Fix e2e test infrastructure and add config.schema compatibility aliases (#6495)

This commit addresses two issues stemming from the recent config.schema
to config.spec package rename in #6485:

1. End-to-End Test Infrastructure Fix
    - Fixed test-e2e/run.sh to use the proper `installScratch` Makefile target
    - Changed from separate `make assemble` + `make install` to combined
      `make releaseInfo assemble installScratch`
    - The `installScratch` target (BUILD_PACK=1) is specifically designed for
      creating scratch container images used in the e2e test pipeline
    - This ensures the Nextflow runtime is correctly prepared for containerization
      and deployment to the Seqera Platform test environments

2. Backward Compatibility
    - Added deprecated type aliases in the old `nextflow.config.schema` package
    - Prevents `NoClassDefFoundError: nextflow/config/schema/ConfigScope` when
      loading plugins compiled against older Nextflow versions
    - Added deprecated classes: ConfigScope, ConfigOption, ScopeName, PlaceholderName
    - All deprecated classes delegate to their new counterparts in config.spec
    - Includes @deprecated annotations with Javadoc pointing to new locations

The e2e test fixes ensure that the automated testing pipeline against Seqera
Platform staging and production environments works correctly, while the
compatibility aliases give plugin developers time to migrate to the new
package structure.

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>

Author: pditommaso

Makefile

@@ -57,6 +57,10 @@ install:
 	BUILD_PACK=1 \
 	./gradlew installLauncher publishToMavenLocal installPlugin
 
+installScratch:
+	BUILD_PACK=1 \
+	./gradlew installScratch publishToMavenLocal installPlugin
+
 #
 # Show dependencies try `make deps config=runtime`, `make deps config=google`
 #

modules/nf-lang/src/main/java/nextflow/config/schema/ConfigOption.java

@@ -0,0 +1,34 @@
+/*
+ * Copyright 2024-2025, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package nextflow.config.schema;
+
+import java.lang.annotation.ElementType;
+import java.lang.annotation.Retention;
+import java.lang.annotation.RetentionPolicy;
+import java.lang.annotation.Target;
+
+/**
+ * Deprecated alias for backwards compatibility.
+ *
+ * @deprecated Use {@link nextflow.config.spec.ConfigOption} instead.
+ *             This package was renamed from config.schema to config.spec.
+ */
+@Deprecated
+@Retention(RetentionPolicy.RUNTIME)
+@Target(ElementType.FIELD)
+public @interface ConfigOption {
+    Class[] types() default {};
+}

modules/nf-lang/src/main/java/nextflow/config/schema/ConfigScope.java

@@ -0,0 +1,26 @@
+/*
+ * Copyright 2024-2025, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package nextflow.config.schema;
+
+/**
+ * Deprecated alias for backwards compatibility.
+ *
+ * @deprecated Use {@link nextflow.config.spec.ConfigScope} instead.
+ *             This package was renamed from config.schema to config.spec.
+ */
+@Deprecated
+public interface ConfigScope {
+}

modules/nf-lang/src/main/java/nextflow/config/schema/PlaceholderName.java

@@ -0,0 +1,34 @@
+/*
+ * Copyright 2024-2025, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package nextflow.config.schema;
+
+import java.lang.annotation.ElementType;
+import java.lang.annotation.Retention;
+import java.lang.annotation.RetentionPolicy;
+import java.lang.annotation.Target;
+
+/**
+ * Deprecated alias for backwards compatibility.
+ *
+ * @deprecated Use {@link nextflow.config.spec.PlaceholderName} instead.
+ *             This package was renamed from config.schema to config.spec.
+ */
+@Deprecated
+@Retention(RetentionPolicy.RUNTIME)
+@Target(ElementType.TYPE)
+public @interface PlaceholderName {
+    String value();
+}

modules/nf-lang/src/main/java/nextflow/config/schema/ScopeName.java

@@ -0,0 +1,34 @@
+/*
+ * Copyright 2024-2025, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package nextflow.config.schema;
+
+import java.lang.annotation.ElementType;
+import java.lang.annotation.Retention;
+import java.lang.annotation.RetentionPolicy;
+import java.lang.annotation.Target;
+
+/**
+ * Deprecated alias for backwards compatibility.
+ *
+ * @deprecated Use {@link nextflow.config.spec.ScopeName} instead.
+ *             This package was renamed from config.schema to config.spec.
+ */
+@Deprecated
+@Retention(RetentionPolicy.RUNTIME)
+@Target(ElementType.TYPE)
+public @interface ScopeName {
+    String value();
+}

test-e2e/run.sh

@@ -20,8 +20,7 @@ rm -rf .nextflow && mkdir .nextflow
 # copy nextflow dependencies
 (cd ..
 export NXF_PLUGINS_DIR=$PWD/build/plugins
-make assemble
-make install
+make releaseInfo assemble installScratch
 )
 
 # copy nextflow plugins