Enable warnings as errors and fix all warnings (#2451)

* Enable warnings as errors and fix all warnings

* Enable skip-metadata-version-check compiler setting

75 files changed, 368 insertions, 333 deletions

diff --git a/build.gradle.kts b/build.gradle.kts
index 0e45f985..d9ee5943 100644
--- a/build.gradle.kts
+++ b/build.gradle.kts
@@ -4,7 +4,7 @@ import org.jetbrains.kotlin.gradle.tasks.KotlinCompile
 plugins {
     kotlin("jvm") apply false
     id("java")
-    id("org.jetbrains.dokka") version "1.5.0"
+    id("org.jetbrains.dokka") version "1.6.20"
     id("io.github.gradle-nexus.publish-plugin")
 }
 
@@ -21,10 +21,13 @@ allprojects {
     tasks.withType(KotlinCompile::class).all {
         kotlinOptions {
             freeCompilerArgs = freeCompilerArgs + listOf(
-                "-Xopt-in=kotlin.RequiresOptIn",
+                "-opt-in=kotlin.RequiresOptIn",
+                "-Xjsr305=strict",
                 "-Xskip-metadata-version-check",
-                "-Xjsr305=strict"
+                // need 1.4 support, otherwise there might be problems with Gradle 6.x (it's bundling Kotlin 1.4)
+                "-Xsuppress-version-warnings"
             )
+            allWarningsAsErrors = true
             languageVersion = language_version
             apiVersion = language_version
             jvmTarget = "1.8"
diff --git a/core/src/main/kotlin/configuration.kt b/core/src/main/kotlin/configuration.kt
index c7feb22e..c26faf28 100644
--- a/core/src/main/kotlin/configuration.kt
+++ b/core/src/main/kotlin/configuration.kt
@@ -235,7 +235,7 @@ interface DokkaConfiguration : Serializable {
 
     interface PackageOptions : Serializable {
         val matchingRegex: String
-        @Deprecated(message = "Use [documentedVisibilities] property for a more flexible control over documented visibilities")
+        @Deprecated("Use [documentedVisibilities] property for a more flexible control over documented visibilities")
         val includeNonPublic: Boolean
         val reportUndocumented: Boolean?
         val skipDeprecated: Boolean
diff --git a/core/src/main/kotlin/defaultConfiguration.kt b/core/src/main/kotlin/defaultConfiguration.kt
index 3ab1782c..8c7c8b5d 100644
--- a/core/src/main/kotlin/defaultConfiguration.kt
+++ b/core/src/main/kotlin/defaultConfiguration.kt
@@ -37,6 +37,7 @@ data class DokkaSourceSetImpl(
     override val dependentSourceSets: Set<DokkaSourceSetID> = emptySet(),
     override val samples: Set<File> = emptySet(),
     override val includes: Set<File> = emptySet(),
+    @Deprecated("Use [documentedVisibilities] property for a more flexible control over documented visibilities")
     override val includeNonPublic: Boolean = DokkaDefaults.includeNonPublic,
     override val reportUndocumented: Boolean = DokkaDefaults.reportUndocumented,
     override val skipEmptyPackages: Boolean = DokkaDefaults.skipEmptyPackages,
@@ -79,6 +80,7 @@ data class SourceLinkDefinitionImpl(
 
 data class PackageOptionsImpl(
     override val matchingRegex: String,
+    @Deprecated("Use [documentedVisibilities] property for a more flexible control over documented visibilities")
     override val includeNonPublic: Boolean,
     override val reportUndocumented: Boolean?,
     override val skipDeprecated: Boolean,
diff --git a/core/src/main/kotlin/pages/PageNodes.kt b/core/src/main/kotlin/pages/PageNodes.kt
index 75e27dcc..c643fd4b 100644
--- a/core/src/main/kotlin/pages/PageNodes.kt
+++ b/core/src/main/kotlin/pages/PageNodes.kt
@@ -21,7 +21,7 @@ interface ContentPage : PageNode {
     val embeddedResources: List<String>
 
     @Deprecated("Deprecated. Remove its usages from your code.",
-        ReplaceWith("documentables.firstOrNull()")
+        ReplaceWith("this.documentables.firstOrNull()")
     )
     val documentable: Documentable?
         get() = if (this is WithDocumentables) this.documentables.firstOrNull() else null
diff --git a/core/test-api/src/main/kotlin/testApi/testRunner/TestDokkaConfigurationBuilder.kt b/core/test-api/src/main/kotlin/testApi/testRunner/TestDokkaConfigurationBuilder.kt
index 623fcc2d..50ab3bad 100644
--- a/core/test-api/src/main/kotlin/testApi/testRunner/TestDokkaConfigurationBuilder.kt
+++ b/core/test-api/src/main/kotlin/testApi/testRunner/TestDokkaConfigurationBuilder.kt
@@ -106,6 +106,7 @@ class DokkaSourceSetBuilder(
     var externalDocumentationLinks: List<ExternalDocumentationLinkImpl> = emptyList(),
     var sourceLinks: List<SourceLinkDefinitionImpl> = emptyList()
 ) {
+    @Suppress("DEPRECATION")
     fun build() = DokkaSourceSetImpl(
         displayName = displayName,
         sourceSetID = DokkaSourceSetID(moduleName, name),
diff --git a/integration-tests/gradle/projects/it-basic-groovy/build.gradle b/integration-tests/gradle/projects/it-basic-groovy/build.gradle
index dc469bba..f368ed10 100644
--- a/integration-tests/gradle/projects/it-basic-groovy/build.gradle
+++ b/integration-tests/gradle/projects/it-basic-groovy/build.gradle
@@ -19,6 +19,23 @@ dokkaHtml {
             displayName.set("custom")
             reportUndocumented.set(true)
         }
+
+        configureEach {
+            perPackageOption { // testing closures
+                matchingRegex.set(".*internal.*")
+                suppress.set(true)
+            }
+
+            sourceLink { // testing closures
+                localDirectory.set(file("src/main"))
+                remoteUrl.set(
+                        new URL(
+                                "https://github.com/Kotlin/dokka/tree/master/" +
+                                        "integration-tests/gradle/projects/it-basic-groovy/src/main"
+                        )
+                )
+            }
+        }
     }
 
 }
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 452b821c..46916705 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
@@ -114,8 +114,11 @@ class AnalysisEnvironment(val messageCollector: MessageCollector, val analysisPl
             JavadocTagInfo.EP_NAME, JavadocTagInfo::class.java
         )
 
+        @Suppress("DEPRECATION")
+        val extensionArea = Extensions.getRootArea()
+
         CoreApplicationEnvironment.registerExtensionPoint(
-            Extensions.getRootArea(),
+            extensionArea,
             CustomJavadocTagProvider.EP_NAME, CustomJavadocTagProvider::class.java
         )
 
@@ -588,8 +591,12 @@ class AnalysisEnvironment(val messageCollector: MessageCollector, val analysisPl
             instances: List<T>,
             disposable: Disposable
         ) {
-            if (Extensions.getRootArea().hasExtensionPoint(appExtension.extensionPointName))
+            @Suppress("DEPRECATION")
+            val extensionArea = Extensions.getRootArea()
+
+            if (extensionArea.hasExtensionPoint(appExtension.extensionPointName)) {
                 return
+            }
 
             appExtension.registerExtensionPoint()
             instances.forEach { extension -> appExtension.registerExtension(extension, disposable) }
diff --git a/kotlin-analysis/src/main/kotlin/org/jetbrains/dokka/analysis/DokkaResolutionFacade.kt b/kotlin-analysis/src/main/kotlin/org/jetbrains/dokka/analysis/DokkaResolutionFacade.kt
index c0fafc25..b278ef6e 100644
--- a/kotlin-analysis/src/main/kotlin/org/jetbrains/dokka/analysis/DokkaResolutionFacade.kt
+++ b/kotlin-analysis/src/main/kotlin/org/jetbrains/dokka/analysis/DokkaResolutionFacade.kt
@@ -75,6 +75,7 @@ class DokkaResolutionFacade(
                     if (key != element) {
                         throw UnsupportedOperationException()
                     }
+                    @Suppress("UNCHECKED_CAST")
                     return when {
                         slice == BindingContext.DECLARATION_TO_DESCRIPTOR -> descriptor as V
                         slice == BindingContext.PRIMARY_CONSTRUCTOR_PARAMETER && (element as KtParameter).hasValOrVar() -> descriptor as V
diff --git a/kotlin-analysis/src/main/kotlin/org/jetbrains/dokka/analysis/JvmDependenciesIndexImpl.kt b/kotlin-analysis/src/main/kotlin/org/jetbrains/dokka/analysis/JvmDependenciesIndexImpl.kt
index 3632337a..c64f2fab 100644
--- a/kotlin-analysis/src/main/kotlin/org/jetbrains/dokka/analysis/JvmDependenciesIndexImpl.kt
+++ b/kotlin-analysis/src/main/kotlin/org/jetbrains/dokka/analysis/JvmDependenciesIndexImpl.kt
@@ -20,7 +20,7 @@ import com.intellij.ide.highlighter.JavaClassFileType
 import com.intellij.ide.highlighter.JavaFileType
 import com.intellij.openapi.vfs.VfsUtilCore
 import com.intellij.openapi.vfs.VirtualFile
-import com.intellij.util.containers.IntArrayList
+import it.unimi.dsi.fastutil.ints.IntArrayList
 import gnu.trove.THashMap
 import org.jetbrains.kotlin.name.ClassId
 import org.jetbrains.kotlin.name.FqName
@@ -54,7 +54,7 @@ class JvmDependenciesIndexImpl(_roots: List<JavaRoot>) : JvmDependenciesIndex {
         Cache().apply {
             roots.indices.forEach(rootIndices::add)
             rootIndices.add(maxIndex)
-            rootIndices.trimToSize()
+            rootIndices.trim()
         }
     }
 
@@ -121,8 +121,8 @@ class JvmDependenciesIndexImpl(_roots: List<JavaRoot>) : JvmDependenciesIndex {
         // NOTE: indices manipulation instead of using caches.reversed() is here for performance reasons
         for (cacheIndex in caches.lastIndex downTo 0) {
             val cacheRootIndices = caches[cacheIndex].rootIndices
-            for (i in 0 until cacheRootIndices.size()) {
-                val rootIndex = cacheRootIndices[i]
+            for (i in 0 until cacheRootIndices.size) {
+                val rootIndex = cacheRootIndices.getInt(i)
                 if (rootIndex <= processedRootsUpTo) continue // roots with those indices have been processed by now
 
                 val directoryInRoot =
@@ -138,7 +138,12 @@ class JvmDependenciesIndexImpl(_roots: List<JavaRoot>) : JvmDependenciesIndex {
                     }
                 }
             }