diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 98b45e82..6074178e 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -60,7 +60,7 @@ jobs:
         with:
           name: nf-quilt-test-reports-${{ matrix.os }}-${{ matrix.java_version }}
           path: |
-            D:\a\nf-quilt\nf-quilt\plugins\nf-quilt\build\reports\
+            D:\a\nf-quilt\nf-quilt\build\reports\
           overwrite: true
       - name: Archive production artifacts (Linux and MacOS)
         uses: actions/upload-artifact@v4
@@ -68,5 +68,5 @@ jobs:
         with:
           name: nf-quilt-test-reports-${{ matrix.os }}-${{ matrix.java_version }}
           path: |
-            ${{ github.workspace }}/plugins/nf-quilt/build/reports/
+            ${{ github.workspace }}/build/reports/
           overwrite: true
diff --git a/Makefile b/Makefile
index ddfb9d50..297c54f5 100644
--- a/Makefile
+++ b/Makefile
@@ -2,152 +2,105 @@ sinclude .env # create from example.env
 PROJECT ?= nf-quilt
 WRITE_BUCKET ?= write-bucket-not-set
 FRAGMENT ?= &path=.
-NF_DIR ?= ../nextflow
-NF_GIT ?= $(NF_DIR)/nextflow
-NF_BIN ?= ./launch.sh
-PID ?= $$$$
 QUERY ?= ?Name=$(USER)&Owner=Kevin+Moore&Date=2023-03-07&Type=CRISPR&Notebook+URL=http%3A%2F%2Fexample.com
-VERSION ?= $(shell grep 'Plugin-Version' plugins/$(PROJECT)/src/resources/META-INF/MANIFEST.MF | awk '{ print $$2 }')
+VERSION ?= $(shell grep "^version" build.gradle | head -1 | awk -F"'" '{ print $$2 }')
 NXF_VER ?= $(shell cat VERSION)
 TEST_URI ?= quilt+s3://$(WRITE_BUCKET)$(QUERY)\#package=nf-quilt/dest-$(VERSION)$(FRAGMENT)
 PIPELINE ?= sarek
-PIPE_OUT ?=  quilt+s3://$(WRITE_BUCKET)\#package=$(PROJECT)/$(PIPELINE)
-NXF_PLUGINS_TEST_REPOSITORY ?= https://github.com/quiltdata/nf-quilt/releases/download/$(VERSION)/nf-quilt-$(VERSION)-meta.json
+PIPE_OUT ?= quilt+s3://$(WRITE_BUCKET)\#package=$(PROJECT)/$(PIPELINE)
 S3_BASE = s3://$(WRITE_BUCKET)/$(PROJECT)
-REPORT ?= ./plugins/$(PROJECT)/build/reports/tests/test/index.html
+REPORT ?= ./build/reports/tests/test/index.html
 
-verify: #compile
+.PHONY: all assemble clean test test-all check rebuild install package release verify fast \
+        check-env pkg-test dyn-test s3-overlay s3-test s3-in s3-out \
+        pkg-fail path-input deps refresh
+
+all: assemble
+
+assemble:
+	./gradlew assemble
+
+clean:
+	rm -rf .nextflow*
+	rm -rf work results null
+	rm -rf build
+	./gradlew clean
+
+test:
+	./gradlew test
+
+check:
+	./gradlew check --warning-mode all
+
+verify:
 	echo $(WRITE_BUCKET)
 	./gradlew test ${ONE} || open $(REPORT)
 
 fast:
 	./gradlew test ${ONE} --fail-fast || open $(REPORT)
 # example: make fast ONE="--tests QuiltProductTest"
+
 check-env:
 	echo $(VERSION)
 	echo $(WRITE_BUCKET)
 	echo "$(TEST_URI)"
-	echo "Use 'make WRITE_BUCKET=<value>' to override" 
+	echo "Use 'make WRITE_BUCKET=<value>' to override"
 	printenv MAKEFLAGS
 
-clean:
-	./gradlew clean
-	rm -rf null results work
-	rm -rf build */build */*/build plugins/nf-quilt/bin
-	rm -f .nextflow.log* .launch*classpath
-
-clean-all: clean
-	rm -rf .gradle buildSrc/.gradle
-
 rebuild:
 	./gradlew clean build --refresh-dependencies
 
-compile:
-	./gradlew compileGroovy exportClasspath
-	@echo "DONE `date`"
-
-nextflow:
-	if [ ! -d "$(NF_DIR)" ]; then git clone https://github.com/nextflow-io/nextflow.git  "$(NF_DIR)"; fi
-	cd "$(NF_DIR)"; git checkout && make compile && git restore .; cd ..
-
-compile-all: nextflow compile
-
-check:
-	./gradlew check --warning-mode all
-
-.PHONY: clean test test-all all pkg-test tower-test
-
-test: clean compile check verifyCoverage
-
-test-nextflow: clean nextflow-git compile check
-
-test-all: clean compile-all check coverage
+test-all: clean test
 
-coverage:
-	./gradlew jacocoTestReport
-	open plugins/nf-quilt/build/reports/jacoco/test/html/index.html
+install: assemble
+	./gradlew installPlugin
 
-verifyCoverage:
-	./gradlew jacocoTestCoverageVerification
+package:
+	./gradlew packagePlugin
 
-groovysh:
-	./gradlew -q --no-daemon --console=plain --init-script groovysh-task.gradle groovysh
+release:
+	./gradlew releasePlugin
 
 #
-# Create packages
+# Create packages (real-S3 integration tests).
+# These run the plugin via `nextflow` directly. Requires `nextflow` on PATH.
 #
 
-pkg-test: compile #-all
+pkg-test: install
 	echo "$(TEST_URI)"
-	$(NF_BIN) run ./main.nf -profile standard -plugins $(PROJECT) --outdir "$(TEST_URI)"
+	nextflow run ./main.nf -profile standard -plugins $(PROJECT)@$(VERSION) --outdir "$(TEST_URI)"
 
-dyn-test: compile #-all
-	$(NF_BIN) run wf/main.dynamic.nf -profile standard -plugins $(PROJECT)
+dyn-test: install
+	nextflow run wf/main.dynamic.nf -profile standard -plugins $(PROJECT)@$(VERSION)
 
-s3-overlay: compile
-	$(NF_BIN) run ./main.nf --plugins $(PROJECT) --outdir "$(S3_BASE)/s3-overlay" --input "$(S3_BASE)/s3-in"  
+s3-overlay: install
+	nextflow run ./main.nf --plugins $(PROJECT)@$(VERSION) --outdir "$(S3_BASE)/s3-overlay" --input "$(S3_BASE)/s3-in"
 
-s3-test: compile
-	$(NF_BIN) run ./main.nf --outdir "$(S3_BASE)/s3-test" --input "$(S3_BASE)/s3-in"
+s3-test: install
+	nextflow run ./main.nf -profile standard -plugins $(PROJECT)@$(VERSION) --outdir "$(S3_BASE)/s3-test" --input "$(S3_BASE)/s3-in"
 
-s3-in: compile
-	$(NF_BIN) run ./main.nf -profile standard -plugins $(PROJECT) --outdir "$(TEST_URI)" --input "$(S3_BASE)/s3-in"
+s3-in: install
+	nextflow run ./main.nf -profile standard -plugins $(PROJECT)@$(VERSION) --outdir "$(TEST_URI)" --input "$(S3_BASE)/s3-in"
 
-s3-out: compile
-	$(NF_BIN) run ./main.nf -profile standard -plugins $(PROJECT) --outdir "$(S3_BASE)/s3-out"
+s3-out: install
+	nextflow run ./main.nf -profile standard -plugins $(PROJECT)@$(VERSION) --outdir "$(S3_BASE)/s3-out"
 
-pkg-fail: compile
+pkg-fail: install
 	echo "$(TEST_URI)"
-	$(NF_BIN) run wf/fail.nf -profile standard -plugins $(PROJECT) --outdir "$(TEST_URI)"
+	nextflow run wf/fail.nf -profile standard -plugins $(PROJECT)@$(VERSION) --outdir "$(TEST_URI)"
 
-path-input: compile
+path-input: install
 	mkdir -p work
 	date > work/COPY_THIS.md
 	echo "$(TEST_URI)"
-	$(NF_BIN) run wf/main.path.nf -profile standard -plugins $(PROJECT) --outdir "./results"
-
-tower-test: $(NF_BIN)
-	$(NF_BIN) run "https://github.com/quiltdata/nf-quilt" -name local_einstein  -with-tower -r main -latest --pub "$(TEST_URI)"
-
-#
-# Production Testing
-#
-
-nf-git-ver: $(NF_GIT)
-	NXF_VER=$(NXF_VER) $(NF_GIT) -v
-
-
-$(PIPELINE): nf-git-ver
-	NXF_PLUGINS_TEST_REPOSITORY=$(NXF_PLUGINS_TEST_REPOSITORY) NXF_VER=$(NXF_VER) $(NF_GIT) run nf-core/$(PIPELINE) -r master -profile test,docker -plugins $(PROJECT)@$(VERSION) --outdir "$(PIPE_OUT)"
-
-fetchngs: nf-git-ver
-	NXF_PLUGINS_TEST_REPOSITORY=$(NXF_PLUGINS_TEST_REPOSITORY) NXF_VER=$(NXF_VER) $(NF_GIT) run nf-core/fetchngs -r master -profile test,docker -plugins $(PROJECT)@$(VERSION) --input ../nf-quilt/wf/ids.csv --outdir s3://$(WRITE_BUCKET)/nf-quilt/fetchngs
+	nextflow run wf/main.path.nf -profile standard -plugins $(PROJECT)@$(VERSION) --outdir "./results"
 
 #
 # Show dependencies
 #
 
 deps:
-	./gradlew -q ${mm}dependencies
-
-update:
-	./gradlew useLatestVersions
-	make check
+	./gradlew -q dependencies
 
 refresh:
 	./gradlew --refresh-dependencies dependencies
-
-install: compile
-	./gradlew copyPluginZip
-	rm -rf ${HOME}/.nextflow/plugins/$(PROJECT)-${VERSION}
-	cp -r build/plugins/$(PROJECT)-${VERSION} ${HOME}/.nextflow/plugins/
-
-#
-# Upload JAR artifacts to Maven Central
-#
-
-publish:
-	echo "Ensure you have set 'github_organization=<owner>' in ~/.gradle/gradle.properties"
-	ls $(HOME)/.gradle/gradle.properties # create locally or globally if it does not exist
-	./gradlew :plugins:$(PROJECT):upload
-	./gradlew :plugins:publishIndex
diff --git a/build.gradle b/build.gradle
index f826d9bb..7056e9aa 100644
--- a/build.gradle
+++ b/build.gradle
@@ -1,207 +1,69 @@
 /*
- * Copyright 2020-2022, Seqera Labs
- * Copyright 2013-2019, Centre for Genomic Regulation (CRG)
+ * Copyright 2024-2026, Quilt Data Inc.
  *
  * 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.
  */
 
 plugins {
-    id 'io.codearte.nexus-staging' version '0.30.0'
-    id 'java'
-    id 'idea'
-    id 'se.patrikerdes.use-latest-versions' version '0.2.18'
-    id 'com.github.ben-manes.versions' version '0.52.0'
-}
-
-// Add ability to test with upcoming versions of Groovy
-def groovyVer = System.getenv('CI_GROOVY_VERSION')
-if (groovyVer) {
-    def repo = groovyVer.startsWith('com.github.apache:') ? 'https://jitpack.io' : 'https://oss.jfrog.org/oss-snapshot-local/'
-    logger.lifecycle "Overriden Groovy dependency to use $groovyVer - repository: $repo"
-    allprojects {
-        repositories {
-            maven { url repo }
-        }
-
-        configurations.configureEach {
-            resolutionStrategy.eachDependency { DependencyResolveDetails details ->
-                force 'cglib:cglib-nodep:3.3.0'
-                force 'org.objenesis:objenesis:3.4'
-
-                // (Optional) If transitive Groovy dependencies cause conflicts
-                force "org.${groovySource}.groovy:groovy-all:$groovyVer"
-                if ((details.requested.group == "org.${groovySource}.groovy") && details.requested.version != groovyVer) {
-                    if (groovyVer.contains(':')) {
-                        details.useTarget(groovyVer)
-                    }
-                    else {
-                        details.useVersion(groovyVer)
-                    }
-                    println ">> Overriding $details.requested with version: $groovyVer"
-                }
-            }
-        }
-    }
+    id 'io.nextflow.nextflow-plugin' version '1.0.0-beta.14'
 }
 
-
+// Plugin version: bump here to release a new version.
+// Keep in sync with any references in CHANGELOG / README until the 1.0.0 release.
+version = '0.9.2'
 group = 'io.nextflow'
 
-allprojects {
-    apply plugin: 'java'
-    apply plugin: 'java-test-fixtures'
-    apply plugin: 'idea'
-    apply plugin: 'groovy'
-    apply plugin: 'java-library'
-
-    java {
-        toolchain {
-            languageVersion = JavaLanguageVersion.of(javaLangVersion)
-        }
-    }
-
-    compileJava {
-        options.release = jdkVersion.toInteger()
-    }
-
-    tasks.withType(GroovyCompile).configureEach {
-        sourceCompatibility = jdkVersion
-        targetCompatibility = jdkVersion
-    }
-
-    idea {
-        module.inheritOutputDirs = true
-    }
-    repositories {
-        mavenCentral()
-        maven { url = 'https://repo.eclipse.org/content/groups/releases' }
-        maven { url = 'https://oss.sonatype.org/content/repositories/snapshots' }
-    }
-    configurations {
-        // see https://docs.gradle.org/4.1/userguide/dependency_management.html#sub:exclude_transitive_dependencies
-        all*.exclude group: 'org.codehaus.groovy', module: 'groovy-all'
-        all*.exclude group: 'org.codehaus.groovy', module: 'groovy-cli-picocli'
-        all*.exclude group: 'org.apache.groovy', module: 'groovy-all'
-        all*.exclude group: 'org.apache.groovy', module: 'groovy-cli-picocli'
-        // groovydoc libs
-        groovyDoc.extendsFrom runtime
-    }
-
-    dependencies {
-        // see https://docs.gradle.org/4.1/userguide/dependency_management.html#sec:module_replacement
-        implementation "org.${groovySource}.groovy:groovy-all:$groovyVersion"
-        implementation 'com.fasterxml.jackson.core:jackson-databind:2.19.0'
-        implementation 'com.fasterxml.jackson.datatype:jackson-datatype-jsr310:2.19.0'
-        implementation 'com.upplication:s3fs:2.2.2'
-
-        modules {
-            module('commons-logging:commons-logging') { replacedBy('org.slf4j:jcl-over-slf4j') }
-        }
-        // Documentation required libraries
-        groovyDoc 'org.fusesource.jansi:jansi:2.4.2'
-        groovyDoc "org.${groovySource}.groovy:groovy-groovydoc:$groovyVersion"
-        groovyDoc "org.${groovySource}.groovy:groovy-ant:$groovyVersion"
-    }
-
-    test {
-        useJUnitPlatform()
-    }
-
-    // this is required due to this IDEA bug
-    // https://youtrack.jetbrains.com/issue/IDEA-129282
-    sourceSets {
-        main {
-            output.resourcesDir = 'build/classes/main'
-        }
-    }
-
-    // Disable strict javadoc checks
-    // See http://blog.joda.org/2014/02/turning-off-doclint-in-jdk-8-javadoc.html
-    if (JavaVersion.current().isJava8Compatible()) {
-        tasks.withType(Javadoc).configureEach {
-            options.addStringOption('Xdoclint:none', '-quiet')
-        }
-    }
-
-    tasks.withType(Jar).configureEach {
-        duplicatesStrategy = DuplicatesStrategy.INCLUDE
-    }
-
-    // patched as described here
-    // http://forums.gradle.org/gradle/topics/gradle_task_groovydoc_failing_with_noclassdeffounderror
-    tasks.withType(Groovydoc).configureEach {
-        groovyClasspath = project.configurations.groovyDoc
-        includes = ['nextflow/**']
-    }
-
-    // Required to run tests on Java 9 and higher in compatibility mode
-    if (JavaVersion.current() >= JavaVersion.VERSION_1_9) {
-        tasks.withType(Test).tap {
-            configureEach {
-                jvmArgs([
-                        '--add-opens=java.base/java.lang=ALL-UNNAMED',
-                        '--add-opens=java.base/java.io=ALL-UNNAMED',
-                        '--add-opens=java.base/java.nio=ALL-UNNAMED',
-                        '--add-opens=java.base/java.nio.file.spi=ALL-UNNAMED',
-                        '--add-opens=java.base/java.net=ALL-UNNAMED',
-                        '--add-opens=java.base/java.util=ALL-UNNAMED',
-                        '--add-opens=java.base/java.util.concurrent.locks=ALL-UNNAMED',
-                        '--add-opens=java.base/java.util.concurrent.atomic=ALL-UNNAMED',
-                        '--add-opens=java.base/sun.nio.ch=ALL-UNNAMED',
-                        '--add-opens=java.base/sun.nio.fs=ALL-UNNAMED',
-                        '--add-opens=java.base/sun.net.www.protocol.http=ALL-UNNAMED',
-                        '--add-opens=java.base/sun.net.www.protocol.https=ALL-UNNAMED',
-                        '--add-opens=java.base/sun.net.www.protocol.ftp=ALL-UNNAMED',
-                        '--add-opens=java.base/sun.net.www.protocol.file=ALL-UNNAMED',
-                        '--add-opens=java.base/jdk.internal.misc=ALL-UNNAMED',
-                ])
-            }
-        }
-    }
+dependencies {
+    implementation 'com.quiltdata:quiltcore:0.1.7'
+    implementation 'com.fasterxml.jackson.core:jackson-databind:2.19.0'
+    implementation 'com.fasterxml.jackson.datatype:jackson-datatype-jsr310:2.19.0'
+    implementation 'commons-io:commons-io:2.19.0'
 }
 
-def getRuntimeConfigs() {
-    def names = subprojects
-            .findAll { prj -> prj.name in ['nextflow', 'nf-commons', 'nf-httpfs'] }
-            .collect { p -> p.name }
-
-    FileCollection result = null
-    for ( def it : names ) {
-        def cfg = project(it).configurations.getByName('runtimeClasspath')
-        if ( result == null ) {
-            result = cfg
-        }
-        else {
-            result += cfg
-        }
-    // this include the module actual jar file
-    // note: migrating to gradle 7 does not work any more
-    //result = result + cfg.getOutgoing().getArtifacts().getFiles()
-    }
-    return result
+// The io.nextflow.nextflow-plugin gradle plugin wires `test` to depend on
+// `assemble` (which transitively runs `packagePlugin`). On Windows,
+// `packagePlugin` fails with "character to be escaped is missing" because
+// the upstream task uses `String.replaceAll(..., File.separator)` and `\`
+// is an escape character in regex replacements
+// (see https://github.com/nextflow-io/nextflow-plugin-gradle/issues/20).
+// Until that upstream bug is fixed, we sever the test->assemble link so the
+// test suite can run on Windows. `make assemble` / `make package` /
+// `make release` still trigger packagePlugin on platforms where it works.
+tasks.named('test') { task ->
+    task.setDependsOn(task.getDependsOn().findAll { it != tasks.assemble && it != 'assemble' })
+    task.dependsOn 'jar'
+    useJUnitPlatform()
+    // Required to run Nextflow / Groovy reflection-heavy tests on JDK 9+.
+    jvmArgs([
+        '--add-opens=java.base/java.lang=ALL-UNNAMED',
+        '--add-opens=java.base/java.io=ALL-UNNAMED',
+        '--add-opens=java.base/java.nio=ALL-UNNAMED',
+        '--add-opens=java.base/java.nio.file.spi=ALL-UNNAMED',
+        '--add-opens=java.base/java.net=ALL-UNNAMED',
+        '--add-opens=java.base/java.util=ALL-UNNAMED',
+        '--add-opens=java.base/java.util.concurrent.locks=ALL-UNNAMED',
+        '--add-opens=java.base/java.util.concurrent.atomic=ALL-UNNAMED',
+        '--add-opens=java.base/sun.nio.ch=ALL-UNNAMED',
+        '--add-opens=java.base/sun.nio.fs=ALL-UNNAMED',
+        '--add-opens=java.base/sun.net.www.protocol.http=ALL-UNNAMED',
+        '--add-opens=java.base/sun.net.www.protocol.https=ALL-UNNAMED',
+        '--add-opens=java.base/sun.net.www.protocol.ftp=ALL-UNNAMED',
+        '--add-opens=java.base/sun.net.www.protocol.file=ALL-UNNAMED',
+        '--add-opens=java.base/jdk.internal.misc=ALL-UNNAMED',
+    ])
 }
 
-/*
- * Save the runtime classpath
- */
-task exportClasspath {
-    dependsOn allprojects.jar
-    doLast {
-        def nextflowVersion = rootProject.file('VERSION').text.trim()
-
-        def all = getRuntimeConfigs()
-        def libs = all.collect { File file -> file.canonicalPath  }
-        ['nextflow', 'nf-commons', 'nf-httfs'].each { libs << file("modules/$it/build/libs/${it}-${nextflowVersion}.jar").canonicalPath }
-        file('.launch.classpath').text = libs.unique().join(':')
-    }
+nextflowPlugin {
+    nextflowVersion = '24.10.0'
+    provider = 'Quilt Data'
+    className = 'nextflow.quilt.QuiltPlugin'
+    extensionPoints = [
+        'nextflow.quilt.QuiltObserverFactory',
+        'nextflow.quilt.nio.QuiltPathFactory',
+        'nextflow.quilt.nio.QuiltPathSerializer'
+    ]
 }
diff --git a/buildSrc/build.gradle b/buildSrc/build.gradle
deleted file mode 100644
index 66a0569c..00000000
--- a/buildSrc/build.gradle
+++ /dev/null
@@ -1,14 +0,0 @@
-/*
- * This file was generated by the Gradle 'init' task.
- */
-
-plugins {
-    // Support convention plugins written in Groovy. Convention plugins are build scripts in 'src/main' that automatically become available as plugins in the main build.
-    id 'groovy-gradle-plugin'
-}
-
-repositories {
-    // Use the plugin portal to apply community plugins in convention plugins.
-    gradlePluginPortal()
-}
-
diff --git a/buildSrc/src/main/groovy/io.nextflow.groovy-application-conventions.gradle b/buildSrc/src/main/groovy/io.nextflow.groovy-application-conventions.gradle
deleted file mode 100644
index ecc029b2..00000000
--- a/buildSrc/src/main/groovy/io.nextflow.groovy-application-conventions.gradle
+++ /dev/null
@@ -1,11 +0,0 @@
-/*
- * This file was generated by the Gradle 'init' task.
- */
-
-plugins {
-    // Apply the common convention plugin for shared build configuration between library and application projects.
-    id 'io.nextflow.groovy-common-conventions'
-
-    // Apply the application plugin to add support for building a CLI application in Java.
-    id 'application'
-}
diff --git a/buildSrc/src/main/groovy/io.nextflow.groovy-common-conventions.gradle b/buildSrc/src/main/groovy/io.nextflow.groovy-common-conventions.gradle
deleted file mode 100644
index bac925f4..00000000
--- a/buildSrc/src/main/groovy/io.nextflow.groovy-common-conventions.gradle
+++ /dev/null
@@ -1,53 +0,0 @@
-/*
- * This file was generated by the Gradle 'init' task.
- */
-
-plugins {
-    // Apply the groovy Plugin to add support for Groovy.
-    id 'groovy'
-}
-
-repositories {
-    // Use Maven Central for resolving dependencies.
-    mavenCentral()
-}
-
-ext {
-    jdkVersion = '11'
-    javaLangVersion = 21
-}
-
-java {
-    toolchain {
-        languageVersion = JavaLanguageVersion.of(javaLangVersion) // from nf-schema
-    }
-}
-
-compileJava {
-    options.release.set(jdkVersion.toInteger())
-}
-
-tasks.withType(GroovyCompile) {
-    sourceCompatibility = jdkVersion
-    targetCompatibility = jdkVersion
-}
-
-tasks.withType(Test) {
-    jvmArgs ([
-            '--add-opens=java.base/java.lang=ALL-UNNAMED',
-            '--add-opens=java.base/java.io=ALL-UNNAMED',
-            '--add-opens=java.base/java.nio=ALL-UNNAMED',
-            '--add-opens=java.base/java.nio.file.spi=ALL-UNNAMED',
-            '--add-opens=java.base/java.net=ALL-UNNAMED',
-            '--add-opens=java.base/java.util=ALL-UNNAMED',
-            '--add-opens=java.base/java.util.concurrent.locks=ALL-UNNAMED',
-            '--add-opens=java.base/java.util.concurrent.atomic=ALL-UNNAMED',
-            '--add-opens=java.base/sun.nio.ch=ALL-UNNAMED',
-            '--add-opens=java.base/sun.nio.fs=ALL-UNNAMED',
-            '--add-opens=java.base/sun.net.www.protocol.http=ALL-UNNAMED',
-            '--add-opens=java.base/sun.net.www.protocol.https=ALL-UNNAMED',
-            '--add-opens=java.base/sun.net.www.protocol.ftp=ALL-UNNAMED',
-            '--add-opens=java.base/sun.net.www.protocol.file=ALL-UNNAMED',
-            '--add-opens=java.base/jdk.internal.misc=ALL-UNNAMED',
-    ])
-}
diff --git a/buildSrc/src/main/groovy/io.nextflow.groovy-library-conventions.gradle b/buildSrc/src/main/groovy/io.nextflow.groovy-library-conventions.gradle
deleted file mode 100644
index 0183e2cc..00000000
--- a/buildSrc/src/main/groovy/io.nextflow.groovy-library-conventions.gradle
+++ /dev/null
@@ -1,11 +0,0 @@
-/*
- * This file was generated by the Gradle 'init' task.
- */
-
-plugins {
-    // Apply the common convention plugin for shared build configuration between library and application projects.
-    id 'io.nextflow.groovy-common-conventions'
-    // Apply the java-library plugin for API and implementation separation.
-    id 'java-library'
-}
-
diff --git a/gradle-groovysh-init.gradle b/gradle-groovysh-init.gradle
deleted file mode 100644
index fa47c759..00000000
--- a/gradle-groovysh-init.gradle
+++ /dev/null
@@ -1,49 +0,0 @@
-gradle.projectsLoaded {
-    rootProject {
-        afterEvaluate { project ->
-            if (!project.repositories.any { it.name == 'MavenRepo' }) {
-                project.repositories {
-                    // To be able to load org.codehaus.groovy:groovy-groovysh
-                    mavenCentral()
-                }
-        }
-
-            project.configurations {
-                groovyshdependencies
-            }
-
-            project.dependencies {
-                groovyshdependencies("org.${groovySource}.groovy:groovy-groovysh:${GroovySystem.version}") {
-                    exclude group: "org.${groovySource}.groovy"
-                }
-            }
-
-            project.tasks.register('groovysh') {
-                group 'debug'
-                description 'Runs an interactive shell in the context of the project.'
-                doLast {
-                    URLClassLoader groovyObjectClassLoader = GroovyObject.classLoader
-                    def groovyshClass
-                    def groovyShell
-
-                    // Add dependency jars to classloader
-                    configurations.groovyshdependencies.each { File file ->
-                        groovyObjectClassLoader.addURL(file.toURL())
-                    }
-                    Class.forName('jline.console.history.FileHistory', true, groovyObjectClassLoader)
-                    groovyshClass = Class.forName("org.${groovySource}.groovy.tools.shell.Groovysh", true, groovyObjectClassLoader)
-
-                    if (groovyshClass) {
-                        groovyShell = groovyshClass.newInstance()
-                    }
-                    if (groovyShell) {
-                        groovyShell.interp.context.variables.put('gradle', gradle)
-                        groovyShell.interp.context.variables.put('settings', gradle.settings)
-                        groovyShell.interp.context.variables.put('project', project)
-                        groovyShell.run('')
-                    }
-                }
-            }
-    }
-}
-}
diff --git a/gradle.properties b/gradle.properties
index 3550e31c..6830d6ee 100644
--- a/gradle.properties
+++ b/gradle.properties
@@ -1,5 +1,3 @@
-groovyVersion = 4.0.26
-groovyV = groovy-4.0
-groovySource = apache
-jdkVersion = 11
-javaLangVersion = 21
+# Gradle configuration for nf-quilt.
+# The Nextflow Gradle plugin (io.nextflow.nextflow-plugin) controls
+# the JVM toolchain and Groovy/Java versions; no overrides required here.
diff --git a/groovysh-task.gradle b/groovysh-task.gradle
deleted file mode 100644
index 64873f26..00000000
--- a/groovysh-task.gradle
+++ /dev/null
@@ -1,54 +0,0 @@
-gradle.projectsLoaded {
-    rootProject {
-        afterEvaluate { project ->
-            if (!project.repositories.any { it.name == 'MavenRepo' }) {
-                project.repositories {
-                    // To be able to load org.codehaus.groovy:groovy-groovysh and dependencies
-                    mavenCentral {
-                        content {
-                            includeGroup "org.${groovySource}.groovy"
-                            includeGroup 'jline'
-                            includeGroup 'com.github.javaparser'
-                            includeGroup 'org.ow2.asm'
-                            includeGroup 'org.abego.treelayout'
-                            includeGroup 'org.apache.ivy'
-                        }
-                    }
-                }
-        }
-            project.configurations {
-                groovyshdependencies
-            }
-
-            project.dependencies {
-                groovyshdependencies "org.${groovySource}.groovy:groovy-groovysh:$groovyVer" {
-                    exclude group: "org.${groovySource}.groovy"
-                }
-            }
-
-            project.tasks.register('groovysh') {
-                group 'debug'
-                description 'Runs an interactive shell in the context of the project. Use :inspect command to inspect project, gradle, settings or other objects.'
-                doLast {
-                    URLClassLoader groovyshClassLoader = new URLClassLoader()
-                    configurations.groovyshdependencies.each { File file ->
-                        groovyshClassLoader.addURL(file.toURI().toURL())
-                    }
-
-                    def groovyshClass
-                    def groovyShell
-                    groovyshClass = Class.forName("org.${groovySource}.groovy.groovysh.Groovysh", true, groovyshClassLoader)
-                    if (groovyshClass) {
-                        groovyShell = groovyshClass.newInstance()
-                        if (groovyShell) {
-                            groovyShell.interp.context.variables.put('gradle', gradle)
-                            groovyShell.interp.context.variables.put('settings', gradle.settings)
-                            groovyShell.interp.context.variables.put('project', project)
-                            groovyShell.run('# Available objects: gradle, settings, project\n# Try :inspect project')
-                        }
-                    }
-                }
-            }
-    }
-}
-}
diff --git a/launch.sh b/launch.sh
deleted file mode 100755
index ebee5335..00000000
--- a/launch.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#!/usr/bin/env bash
-export NXF_PLUGINS_DEV=$PWD/plugins
-../nextflow/launch.sh "$@"
diff --git a/plugins/build.gradle b/plugins/build.gradle
deleted file mode 100644
index 84d7077d..00000000
--- a/plugins/build.gradle
+++ /dev/null
@@ -1,182 +0,0 @@
-import io.nextflow.gradle.tasks.GithubRepositoryPublisher
-import io.nextflow.gradle.tasks.GithubUploader
-import org.apache.commons.codec.digest.DigestUtils
-import org.codehaus.groovy.runtime.GStringImpl
-
-import java.time.OffsetDateTime
-import java.time.format.DateTimeFormatter
-
-/*
- * Copyright 2021-2022, 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
- *
- * This file is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS
- * of any kind, either express or implied.
- * See the License for specific language governing permissions and limitations.
- */
-
-plugins {
-    id 'java'
-    id 'groovy'
-    id 'io.nextflow.nf-build-plugin' version '1.0.1'
-}
-
-/* Project Constants */
-ext {
-    github_organization = project.findProperty('github_organization') ?: 'nextflow-io'
-    github_username = project.findProperty('github_username') ?: 'pditommaso'
-    github_access_token = project.findProperty('github_access_token') ?: System.getenv('GITHUB_TOKEN')
-    github_commit_email = project.findProperty('github_commit_email') ?: 'paolo.ditommaso@gmail.com'
-    github_index_url = "https://github.com/${github_organization}/plugins/main/plugins.json" as GStringImpl
-}
-
-// Disable default JAR generation
-jar.enabled = false
-
-/* Utility Functions */
-static String computeSha512(File file) {
-    if (!file.exists()) {
-        throw new GradleException("Missing file: $file -- cannot compute SHA-512")
-    }
-    return DigestUtils.sha512Hex(file.bytes)
-}
-
-static String now() {
-    "${OffsetDateTime.now().format(DateTimeFormatter.ISO_DATE_TIME)}"
-}
-
-List<String> allPlugins() {
-    def plugins = []
-    new File(rootProject.rootDir, 'plugins').eachDir {
-        if (it.name.startsWith('nf-')) plugins.add(it.name)
-    }
-    return plugins
-}
-
-String metaFromManifest(String meta, File file) {
-    def str = file.text
-    def regex = ~/(?m)^$meta:\s*([\w-\.<>=]+)$/
-    def m = regex.matcher(str)
-    if (m.find()) {
-        def ver = m.group(1)
-        println "Set plugin '${file.parentFile.parentFile.parentFile.parentFile.name}' version=$ver"
-        return ver
-    }
-    throw new GradleException("Cannot find '$meta' for plugin: $file")
-}
-
-def timestamp = now()
-
-/* Configure Subprojects */
-subprojects {
-    apply plugin: 'java'
-    apply plugin: 'groovy'
-    apply plugin: 'io.nextflow.nf-build-plugin'
-
-    repositories {
-        mavenLocal()
-        mavenCentral()
-    }
-
-    version = metaFromManifest('Plugin-Version', file('src/resources/META-INF/MANIFEST.MF'))
-
-    tasks.withType(Jar).configureEach {
-        duplicatesStrategy = DuplicatesStrategy.INCLUDE
-    }
-
-    /* Plugin Variables */
-    String pluginVersion = project.version
-    String archiveName = "${project.name}-${pluginVersion}"
-    File zipFile = layout.buildDirectory.file("libs/${archiveName}.zip").get().asFile
-    File jsonFile = layout.buildDirectory.file("libs/${archiveName}-meta.json").get().asFile
-    File pluginsDir = layout.buildDirectory.dir("plugins").get().asFile
-
-    /* Task to Create Plugin Zip and Metadata */
-    tasks.register('makeZip', Jar) {
-        into('classes') { with jar }
-        into('lib') { from configurations.runtimeClasspath }
-        manifest.from file('src/resources/META-INF/MANIFEST.MF')
-        archiveExtension = 'zip'
-        preserveFileTimestamps = false
-        reproducibleFileOrder = true
-
-        String downloadUrl = "https://github.com/${github_organization}/${project.name}/releases/download/${pluginVersion}/${archiveName}.zip"
-        doLast {
-            // Generate the metadata file
-            jsonFile.text = """\
-{
-    "version": "${pluginVersion}",
-    "date": "${timestamp}",
-    "url": "${downloadUrl}",
-    "requires": "${metaFromManifest('Plugin-Requires', file('src/resources/META-INF/MANIFEST.MF'))}",
-    "sha512sum": "${computeSha512(zipFile)}"
-}
-"""
-        }
-        outputs.file(zipFile)
-    }
-
-    /* Task to Copy Plugin Dependencies */
-    tasks.register('copyPluginLibs', Sync) {
-        from configurations.runtimeClasspath
-        into 'build/target/libs'
-        duplicatesStrategy = DuplicatesStrategy.EXCLUDE
-    }
-
-    /* Task to Copy Plugin ZIP to Plugins Directory */
-    tasks.register('copyPluginZip', Copy) {
-        dependsOn project.tasks.named('makeZip')
-        from { tasks.named('makeZip').get().outputs.files.singleFile }
-        into pluginsDir.absolutePath
-        outputs.file(zipFile)
-
-        def destDirPath = new File(pluginsDir, archiveName).absolutePath
-        doLast {
-            if (!zipFile.exists()) {
-                throw new GradleException("File ${zipFile} does not exist! Cannot unzip.")
-            }
-            ant.unzip(
-                    src: zipFile.absolutePath,
-                    dest: destDirPath
-            )
-        }
-    }
-
-    /* "Install" the Plugin */
-    def providerList = [zipFile.absolutePath, jsonFile.absolutePath]
-    project.parent.tasks.named('assemble').configure {
-        dependsOn(copyPluginZip)
-    }
-    tasks.register('uploadPlugin', GithubUploader) {
-        dependsOn tasks.named('makeZip') // Lazy dependency
-        repo = providers.provider { project.name }
-        owner = github_organization
-        userName = github_username
-        authToken = github_access_token
-        skipExisting = true
-        release = providers.provider { project.version } as Provider<? extends String>
-        assets = providers.provider { providerList } as Provider<? extends Iterable<? extends String>>
-    }
-}
-
-/* Upload Task */
-tasks.register('upload') {
-    dependsOn subprojects.uploadPlugin
-}
-
-classes.dependsOn subprojects.copyPluginLibs
-
-/* Publish Plugins Index File */
-tasks.register('publishIndex', GithubRepositoryPublisher) {
-    indexUrl = github_index_url
-    repos = allPlugins()
-    owner = github_organization
-    githubUser = github_username
-    githubEmail = github_commit_email
-    githubToken = github_access_token
-}
diff --git a/plugins/nf-quilt/build.gradle b/plugins/nf-quilt/build.gradle
deleted file mode 100644
index a350d91f..00000000
--- a/plugins/nf-quilt/build.gradle
+++ /dev/null
@@ -1,149 +0,0 @@
-/*
- * Copyright 2021-2022, 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
- *
- * This file 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.
- */
-
-plugins {
-    // Apply the conventions and plugins required by the build
-    id 'io.nextflow.groovy-library-conventions'
-    id 'idea'
-    id 'jacoco'
-}
-
-group = 'io.nextflow'
-
-// DO NOT SET THE VERSION HERE
-// PLUGIN VERSION IS DEFINED IN THE `META-INF/MANIFEST.MF` FILE
-
-java {
-    toolchain {
-        languageVersion = JavaLanguageVersion.of(javaLangVersion)
-    }
-}
-
-compileJava {
-    options.release = jdkVersion.toInteger()
-}
-
-tasks.withType(GroovyCompile).configureEach {
-    sourceCompatibility = jdkVersion
-    targetCompatibility = jdkVersion
-}
-
-idea {
-    module.inheritOutputDirs = true
-}
-
-repositories {
-    mavenCentral()
-    maven { url = 'https://jitpack.io' }
-    maven { url = 'https://s3-eu-west-1.amazonaws.com/maven.seqera.io/releases' }
-    maven { url = 'https://s3-eu-west-1.amazonaws.com/maven.seqera.io/snapshots' }
-}
-
-configurations {
-    // Exclude transitive dependencies
-    runtimeClasspath.exclude(group: 'org.slf4j', module: 'slf4j-api')
-}
-
-sourceSets {
-    main {
-        java.srcDirs = []               // Disable Java sources
-        groovy.srcDirs = ['src/main']   // Use Groovy sources
-        resources.srcDirs = ['src/resources'] // Use resources
-    }
-    test {
-        java.srcDirs = []               // Disable Java sources for tests
-        groovy.srcDirs = ['src/test']   // Use Groovy test sources
-        resources.srcDirs = ['src/testResources'] // Use test resources
-    }
-}
-
-dependencies {
-    def nextflowVersion = rootProject.file('VERSION').text.trim()
-
-    // Quiltcore
-    implementation 'com.quiltdata:quiltcore:0.1.7'
-
-    // Compile-only dependencies
-    compileOnly "io.nextflow:nextflow:$nextflowVersion"
-    compileOnly 'org.slf4j:slf4j-api:2.1.0-alpha1'
-    compileOnly 'org.pf4j:pf4j:3.13.0'
-
-    // Runtime-only dependencies
-    runtimeOnly 'org.junit.platform:junit-platform-launcher:1.12.2'
-    implementation 'commons-io:commons-io:2.19.0'
-
-    // Test dependencies
-    testImplementation "io.nextflow:nextflow:$nextflowVersion"
-    testImplementation "org.${groovySource}.groovy:groovy:$groovyVersion"
-    testImplementation "org.${groovySource}.groovy:groovy-nio:$groovyVersion"
-    testImplementation("org.${groovySource}.groovy:groovy-test:$groovyVersion") {
-        exclude group: "org.${groovySource}.groovy"
-    }
-    testImplementation('cglib:cglib-nodep:3.3.0')
-    testImplementation('org.objenesis:objenesis:3.4')
-
-    // Spock framework
-    testImplementation("org.spockframework:spock-core:2.3-$groovyV") {
-        exclude group: "org.${groovySource}.groovy"
-        exclude group: 'net.bytebuddy'
-    }
-    testImplementation("org.spockframework:spock-junit4:2.3-$groovyV") {
-        exclude group: "org.${groovySource}.groovy"
-        exclude group: 'net.bytebuddy'
-    }
-
-    // Miscellaneous test dependencies
-    testImplementation('com.google.jimfs:jimfs:1.3.0')
-    testImplementation(testFixtures("io.nextflow:nextflow:$nextflowVersion"))
-    testImplementation(testFixtures("io.nextflow:nf-commons:$nextflowVersion"))
-
-    // Module replacement
-    modules {
-        module('commons-logging:commons-logging') {
-            replacedBy('org.slf4j:jcl-over-slf4j')
-        }
-    }
-}
-
-// Use JUnit 5 platform for testing
-test {
-    useJUnitPlatform()
-}
-
-jacocoTestReport {
-    dependsOn test // The report depends on the completion of tests
-}
-
-jacocoTestCoverageVerification {
-    dependsOn jacocoTestReport // Ensure the test report is generated first
-    violationRules {
-        rule {
-            limit {
-                minimum = 0.7 // Ensure at least 70% coverage
-            }
-        }
-
-        rule {
-            enabled = false
-            element = 'CLASS'
-            includes = ['org.gradle.*']
-
-            limit {
-                counter = 'LINE'
-                value = 'TOTALCOUNT'
-                maximum = 0.3 // Coverage limit for lines
-            }
-        }
-    }
-}
diff --git a/plugins/nf-quilt/src/resources/META-INF/MANIFEST.MF b/plugins/nf-quilt/src/resources/META-INF/MANIFEST.MF
deleted file mode 100644
index b5f05245..00000000
--- a/plugins/nf-quilt/src/resources/META-INF/MANIFEST.MF
+++ /dev/null
@@ -1,7 +0,0 @@
-Manifest-Version: 1.0
-Plugin-Class: nextflow.quilt.QuiltPlugin
-Plugin-Id: nf-quilt
-Plugin-Version: 0.9.2
-Plugin-Provider: Quilt Data
-Plugin-Requires: >=24.10.0
-
diff --git a/plugins/nf-quilt/src/resources/META-INF/extensions.idx b/plugins/nf-quilt/src/resources/META-INF/extensions.idx
deleted file mode 100644
index 890194be..00000000
--- a/plugins/nf-quilt/src/resources/META-INF/extensions.idx
+++ /dev/null
@@ -1,20 +0,0 @@
-#
-# Copyright 2020-2022, Seqera Labs
-# Copyright 2013-2019, Centre for Genomic Regulation (CRG)
-#
-# 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.
-#
-
-nextflow.quilt.nio.QuiltPathSerializer
-nextflow.quilt.nio.QuiltPathFactory
-nextflow.quilt.QuiltObserverFactory
\ No newline at end of file
diff --git a/settings.gradle b/settings.gradle
index 859f3248..e9cf8e52 100644
--- a/settings.gradle
+++ b/settings.gradle
@@ -1,23 +1 @@
-/*
- * Copyright 2022, 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.
- */
-
-plugins {
-    id('org.gradle.toolchains.foojay-resolver-convention') version '0.10.0'
-}
-
 rootProject.name = 'nf-quilt'
-include 'plugins'
-include('plugins:nf-quilt')
diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/QuiltObserver.groovy b/src/main/groovy/nextflow/quilt/QuiltObserver.groovy
similarity index 100%
rename from plugins/nf-quilt/src/main/nextflow/quilt/QuiltObserver.groovy
rename to src/main/groovy/nextflow/quilt/QuiltObserver.groovy
diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/QuiltObserverFactory.groovy b/src/main/groovy/nextflow/quilt/QuiltObserverFactory.groovy
similarity index 100%
rename from plugins/nf-quilt/src/main/nextflow/quilt/QuiltObserverFactory.groovy
rename to src/main/groovy/nextflow/quilt/QuiltObserverFactory.groovy
diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/QuiltPathify.groovy b/src/main/groovy/nextflow/quilt/QuiltPathify.groovy
similarity index 100%
rename from plugins/nf-quilt/src/main/nextflow/quilt/QuiltPathify.groovy
rename to src/main/groovy/nextflow/quilt/QuiltPathify.groovy
diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/QuiltPlugin.groovy b/src/main/groovy/nextflow/quilt/QuiltPlugin.groovy
similarity index 100%
rename from plugins/nf-quilt/src/main/nextflow/quilt/QuiltPlugin.groovy
rename to src/main/groovy/nextflow/quilt/QuiltPlugin.groovy
diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/QuiltProduct.groovy b/src/main/groovy/nextflow/quilt/QuiltProduct.groovy
similarity index 100%
rename from plugins/nf-quilt/src/main/nextflow/quilt/QuiltProduct.groovy
rename to src/main/groovy/nextflow/quilt/QuiltProduct.groovy
diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltID.groovy b/src/main/groovy/nextflow/quilt/jep/QuiltID.groovy
similarity index 100%
rename from plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltID.groovy
rename to src/main/groovy/nextflow/quilt/jep/QuiltID.groovy
diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltPackage.groovy b/src/main/groovy/nextflow/quilt/jep/QuiltPackage.groovy
similarity index 100%
rename from plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltPackage.groovy
rename to src/main/groovy/nextflow/quilt/jep/QuiltPackage.groovy
diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltParser.groovy b/src/main/groovy/nextflow/quilt/jep/QuiltParser.groovy
similarity index 100%
rename from plugins/nf-quilt/src/main/nextflow/quilt/jep/QuiltParser.groovy
rename to src/main/groovy/nextflow/quilt/jep/QuiltParser.groovy
diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltBashLib.groovy b/src/main/groovy/nextflow/quilt/nio/QuiltBashLib.groovy
similarity index 100%
rename from plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltBashLib.groovy
rename to src/main/groovy/nextflow/quilt/nio/QuiltBashLib.groovy
diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltFileAttributes.groovy b/src/main/groovy/nextflow/quilt/nio/QuiltFileAttributes.groovy
similarity index 100%
rename from plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltFileAttributes.groovy
rename to src/main/groovy/nextflow/quilt/nio/QuiltFileAttributes.groovy
diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltFileAttributesView.groovy b/src/main/groovy/nextflow/quilt/nio/QuiltFileAttributesView.groovy
similarity index 100%
rename from plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltFileAttributesView.groovy
rename to src/main/groovy/nextflow/quilt/nio/QuiltFileAttributesView.groovy
diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltFileCopyStrategy.groovy b/src/main/groovy/nextflow/quilt/nio/QuiltFileCopyStrategy.groovy
similarity index 100%
rename from plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltFileCopyStrategy.groovy
rename to src/main/groovy/nextflow/quilt/nio/QuiltFileCopyStrategy.groovy
diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltFileSystem.groovy b/src/main/groovy/nextflow/quilt/nio/QuiltFileSystem.groovy
similarity index 100%
rename from plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltFileSystem.groovy
rename to src/main/groovy/nextflow/quilt/nio/QuiltFileSystem.groovy
diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltFileSystemProvider.groovy b/src/main/groovy/nextflow/quilt/nio/QuiltFileSystemProvider.groovy
similarity index 100%
rename from plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltFileSystemProvider.groovy
rename to src/main/groovy/nextflow/quilt/nio/QuiltFileSystemProvider.groovy
diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltPath.groovy b/src/main/groovy/nextflow/quilt/nio/QuiltPath.groovy
similarity index 100%
rename from plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltPath.groovy
rename to src/main/groovy/nextflow/quilt/nio/QuiltPath.groovy
diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltPathFactory.groovy b/src/main/groovy/nextflow/quilt/nio/QuiltPathFactory.groovy
similarity index 100%
rename from plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltPathFactory.groovy
rename to src/main/groovy/nextflow/quilt/nio/QuiltPathFactory.groovy
diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltPathIterator.groovy b/src/main/groovy/nextflow/quilt/nio/QuiltPathIterator.groovy
similarity index 100%
rename from plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltPathIterator.groovy
rename to src/main/groovy/nextflow/quilt/nio/QuiltPathIterator.groovy
diff --git a/plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltPathSerializer.groovy b/src/main/groovy/nextflow/quilt/nio/QuiltPathSerializer.groovy
similarity index 100%
rename from plugins/nf-quilt/src/main/nextflow/quilt/nio/QuiltPathSerializer.groovy
rename to src/main/groovy/nextflow/quilt/nio/QuiltPathSerializer.groovy
diff --git a/plugins/nf-quilt/src/resources/logback-test.xml b/src/main/resources/logback-test.xml
similarity index 100%
rename from plugins/nf-quilt/src/resources/logback-test.xml
rename to src/main/resources/logback-test.xml
diff --git a/plugins/nf-quilt/src/test/nextflow/quilt/QuiltObserverTest.groovy b/src/test/groovy/nextflow/quilt/QuiltObserverTest.groovy
similarity index 100%
rename from plugins/nf-quilt/src/test/nextflow/quilt/QuiltObserverTest.groovy
rename to src/test/groovy/nextflow/quilt/QuiltObserverTest.groovy
diff --git a/plugins/nf-quilt/src/test/nextflow/quilt/QuiltPathifyTest.groovy b/src/test/groovy/nextflow/quilt/QuiltPathifyTest.groovy
similarity index 100%
rename from plugins/nf-quilt/src/test/nextflow/quilt/QuiltPathifyTest.groovy
rename to src/test/groovy/nextflow/quilt/QuiltPathifyTest.groovy
diff --git a/plugins/nf-quilt/src/test/nextflow/quilt/QuiltPkgTest.groovy b/src/test/groovy/nextflow/quilt/QuiltPkgTest.groovy
similarity index 74%
rename from plugins/nf-quilt/src/test/nextflow/quilt/QuiltPkgTest.groovy
rename to src/test/groovy/nextflow/quilt/QuiltPkgTest.groovy
index 778f5415..bba06d3c 100644
--- a/plugins/nf-quilt/src/test/nextflow/quilt/QuiltPkgTest.groovy
+++ b/src/test/groovy/nextflow/quilt/QuiltPkgTest.groovy
@@ -49,12 +49,25 @@ class QuiltPkgTest extends QuiltSpecification {
     }
 
     static String manifestVersion() {
-        String subPath = 'src/resources/META-INF/MANIFEST.MF'
-        File manifestFile = new File(subPath)
-        def manifest = new Manifest(new FileInputStream(manifestFile))
-        def attrs = manifest.getMainAttributes()
-        String version = attrs.getValue('Plugin-Version')
-        return version
+        // Under the new Nextflow Gradle plugin the MANIFEST.MF is generated
+        // into build/tmp/jar/MANIFEST.MF by the `jar` task. Fall back to the
+        // legacy source path for transitional builds.
+        for (String subPath : [
+            'build/tmp/jar/MANIFEST.MF',
+            'src/resources/META-INF/MANIFEST.MF',
+            'src/main/resources/META-INF/MANIFEST.MF',
+        ]) {
+            File manifestFile = new File(subPath)
+            if (manifestFile.exists()) {
+                String version = manifestFile.withInputStream { stream ->
+                    new Manifest(stream).getMainAttributes().getValue('Plugin-Version')
+                }
+                if (version) {
+                    return version
+                }
+            }
+        }
+        throw new FileNotFoundException('Could not locate plugin MANIFEST.MF')
     }
 
     static String destPackage() {
diff --git a/plugins/nf-quilt/src/test/nextflow/quilt/QuiltProductTest.groovy b/src/test/groovy/nextflow/quilt/QuiltProductTest.groovy
similarity index 100%
rename from plugins/nf-quilt/src/test/nextflow/quilt/QuiltProductTest.groovy
rename to src/test/groovy/nextflow/quilt/QuiltProductTest.groovy
diff --git a/plugins/nf-quilt/src/test/nextflow/quilt/QuiltSpecification.groovy b/src/test/groovy/nextflow/quilt/QuiltSpecification.groovy
similarity index 86%
rename from plugins/nf-quilt/src/test/nextflow/quilt/QuiltSpecification.groovy
rename to src/test/groovy/nextflow/quilt/QuiltSpecification.groovy
index 8b648e54..124f4588 100644
--- a/plugins/nf-quilt/src/test/nextflow/quilt/QuiltSpecification.groovy
+++ b/src/test/groovy/nextflow/quilt/QuiltSpecification.groovy
@@ -85,12 +85,22 @@ class QuiltSpecification extends Specification {
                         if (!Files.isDirectory(pluginPath)) {
                             return null
                         }
-                        final manifestPath = pluginPath.resolve('src/resources/META-INF/MANIFEST.MF')
-                        if (!Files.exists(manifestPath)) {
-                            return null
+                        // Under the new Nextflow Gradle plugin (io.nextflow.nextflow-plugin)
+                        // the MANIFEST.MF is generated into build/tmp/jar/ during the `jar`
+                        // task. The legacy path src/resources/META-INF/MANIFEST.MF is
+                        // retained as a fallback for transitional builds.
+                        final candidates = [
+                            pluginPath.resolve('build/tmp/jar/MANIFEST.MF'),
+                            pluginPath.resolve('src/resources/META-INF/MANIFEST.MF'),
+                            pluginPath.resolve('src/main/resources/META-INF/MANIFEST.MF'),
+                        ]
+                        for (Path manifestPath : candidates) {
+                            if (Files.exists(manifestPath)) {
+                                final input = Files.newInputStream(manifestPath)
+                                return new Manifest(input)
+                            }
                         }
-                        final input = Files.newInputStream(manifestPath)
-                        return new Manifest(input)
+                        return null
                     }
 
                 }
diff --git a/plugins/nf-quilt/src/test/nextflow/quilt/jep/QuiltIDTest.groovy b/src/test/groovy/nextflow/quilt/jep/QuiltIDTest.groovy
similarity index 100%
rename from plugins/nf-quilt/src/test/nextflow/quilt/jep/QuiltIDTest.groovy
rename to src/test/groovy/nextflow/quilt/jep/QuiltIDTest.groovy
diff --git a/plugins/nf-quilt/src/test/nextflow/quilt/jep/QuiltPackageTest.groovy b/src/test/groovy/nextflow/quilt/jep/QuiltPackageTest.groovy
similarity index 100%
rename from plugins/nf-quilt/src/test/nextflow/quilt/jep/QuiltPackageTest.groovy
rename to src/test/groovy/nextflow/quilt/jep/QuiltPackageTest.groovy
diff --git a/plugins/nf-quilt/src/test/nextflow/quilt/jep/QuiltParserTest.groovy b/src/test/groovy/nextflow/quilt/jep/QuiltParserTest.groovy
similarity index 100%
rename from plugins/nf-quilt/src/test/nextflow/quilt/jep/QuiltParserTest.groovy
rename to src/test/groovy/nextflow/quilt/jep/QuiltParserTest.groovy
diff --git a/plugins/nf-quilt/src/test/nextflow/quilt/nio/QuiltFileSystemProviderTest.groovy b/src/test/groovy/nextflow/quilt/nio/QuiltFileSystemProviderTest.groovy
similarity index 100%
rename from plugins/nf-quilt/src/test/nextflow/quilt/nio/QuiltFileSystemProviderTest.groovy
rename to src/test/groovy/nextflow/quilt/nio/QuiltFileSystemProviderTest.groovy
diff --git a/plugins/nf-quilt/src/test/nextflow/quilt/nio/QuiltFileSystemTest.groovy b/src/test/groovy/nextflow/quilt/nio/QuiltFileSystemTest.groovy
similarity index 100%
rename from plugins/nf-quilt/src/test/nextflow/quilt/nio/QuiltFileSystemTest.groovy
rename to src/test/groovy/nextflow/quilt/nio/QuiltFileSystemTest.groovy
diff --git a/plugins/nf-quilt/src/test/nextflow/quilt/nio/QuiltNioTest.groovy b/src/test/groovy/nextflow/quilt/nio/QuiltNioTest.groovy
similarity index 100%
rename from plugins/nf-quilt/src/test/nextflow/quilt/nio/QuiltNioTest.groovy
rename to src/test/groovy/nextflow/quilt/nio/QuiltNioTest.groovy
diff --git a/plugins/nf-quilt/src/test/nextflow/quilt/nio/QuiltPathFactoryTest.groovy b/src/test/groovy/nextflow/quilt/nio/QuiltPathFactoryTest.groovy
similarity index 100%
rename from plugins/nf-quilt/src/test/nextflow/quilt/nio/QuiltPathFactoryTest.groovy
rename to src/test/groovy/nextflow/quilt/nio/QuiltPathFactoryTest.groovy
diff --git a/plugins/nf-quilt/src/test/nextflow/quilt/nio/QuiltPathSerializerTest.groovy b/src/test/groovy/nextflow/quilt/nio/QuiltPathSerializerTest.groovy
similarity index 100%
rename from plugins/nf-quilt/src/test/nextflow/quilt/nio/QuiltPathSerializerTest.groovy
rename to src/test/groovy/nextflow/quilt/nio/QuiltPathSerializerTest.groovy
diff --git a/plugins/nf-quilt/src/test/nextflow/quilt/nio/QuiltPathTest.groovy b/src/test/groovy/nextflow/quilt/nio/QuiltPathTest.groovy
similarity index 100%
rename from plugins/nf-quilt/src/test/nextflow/quilt/nio/QuiltPathTest.groovy
rename to src/test/groovy/nextflow/quilt/nio/QuiltPathTest.groovy