Replace SetProperty<Configuration> with ConfigurableFileCollection on ShadowJar

src/functionalTest/kotlin/com/github/jengelman/gradle/plugins/shadow/JavaPluginsTest.kt

@@ -714,7 +714,7 @@ class JavaPluginsTest : BasePluginTest() {
           description = 'Create a combined JAR of project and test dependencies'
           archiveClassifier = 'test'
           from sourceSets.named('test').map { it.output }
-          configurations = project.configurations.named('testRuntimeClasspath').map { [it] }
+          setConfigurations([project.configurations.testRuntimeClasspath])
           manifest {
             attributes '$mainClassAttributeKey': 'my.Main'
           }
@@ -751,7 +751,7 @@ class JavaPluginsTest : BasePluginTest() {
           description = 'Create a combined JAR of project and test dependencies'
           archiveClassifier = 'test'
           from sourceSets.named('test').map { it.output }
-          configurations = project.configurations.named('testRuntimeClasspath').map { [it] }
+          setConfigurations([project.configurations.testRuntimeClasspath])
           manifest {
             attributes '$mainClassAttributeKey': 'my.Main'
           }
@@ -795,7 +795,7 @@ class JavaPluginsTest : BasePluginTest() {
         def $dependencyShadowJar = tasks.register('$dependencyShadowJar', ${ShadowJar::class.java.name}) {
           description = 'Create a shadow JAR of all dependencies'
           archiveClassifier = 'dep'
-          configurations = project.configurations.named('runtimeClasspath').map { [it] }
+          setConfigurations([project.configurations.runtimeClasspath])
         }
       """
         .trimIndent()
@@ -1185,7 +1185,7 @@ class JavaPluginsTest : BasePluginTest() {
         }
 
         $shadowJarTask {
-          configurations = [project.configurations.runtimeClasspath]
+          setConfigurations([project.configurations.runtimeClasspath])
         }
 
         configurations.runtimeClasspath {

src/functionalTest/kotlin/com/github/jengelman/gradle/plugins/shadow/PublishingTest.kt

@@ -305,7 +305,7 @@ class PublishingTest : BasePluginTest() {
             description = 'Create a combined JAR of project and test dependencies'
             archiveClassifier = 'tests'
             from sourceSets.named('test').map { it.output }
-            configurations = project.configurations.named('testRuntimeClasspath').map { [it] }
+            setConfigurations([project.configurations.testRuntimeClasspath])
           }
         """
             .trimIndent(),

src/functionalTest/kotlin/com/github/jengelman/gradle/plugins/shadow/RelocationTest.kt

@@ -466,7 +466,7 @@ class RelocationTest : BasePluginTest() {
           implementation 'junit:junit:3.8.2'
         }
         $shadowJarTask {
-          configurations = []
+          clearConfigurations()
           relocate('', 'foo/')
         }
       """

src/main/kotlin/com/github/jengelman/gradle/plugins/shadow/ShadowJavaPlugin.kt

@@ -42,7 +42,7 @@ constructor(private val softwareComponentFactory: SoftwareComponentFactory) : Pl
     val taskProvider =
       registerShadowJarCommon(tasks.named("jar", Jar::class.java)) { task ->
         task.from(sourceSets.named("main").map { it.output })
-        task.configurations.convention(provider { listOf(runtimeConfiguration) })
+        task.addConfiguration(runtimeConfiguration)
       }
     artifacts.add(configurations.shadow.name, taskProvider)
   }

src/main/kotlin/com/github/jengelman/gradle/plugins/shadow/ShadowKmpPlugin.kt

@@ -36,10 +36,8 @@ public abstract class ShadowKmpPlugin : Plugin<Project> {
     val kotlinJvmMain = target.compilations.named("main")
     registerShadowJarCommon(tasks.named(target.artifactsTaskName, Jar::class.java)) { task ->
       task.from(kotlinJvmMain.map { it.output.allOutputs })
-      task.configurations.convention(
-        provider {
-          listOf(configurations.getByName(kotlinJvmMain.get().runtimeDependencyConfigurationName))
-        }
+      task.addConfiguration(
+        configurations.getByName(kotlinJvmMain.get().runtimeDependencyConfigurationName)
       )
 
       if (!isAtLeastKgp("1.9.0")) return@registerShadowJarCommon

src/main/kotlin/com/github/jengelman/gradle/plugins/shadow/tasks/ShadowJar.kt

@@ -72,6 +72,9 @@ public abstract class ShadowJar : Jar() {
     project.configurations.findByName(ShadowBasePlugin.CONFIGURATION_NAME) ?: project.files()
   }
 
+  @Transient
+  private val _sourceConfigurations = mutableListOf<Configuration>()
+
   init {
     group = LifecycleBasePlugin.BUILD_GROUP
     description = "Create a combined JAR of project and runtime dependencies"
@@ -101,7 +104,7 @@ public abstract class ShadowJar : Jar() {
   @get:Classpath
   public open val toMinimize: ConfigurableFileCollection = objectFactory.fileCollection {
     minimizeJar.map {
-      if (it) (dependencyFilterForMinimize.resolve(configurations.get()) - apiJars) else emptySet()
+      if (it) (dependencyFilterForMinimize.resolve(_sourceConfigurations) - apiJars) else emptySet()
     }
   }
 
@@ -132,12 +135,34 @@ public abstract class ShadowJar : Jar() {
   @get:Nested public open val relocators: SetProperty<Relocator> = objectFactory.setProperty()
 
   /**
-   * The configurations to include dependencies from.
+   * The resolved files from configurations to include dependencies from.
+   *
+   * Do not add to this file collection directly. Use [addConfiguration], [setConfigurations],
+   * or [clearConfigurations] instead, so that dependency filtering works correctly.
    *
    * Defaults to a set that contains `runtimeClasspath` or `runtime` configuration.
    */
   @get:Classpath
-  public open val configurations: SetProperty<Configuration> = objectFactory.setProperty()
+  public open val configurations: ConfigurableFileCollection = objectFactory.fileCollection()
+
+  /** Add a [Configuration] whose dependencies should be shadowed. */
+  public open fun addConfiguration(config: Configuration) {
+    _sourceConfigurations.add(config)
+    configurations.from(config)
+  }
+
+  /** Replace all configurations with the given set. */
+  public open fun setConfigurations(configs: Iterable<Configuration>) {
+    _sourceConfigurations.clear()
+    configurations.setFrom()
+    configs.forEach { addConfiguration(it) }
+  }
+
+  /** Remove all configurations. */
+  public open fun clearConfigurations() {
+    _sourceConfigurations.clear()
+    configurations.setFrom()
+  }
 
   @get:Input
   public open val dependencyFilter: Property<DependencyFilter> =
@@ -146,7 +171,7 @@ public abstract class ShadowJar : Jar() {
   /** Final dependencies to be shadowed. */
   @get:Classpath
   public open val includedDependencies: ConfigurableFileCollection = objectFactory.fileCollection {
-    dependencyFilter.zip(configurations) { df, cs -> df.resolve(cs) }
+    dependencyFilter.map { df -> df.resolve(_sourceConfigurations) }
   }
 
   /**

src/test/kotlin/com/github/jengelman/gradle/plugins/shadow/ShadowPropertiesTest.kt

@@ -154,7 +154,7 @@ class ShadowPropertiesTest {
         assertThat(mainClass.orNull).isNull()
 
         assertThat(relocationPrefix.get()).isEqualTo(ShadowBasePlugin.SHADOW)
-        assertThat(configurations.get()).containsOnly(runtimeConfiguration)
+        assertThat(configurations.files).isEqualTo(runtimeConfiguration.files)
       }
     }