Fix failing for non-existent class directories (#1976)

* Initial plan

* fix: skip non-existent dependency directories in shadowJar task

Fixes #1975. When a project dependency includes a class output directory
that does not exist (e.g., build/classes/java/api from a custom source
set with no Java sources), shadowJar now gracefully skips it instead of
failing with "Cannot expand ZIP ... as it does not exist."

Also adds a functional test to verify the fix.

Co-authored-by: Goooler <10363352+Goooler@users.noreply.github.com>

* Logging for info level

* Update changelog

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: Goooler <10363352+Goooler@users.noreply.github.com>
Co-authored-by: Goooler <wangzongler@gmail.com>

Author: Copilot

docs/changes/README.md

@@ -22,6 +22,7 @@
 
 - Fix interaction with Gradle artifact transforms. ([#1345](https://github.com/GradleUp/shadow/pull/1345))
 - Fix `skipStringConstants` per-relocator behavior in `mapName`. ([#1968](https://github.com/GradleUp/shadow/pull/1968))
+- Fix failing for non-existent class directories. ([#1976](https://github.com/GradleUp/shadow/pull/1976))
 
 ## [9.3.2](https://github.com/GradleUp/shadow/releases/tag/9.3.2) - 2026-02-27
 

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

@@ -813,6 +813,25 @@ class JavaPluginsTest : BasePluginTest() {
     }
   }
 
+  @Issue("https://github.com/GradleUp/shadow/issues/1975")
+  @Test
+  fun skipNonExistentDependencyDirectory() {
+    val nonExistentDir = projectRoot.resolve("non-existent-dir")
+
+    projectScript.appendText(
+      """
+        dependencies {
+          ${implementationFiles(nonExistentDir)}
+        }
+      """
+        .trimIndent()
+    )
+
+    val result = runWithSuccess(shadowJarPath)
+
+    assertThat(result.task(shadowJarPath)).isNotNull().transform { it.outcome }.isEqualTo(SUCCESS)
+  }
+
   @Issue("https://github.com/GradleUp/shadow/issues/915")
   @Test
   fun failBuildIfProcessingBadJar() {

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

@@ -451,6 +451,9 @@ public abstract class ShadowJar : Jar() {
   override fun copy() {
     includedDependencies.files.forEach { file ->
       when {
+        !file.exists() -> {
+          logger.info("Skipping non-existent dependency: {}", file)
+        }
         file.isDirectory -> {
           from(file)
         }