Fixes: #601 and #562

I tested this on the java-application-with-resources sample. If I set <scope> of org.apache.commons to provided:

• without this fix classpath looks like this:

[INFO] Executing: /.sdkman/candidates/java/21.0.4-graal/bin/native-image -cp /native-build-tools/samples/java-application-with-resources/target/classes:/native-build-tools/samples/java-application-with-resources/target/test-classes:/native-build-tools/samples/java-application-with-resources/src/test/resources:/.m2/repository/org/junit/jupiter/junit-jupiter/5.10.0/junit-jupiter-5.10.0.jar:/.m2/repository/org/junit/jupiter/junit-jupiter-api/5.10.0/junit-jupiter-api-5.10.0.jar:/.m2/repository/org/opentest4j/opentest4j/1.3.0/opentest4j-1.3.0.jar:/.m2/repository/org/junit/platform/junit-platform-commons/1.10.0/junit-platform-commons-1.10.0.jar:/.m2/repository/org/apiguardian/apiguardian-api/1.1.2/apiguardian-api-1.1.2.jar:/.m2/repository/org/junit/jupiter/junit-jupiter-params/5.10.0/junit-jupiter-params-5.10.0.jar:/.m2/repository/org/junit/jupiter/junit-jupiter-engine/5.10.0/junit-jupiter-engine-5.10.0.jar:/.m2/repository/org/junit/platform/junit-platform-engine/1.10.0/junit-platform-engine-1.10.0.jar:/.m2/repository/org/graalvm/buildtools/native-maven-plugin/0.10.7-SNAPSHOT/native-maven-plugin-0.10.7-SNAPSHOT.jar:/.m2/repository/org/graalvm/buildtools/utils/0.10.7-SNAPSHOT/utils-0.10.7-SNAPSHOT.jar:/.m2/repository/org/graalvm/buildtools/graalvm-reachability-metadata/0.10.7-SNAPSHOT/graalvm-reachability-metadata-0.10.7-SNAPSHOT.jar:/.m2/repository/org/graalvm/buildtools/junit-platform-native/0.10.7-SNAPSHOT/junit-platform-native-0.10.7-SNAPSHOT.jar:/.m2/repository/org/junit/platform/junit-platform-console/1.10.0/junit-platform-console-1.10.0.jar:/.m2/repository/org/junit/platform/junit-platform-reporting/1.10.0/junit-platform-reporting-1.10.0.jar:/.m2/repository/org/apiguardian/apiguardian-api/1.1.2/apiguardian-api-1.1.2.jar:/.m2/repository/org/junit/platform/junit-platform-launcher/1.10.0/junit-platform-launcher-1.10.0.jar:/.m2/repository/org/junit/platform/junit-platform-engine/1.10.0/junit-platform-engine-1.10.0.jar:/.m2/repository/org/opentest4j/opentest4j/1.3.0/opentest4j-1.3.0.jar:/.m2/repository/org/junit/platform/junit-platform-commons/1.10.0/junit-platform-commons-1.10.0.jar:/.m2/repository/org/junit/jupiter/junit-jupiter/5.10.0/junit-jupiter-5.10.0.jar:/.m2/repository/org/junit/jupiter/junit-jupiter-api/5.10.0/junit-jupiter-api-5.10.0.jar:/.m2/repository/org/junit/jupiter/junit-jupiter-params/5.10.0/junit-jupiter-params-5.10.0.jar:/.m2/repository/org/junit/jupiter/junit-jupiter-engine/5.10.0/junit-jupiter-engine-5.10.0.jar --no-fallback -o /native-build-tools/samples/java-application-with-resources/target/native-tests -Djunit.platform.listeners.uid.tracking.output.dir=/native-build-tools/samples/java-application-with-resources/target/test-ids --features=org.graalvm.junit.platform.JUnitPlatformFeature -H:ConfigurationFileDirectories=/native-build-tools/samples/java-application-with-resources/target/native/generated/generateTestResourceConfig org.graalvm.junit.platform.NativeImageJUnitLauncher

and there is no org.apache.commons dependency.

• with this fix classpath looks like this:

[INFO] Executing: /.sdkman/candidates/java/21.0.4-graal/bin/native-image -cp /native-build-tools/samples/java-application-with-resources/target/classes:/native-build-tools/samples/java-application-with-resources/target/test-classes:/native-build-tools/samples/java-application-with-resources/src/test/resources:/.m2/repository/org/apache/commons/commons-lang3/3.12.0/commons-lang3-3.12.0.jar:/.m2/repository/org/junit/jupiter/junit-jupiter/5.10.0/junit-jupiter-5.10.0.jar:/.m2/repository/org/junit/jupiter/junit-jupiter-api/5.10.0/junit-jupiter-api-5.10.0.jar:/.m2/repository/org/opentest4j/opentest4j/1.3.0/opentest4j-1.3.0.jar:/.m2/repository/org/junit/platform/junit-platform-commons/1.10.0/junit-platform-commons-1.10.0.jar:/.m2/repository/org/apiguardian/apiguardian-api/1.1.2/apiguardian-api-1.1.2.jar:/.m2/repository/org/junit/jupiter/junit-jupiter-params/5.10.0/junit-jupiter-params-5.10.0.jar:/.m2/repository/org/junit/jupiter/junit-jupiter-engine/5.10.0/junit-jupiter-engine-5.10.0.jar:/.m2/repository/org/junit/platform/junit-platform-engine/1.10.0/junit-platform-engine-1.10.0.jar:/.m2/repository/org/graalvm/buildtools/native-maven-plugin/0.10.7-SNAPSHOT/native-maven-plugin-0.10.7-SNAPSHOT.jar:/.m2/repository/org/graalvm/buildtools/utils/0.10.7-SNAPSHOT/utils-0.10.7-SNAPSHOT.jar:/.m2/repository/org/graalvm/buildtools/graalvm-reachability-metadata/0.10.7-SNAPSHOT/graalvm-reachability-metadata-0.10.7-SNAPSHOT.jar:/.m2/repository/org/graalvm/buildtools/junit-platform-native/0.10.7-SNAPSHOT/junit-platform-native-0.10.7-SNAPSHOT.jar:/.m2/repository/org/junit/platform/junit-platform-console/1.10.0/junit-platform-console-1.10.0.jar:/.m2/repository/org/junit/platform/junit-platform-reporting/1.10.0/junit-platform-reporting-1.10.0.jar:/.m2/repository/org/apiguardian/apiguardian-api/1.1.2/apiguardian-api-1.1.2.jar:/.m2/repository/org/junit/platform/junit-platform-launcher/1.10.0/junit-platform-launcher-1.10.0.jar:/.m2/repository/org/junit/platform/junit-platform-engine/1.10.0/junit-platform-engine-1.10.0.jar:/.m2/repository/org/opentest4j/opentest4j/1.3.0/opentest4j-1.3.0.jar:/.m2/repository/org/junit/platform/junit-platform-commons/1.10.0/junit-platform-commons-1.10.0.jar:/.m2/repository/org/junit/jupiter/junit-jupiter/5.10.0/junit-jupiter-5.10.0.jar:/.m2/repository/org/junit/jupiter/junit-jupiter-api/5.10.0/junit-jupiter-api-5.10.0.jar:/.m2/repository/org/junit/jupiter/junit-jupiter-params/5.10.0/junit-jupiter-params-5.10.0.jar:/.m2/repository/org/junit/jupiter/junit-jupiter-engine/5.10.0/junit-jupiter-engine-5.10.0.jar --no-fallback -o /native-build-tools/samples/java-application-with-resources/target/native-tests -Djunit.platform.listeners.uid.tracking.output.dir=/native-build-tools/samples/java-application-with-resources/target/test-ids --features=org.graalvm.junit.platform.JUnitPlatformFeature -H:ConfigurationFileDirectories=/native-build-tools/samples/java-application-with-resources/target/native/generated/generateTestResourceConfig org.graalvm.junit.platform.NativeImageJUnitLauncher

and we can see that there is an entry fororg.apache.commons (/.m2/repository/org/apache/commons/commons-lang3/3.12.0/commons-lang3-3.12.0.jar)

NOTE: when I run mvn -Pnative package -DskipNativeTests classpath doesn't have org.apache.commons dependency if it has <scope>provided</scope>:

[INFO] Executing: /.sdkman/candidates/java/21.0.4-graal/bin/native-image -cp /native-build-tools/samples/java-application-with-resources/target/maven-app-with-tests.jar --no-fallback -o /native-build-tools/samples/java-application-with-resources/target/example-app -H:ConfigurationFileDirectories=/native-build-tools/samples/java-application-with-resources/target/native/generated/generateTestResourceConfig,/native-build-tools/samples/java-application-with-resources/target/native/generated/generateResourceConfig -H:ConfigurationFileDirectories=/native-build-tools/samples/java-application-with-resources/target/native/generated/generateTestResourceConfig,/native-build-tools/samples/java-application-with-resources/target/native/generated/generateResourceConfig -H:ConfigurationFileDirectories=/native-build-tools/samples/java-application-with-resources/target/native/generated/generateTestResourceConfig,/native-build-tools/samples/java-application-with-resources/target/native/generated/generateResourceConfig org.graalvm.demo.Application

(without explicitly defined <scope> the dependency appears on classpath)