Expected and Results

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 should gracefully skip it or treat it as an empty directory, rather than failing.

Actual behavior
shadowJar fails with:
Cannot expand ZIP '/path/to/project/build/classes/java/api' as it does not exist.

Related environment and versions

No response

Reproduction steps

1. Create a multi-module Gradle project with a custom api source set:

  // root build.gradle.kts
  subprojects {
      sourceSets {
          val api by creating
          val main by getting {
              compileClasspath += api.output
              runtimeClasspath += api.output
          }
      }
  }

2. In one of the submodules, apply the Shadow plugin and have Kotlin-only sources in the api source set (no Java files under src/api/java/).
3. Run ./gradlew :module:shadowJar.
4. The task fails because build/classes/java/api is included in runtimeClasspath via api.output, but the directory was never created since there are no Java sources to compile in that source set.

Anything else?

No response