base/src/main/kotlin/translators/psi/DefaultPsiToDocumentableTranslator.kt
@@ -44,7 +44,7 @@ class DefaultPsiToDocumentableTranslator(
     override fun invoke(sourceSet: DokkaSourceSet, context: DokkaContext): DModule {
 
         fun isFileInSourceRoots(file: File): Boolean {
-            return sourceSet.sourceRoots.any { root -> file.startsWith(root.directory) }
+            return sourceSet.sourceRoots.any { root -> file.startsWith(root) }
         }
 
         val (environment, _) = kotlinAnalysis[sourceSet]
diff --git a/plugins/base/src/test/kotlin/renderers/html/DivergentTest.kt b/plugins/base/src/test/kotlin/renderers/html/DivergentTest.kt
index 8ab277f1..b4de5aed 100644
--- a/plugins/base/src/test/kotlin/renderers/html/DivergentTest.kt
+++ b/plugins/base/src/test/kotlin/renderers/html/DivergentTest.kt
@@ -1,12 +1,10 @@
 package renderers.html
 
-import org.jetbrains.dokka.Platform
-import org.jetbrains.dokka.SourceRootImpl
 import org.jetbrains.dokka.base.renderers.html.HtmlRenderer
 import org.jetbrains.dokka.links.DRI
 import org.jetbrains.dokka.pages.ContentDivergentGroup
 import org.junit.jupiter.api.Test
-import renderers.*
+import renderers.TestPage
 import utils.Div
 import utils.Span
 import utils.match
diff --git a/plugins/base/src/test/kotlin/renderers/html/HtmlRenderingOnlyTestBase.kt b/plugins/base/src/test/kotlin/renderers/html/HtmlRenderingOnlyTestBase.kt
index ae494929..eea4dc0c 100644
--- a/plugins/base/src/test/kotlin/renderers/html/HtmlRenderingOnlyTestBase.kt
+++ b/plugins/base/src/test/kotlin/renderers/html/HtmlRenderingOnlyTestBase.kt
@@ -2,7 +2,6 @@ package renderers.html
 
 import org.jetbrains.dokka.DokkaConfigurationImpl
 import org.jetbrains.dokka.Platform
-import org.jetbrains.dokka.SourceRootImpl
 import org.jetbrains.dokka.base.DokkaBase
 import org.jetbrains.dokka.base.renderers.DefaultTabSortingStrategy
 import org.jetbrains.dokka.base.renderers.RootCreator
@@ -17,6 +16,7 @@ import org.jsoup.nodes.TextNode
 import renderers.RenderingOnlyTestBase
 import utils.TestOutputWriter
 import renderers.defaultSourceSet
+import java.io.File
 
 abstract class HtmlRenderingOnlyTestBase : RenderingOnlyTestBase<Element>() {
 
@@ -25,7 +25,7 @@ abstract class HtmlRenderingOnlyTestBase : RenderingOnlyTestBase<Element>() {
         "JS",
         defaultSourceSet.sourceSetID.copy(sourceSetName = "js"),
         analysisPlatform = Platform.js,
-        sourceRoots = listOf(SourceRootImpl("pl1"))
+        sourceRoots = setOf(File("pl1"))
     )
     protected val jvm = defaultSourceSet.copy(
         "root",
@@ -33,14 +33,14 @@ abstract class HtmlRenderingOnlyTestBase : RenderingOnlyTestBase<Element>() {
         defaultSourceSet.sourceSetID.copy(sourceSetName = "jvm"),
 
         analysisPlatform = Platform.jvm,
-        sourceRoots = listOf(SourceRootImpl("pl1"))
+        sourceRoots = setOf(File("pl1"))
     )
     protected val native = defaultSourceSet.copy(
         "root",
         "NATIVE",
         defaultSourceSet.sourceSetID.copy(sourceSetName = "native"),
         analysisPlatform = Platform.native,
-        sourceRoots = listOf(SourceRootImpl("pl1"))
+        sourceRoots = setOf(File("pl1"))
     )
 
     val files = TestOutputWriter()
diff --git a/plugins/base/src/test/kotlin/renderers/html/SourceSetDependentHintTest.kt b/plugins/base/src/test/kotlin/renderers/html/SourceSetDependentHintTest.kt
index cf7f47e6..77ba390e 100644
--- a/plugins/base/src/test/kotlin/renderers/html/SourceSetDependentHintTest.kt
+++ b/plugins/base/src/test/kotlin/renderers/html/SourceSetDependentHintTest.kt
@@ -1,7 +1,6 @@
 package renderers.html
 
 import org.jetbrains.dokka.Platform
-import org.jetbrains.dokka.SourceRootImpl
 import org.jetbrains.dokka.base.renderers.html.HtmlRenderer
 import org.jetbrains.dokka.pages.TextStyle
 import org.junit.jupiter.api.Test
@@ -10,6 +9,7 @@ import renderers.defaultSourceSet
 import renderers.RenderingOnlyTestBase
 import utils.Div
 import utils.match
+import java.io.File
 
 class SourceSetDependentHintTest : HtmlRenderingOnlyTestBase() {
 
@@ -18,21 +18,21 @@ class SourceSetDependentHintTest : HtmlRenderingOnlyTestBase() {
         "pl1",
         defaultSourceSet.sourceSetID.copy(sourceSetName =  "pl1"),
         analysisPlatform = Platform.js,
-        sourceRoots = listOf(SourceRootImpl("pl1"))
+        sourceRoots = setOf(File("pl1"))
     )
     private val pl2 = defaultSourceSet.copy(
         "root",
         "pl2",
         defaultSourceSet.sourceSetID.copy(sourceSetName =  "pl2"),
         analysisPlatform = Platform.jvm,
-        sourceRoots = listOf(SourceRootImpl("pl1"))
+        sourceRoots = setOf(File("pl1"))
     )
     private val pl3 = defaultSourceSet.copy(
         "root",
         "pl3",
         defaultSourceSet.sourceSetID.copy(sourceSetName =  "pl3"),
         analysisPlatform = Platform.native,
-        sourceRoots = listOf(SourceRootImpl("pl1"))
+        sourceRoots = setOf(File("pl1"))
     )
 
     @Test
diff --git a/plugins/base/test-utils/src/main/kotlin/renderers/defaultSourceSet.kt b/plugins/base/test-utils/src/main/kotlin/renderers/defaultSourceSet.kt
index 7358d2c2..8d19870c 100644
--- a/plugins/base/test-utils/src/main/kotlin/renderers/defaultSourceSet.kt
+++ b/plugins/base/test-utils/src/main/kotlin/renderers/defaultSourceSet.kt
@@ -8,24 +8,24 @@ val defaultSourceSet = DokkaSourceSetImpl(
     moduleDisplayName = "DEFAULT",
     displayName = "DEFAULT",
     sourceSetID = DokkaSourceSetID("DEFAULT", "DEFAULT"),
-    classpath = emptyList(),
-    sourceRoots = emptyList(),
+    classpath = emptySet(),
+    sourceRoots = emptySet(),
     dependentSourceSets = emptySet(),
-    samples = emptyList(),
-    includes = emptyList(),
+    samples = emptySet(),
+    includes = emptySet(),
     includeNonPublic = false,
     includeRootPackage = false,
     reportUndocumented = false,
     skipEmptyPackages = true,
     skipDeprecated = false,
     jdkVersion = 8,
-    sourceLinks = emptyList(),
+    sourceLinks = emptySet(),
     perPackageOptions = emptyList(),
-    externalDocumentationLinks = emptyList(),
+    externalDocumentationLinks = emptySet(),
     languageVersion = null,
     apiVersion = null,
     noStdlibLink = false,
     noJdkLink = false,
-    suppressedFiles = emptyList(),
+    suppressedFiles = emptySet(),
     analysisPlatform = Platform.DEFAULT
 )
diff --git a/plugins/gfm/src/test/kotlin/renderers/gfm/DivergentTest.kt b/plugins/gfm/src/test/kotlin/renderers/gfm/DivergentTest.kt
index 2381ad07..cd9b9dfc 100644
--- a/plugins/gfm/src/test/kotlin/renderers/gfm/DivergentTest.kt
+++ b/plugins/gfm/src/test/kotlin/renderers/gfm/DivergentTest.kt
@@ -2,7 +2,6 @@ package renderers.gfm
 
 import org.jetbrains.dokka.DokkaSourceSetID
 import org.jetbrains.dokka.Platform
-import org.jetbrains.dokka.SourceRootImpl
 import org.jetbrains.dokka.gfm.CommonmarkRenderer
 import org.jetbrains.dokka.links.DRI
 import org.jetbrains.dokka.pages.ContentDivergentGroup
@@ -17,21 +16,21 @@ class DivergentTest : GfmRenderingOnlyTestBase() {
         "js",
         DokkaSourceSetID("root", "js"),
         analysisPlatform = Platform.js,
-        sourceRoots = listOf(SourceRootImpl("pl1"))
+        sourceRoots = setOf(File("pl1"))
     )
     private val jvm = defaultSourceSet.copy(
         "root",
         "jvm",
         DokkaSourceSetID("root", "jvm"),
         analysisPlatform = Platform.jvm,
-        sourceRoots = listOf(SourceRootImpl("pl1"))
+        sourceRoots = setOf(File("pl1"))
     )
     private val native = defaultSourceSet.copy(
         "root",
         "native",
         DokkaSourceSetID("root", "native"),
         analysisPlatform = Platform.native,
-        sourceRoots = listOf(SourceRootImpl("pl1"))
+        sourceRoots = setOf(File("pl1"))
     )
 
     @Test
diff --git a/plugins/gfm/src/test/kotlin/renderers/gfm/SourceSetDependentHintTest.kt b/plugins/gfm/src/test/kotlin/renderers/gfm/SourceSetDependentHintTest.kt
index e181e3a2..de473db0 100644
--- a/plugins/gfm/src/test/kotlin/renderers/gfm/SourceSetDependentHintTest.kt
+++ b/plugins/gfm/src/test/kotlin/renderers/gfm/SourceSetDependentHintTest.kt
@@ -2,12 +2,12 @@ package renderers.gfm
 
 import org.jetbrains.dokka.DokkaSourceSetID
 import org.jetbrains.dokka.Platform
-import org.jetbrains.dokka.SourceRootImpl
 import org.jetbrains.dokka.gfm.CommonmarkRenderer
 import org.jetbrains.dokka.pages.TextStyle
 import org.junit.jupiter.api.Test
 import renderers.TestPage
 import renderers.defaultSourceSet
+import java.io.File
 
 class SourceSetDependentHintTest : GfmRenderingOnlyTestBase() {
 
@@ -16,21 +16,21 @@ class SourceSetDependentHintTest : GfmRenderingOnlyTestBase() {
         "pl1",
         DokkaSourceSetID("root", "pl1"),
         analysisPlatform = Platform.js,
-        sourceRoots = listOf(SourceRootImpl("pl1"))
+        sourceRoots = setOf(File("pl1"))
     )
     private val pl2 = defaultSourceSet.copy(
         "root",
         "pl2",
         DokkaSourceSetID("root", "pl2"),
         analysisPlatform = Platform.jvm,
-        sourceRoots = listOf(SourceRootImpl("pl1"))
+        sourceRoots = setOf(File("pl1"))
     )
     private val pl3 = defaultSourceSet.copy(
         "root",
         "pl3",
         DokkaSourceSetID("root", "pl3"),
         analysisPlatform = Platform.native,
-        sourceRoots = listOf(SourceRootImpl("pl1"))
+        sourceRoots = setOf(File("pl1"))
     )
 
     @Test
@@ -134,4 +134,4 @@ class SourceSetDependentHintTest : GfmRenderingOnlyTestBase() {
         CommonmarkRenderer(context).render(page)
         assert(renderedContent == "//[testPage](test-page.md)\n\n [pl1, pl2] a  \n   \n [pl3] b  \n   \n")
     }
-}
\ No newline at end of file
+}
diff --git a/plugins/javadoc/src/test/kotlin/org/jetbrains/dokka/javadoc/JavadocPackageTemplateMapTest.kt b/plugins/javadoc/src/test/kotlin/org/jetbrains/dokka/javadoc/JavadocPackageTemplateMapTest.kt
index 89d5b286..aa5013e5 100644
--- a/plugins/javadoc/src/test/kotlin/org/jetbrains/dokka/javadoc/JavadocPackageTemplateMapTest.kt
+++ b/plugins/javadoc/src/test/kotlin/org/jetbrains/dokka/javadoc/JavadocPackageTemplateMapTest.kt
@@ -110,7 +110,7 @@ internal class JavadocPackageTemplateMapTest : AbstractJavadocTemplateMapTest()
             configuration = config.copy(
                 sourceSets = config.sourceSets.map { sourceSet ->
                     sourceSet.copy(
-                        includes = listOf(File("packages.md"))
+                        includes = setOf(File("packages.md"))
                     )
                 }
             )
diff --git a/runners/cli/src/main/kotlin/cli/main.kt b/runners/cli/src/main/kotlin/cli/main.kt
index df763596..a9c15ec1 100644
--- a/runners/cli/src/main/kotlin/cli/main.kt
+++ b/runners/cli/src/main/kotlin/cli/main.kt
@@ -36,11 +36,13 @@ class GlobalArguments(args: Array<String>) : DokkaConfiguration {
         description = "Configuration for plugins in format fqPluginName=json^^fqPluginName=json..."
     ).default(emptyMap())
 
-    override val pluginsClasspath by parser.option(
+    private val pluginsClasspathList by parser.option(
         ArgTypeFile,
+        fullName = "pluginsClasspath",
         description = "List of jars with dokka plugins (allows many paths separated by the semicolon `;`)"
     ).delimiter(";")
 
+    override val pluginsClasspath: Set<File> by lazy { pluginsClasspathList.toMutableSet() }
 
     override val offlineMode by parser.option(
         ArgType.Boolean,
@@ -77,19 +79,19 @@ class GlobalArguments(args: Array<String>) : DokkaConfiguration {
     init {
         parser.parse(args)
 
-        sourceSets.all {
+        sourceSets.forEach {
             it.perPackageOptions.cast<MutableList<DokkaConfiguration.PackageOptions>>()
                 .addAll(parsePerPackageOptions(globalPackageOptions))
         }
 
-        sourceSets.all {
-            it.externalDocumentationLinks.cast<MutableList<ExternalDocumentationLink>>().addAll(parseLinks(globalLinks))
+        sourceSets.forEach {
+            it.externalDocumentationLinks.cast<MutableSet<ExternalDocumentationLink>>().addAll(parseLinks(globalLinks))
         }
 
         globalSrcLink.forEach {
             if (it.isNotEmpty() && it.contains("="))
                 sourceSets.all { sourceSet ->
-                    sourceSet.sourceLinks.cast<MutableList<SourceLinkDefinitionImpl>>()
+                    sourceSet.sourceLinks.cast<MutableSet<SourceLinkDefinitionImpl>>()
                         .add(SourceLinkDefinitionImpl.parseSourceLinkDefinition(it))
                 }
             else {
@@ -98,10 +100,7 @@ class GlobalArguments(args: Array<String>) : DokkaConfiguration {
         }
 
         sourceSets.forEach {
-            it.externalDocumentationLinks.cast<MutableList<ExternalDocumentationLink>>().addAll(defaultLinks(it))
-            it.externalDocumentationLinks.cast<MutableList<ExternalDocumentationLink>>().replaceAll { link ->
-                ExternalDocumentationLink.Builder(link.url, link.packageListUrl).build()
-            }
+            it.externalDocumentationLinks.cast<MutableSet<ExternalDocumentationLink>>().addAll(defaultLinks(it))
         }
     }
 }
@@ -227,28 +226,28 @@ private fun parseSourceSet(args: Array<String>): DokkaConfiguration.DokkaSourceS
         override val moduleDisplayName = moduleDisplayName ?: moduleName
         override val displayName = displayName
         override val sourceSetID = DokkaSourceSetID(moduleName, sourceSetName)
-        override val classpath = classpath
-        override val sourceRoots = sourceRoots.map { SourceRootImpl(it) }
-        override val dependentSourceSets: Set<DokkaSourceSetID> = dependentSourceSets
+        override val classpath = classpath.toMutableSet()
+        override val sourceRoots = sourceRoots.toMutableSet()
+        override val dependentSourceSets = dependentSourceSets
             .map { dependentSourceSetName -> dependentSourceSetName.split('/').let { DokkaSourceSetID(it[0], it[1]) } }
-            .toSet()
-        override val samples = samples
-        override val includes = includes
+            .toMutableSet()
+        override val samples = samples.toMutableSet()
+        override val includes = includes.toMutableSet()
         override val includeNonPublic = includeNonPublic
         override val includeRootPackage = includeRoo