reduce .gitignore

k8s-dvfs/.gitignore

@@ -0,0 +1,10 @@
+# Ignore Gradle project-specific cache directory
+.gradle
+.idea
+.nextflow*
+
+# Ignore Gradle build output directory
+build
+work
+lib/groovy-6.0.0-beta-1.jar lib/groovy-6.0.0-beta-1-sources.jar lib/groovy-ant-6.0.0-beta-1.jar lib/groovy-ant-6.0.0-beta-1-sources.jar lib/groovy-astbuilder-6.0.0-beta-1.jar lib/groovy-astbuilder-6.0.0-beta-1-sources.jar lib/groovy-cli-commons-6.0.0-beta-1.jar lib/groovy-cli-commons-6.0.0-beta-1-sources.jar lib/groovy-cli-picocli-6.0.0-beta-1.jar lib/groovy-cli-picocli-6.0.0-beta-1-sources.jar lib/groovy-console-6.0.0-beta-1.jar lib/groovy-console-6.0.0-beta-1-sources.jar lib/groovy-contracts-6.0.0-beta-1.jar lib/groovy-contracts-6.0.0-beta-1-sources.jar lib/groovy-csv-6.0.0-beta-1.jar lib/groovy-csv-6.0.0-beta-1-sources.jar lib/groovy-datetime-6.0.0-beta-1.jar lib/groovy-datetime-6.0.0-beta-1-sources.jar lib/groovy-dateutil-6.0.0-beta-1.jar lib/groovy-dateutil-6.0.0-beta-1-sources.jar lib/groovy-docgenerator-6.0.0-beta-1.jar lib/groovy-docgenerator-6.0.0-beta-1-sources.jar lib/groovy-ginq-6.0.0-beta-1.jar lib/groovy-ginq-6.0.0-beta-1-sources.jar lib/groovy-grape-ivy-6.0.0-beta-1.jar lib/groovy-grape-ivy-6.0.0-beta-1-sources.jar lib/groovy-grape-maven-6.0.0-beta-1.jar lib/groovy-grape-maven-6.0.0-beta-1-sources.jar lib/groovy-groovydoc-6.0.0-beta-1.jar lib/groovy-groovydoc-6.0.0-beta-1-sources.jar lib/groovy-groovysh-6.0.0-beta-1.jar lib/groovy-groovysh-6.0.0-beta-1-sources.jar lib/groovy-http-builder-6.0.0-beta-1.jar lib/groovy-http-builder-6.0.0-beta-1-sources.jar lib/groovy-jmx-6.0.0-beta-1.jar lib/groovy-jmx-6.0.0-beta-1-sources.jar lib/groovy-json-6.0.0-beta-1.jar lib/groovy-json-6.0.0-beta-1-sources.jar lib/groovy-jsr223-6.0.0-beta-1.jar lib/groovy-jsr223-6.0.0-beta-1-sources.jar lib/groovy-macro-6.0.0-beta-1.jar lib/groovy-macro-6.0.0-beta-1-sources.jar lib/groovy-macro-library-6.0.0-beta-1.jar lib/groovy-macro-library-6.0.0-beta-1-sources.jar lib/groovy-markdown-6.0.0-beta-1.jar lib/groovy-markdown-6.0.0-beta-1-sources.jar lib/groovy-nio-6.0.0-beta-1.jar lib/groovy-nio-6.0.0-beta-1-sources.jar lib/groovy-reactor-6.0.0-beta-1.jar lib/groovy-reactor-6.0.0-beta-1-sources.jar lib/groovy-rxjava-6.0.0-beta-1.jar lib/groovy-rxjava-6.0.0-beta-1-sources.jar lib/groovy-servlet-6.0.0-beta-1.jar lib/groovy-servlet-6.0.0-beta-1-sources.jar lib/groovy-sql-6.0.0-beta-1.jar lib/groovy-sql-6.0.0-beta-1-sources.jar lib/groovy-swing-6.0.0-beta-1.jar lib/groovy-swing-6.0.0-beta-1-sources.jar lib/groovy-templates-6.0.0-beta-1.jar lib/groovy-templates-6.0.0-beta-1-sources.jar lib/groovy-test-6.0.0-beta-1.jar lib/groovy-test-6.0.0-beta-1-sources.jar lib/groovy-test-junit5-6.0.0-beta-1.jar lib/groovy-test-junit5-6.0.0-beta-1-sources.jar lib/groovy-test-junit6-6.0.0-beta-1.jar lib/groovy-test-junit6-6.0.0-beta-1-sources.jar lib/groovy-testng-6.0.0-beta-1.jar lib/groovy-testng-6.0.0-beta-1-sources.jar lib/groovy-toml-6.0.0-beta-1.jar lib/groovy-toml-6.0.0-beta-1-sources.jar lib/groovy-typecheckers-6.0.0-beta-1.jar lib/groovy-typecheckers-6.0.0-beta-1-sources.jar lib/groovy-xml-6.0.0-beta-1.jar lib/groovy-xml-6.0.0-beta-1-sources.jar lib/groovy-yaml-6.0.0-beta-1.jar lib/groovy-yaml-6.0.0-beta-1-sources.jar
+lib

k8s-dvfs/Makefile

@@ -0,0 +1,25 @@
+# Use the Gradle wrapper by default; override with e.g. `make GRADLE=gradle ...`
+# or `export GRADLE=gradle` (useful in pixi/conda environments).
+GRADLE ?= ./gradlew
+
+# Build the plugin
+assemble:
+	$(GRADLE) assemble
+
+clean:
+	rm -rf .nextflow*
+	rm -rf work
+	rm -rf build
+	$(GRADLE) clean
+
+# Run plugin unit tests
+test:
+	$(GRADLE) test
+
+# Install the plugin into local nextflow plugins dir
+install:
+	$(GRADLE) install
+
+# Publish the plugin
+release:
+	$(GRADLE) releasePlugin

k8s-dvfs/README.md

@@ -0,0 +1,86 @@
+# k8s-dvfs
+
+## Summary
+
+`k8s-dvfs` is a Nextflow plugin scaffolded from the official plugin
+template. Out of the box it provides:
+
+- A custom function `sayHello` that can be imported into Nextflow scripts.
+- A workflow observer that reacts to pipeline lifecycle events (start and
+  completion).
+
+Replace this section with a description of what your plugin actually does.
+
+Note: The **Summary**, **Get Started**, **Examples**, and **License** sections are
+mandatory: they are required by the Nextflow Registry, which uses this
+file as the plugin description. The **Plugin development** section below is
+guidance for working on the plugin and can be removed before publishing.
+
+## Get Started
+
+Enable the plugin in your pipeline `nextflow.config`:
+
+```groovy
+plugins {
+    id 'k8s-dvfs@0.1.0'
+}
+```
+
+Nextflow downloads the plugin from the Nextflow Registry the first time
+the pipeline runs.
+
+## Examples
+
+Import and call the `sayHello` function from a Nextflow script:
+
+```nextflow
+include { sayHello } from 'plugin/k8s-dvfs'
+
+workflow {
+    channel.of('Mundo', 'World').map { target -> sayHello(target) }
+}
+```
+
+The bundled observer prints a message when the pipeline starts and completes,
+so running any pipeline with the plugin enabled produces:
+
+```
+Pipeline is starting! 🚀
+Pipeline complete! 👋
+```
+
+## Plugin development
+
+This project was created from the [Nextflow plugin template](https://www.nextflow.io/docs/latest/guides/gradle-plugin.html#gradle-plugin-create).
+
+### Building
+
+To build the plugin:
+
+```bash
+make assemble
+```
+
+### Testing with Nextflow
+
+The plugin can be tested without a local Nextflow installation:
+
+1. Build and install the plugin to your local Nextflow installation: `make install`
+2. Run a pipeline with the plugin: `nextflow run hello -plugins k8s-dvfs@0.1.0`
+
+### Publishing
+
+Plugins can be published to a central Nextflow registry to make them accessible to the Nextflow community.
+
+Follow these steps to publish the plugin to the Nextflow Registry:
+
+1. Create a file named `$HOME/.gradle/gradle.properties`, where `$HOME` is your home directory. Add the following properties:
+    * `npr.apiKey`: Your Nextflow Registry access token.
+2. Package your plugin and publish it to the registry: `make release`.
+
+## License
+
+Apache License 2.0. See the [`COPYING`](COPYING) file for details.
+
+Note: The above license is given for guidance only; however the Nextflow Registry
+requires the plugin to include an OSS (open source software) license.

k8s-dvfs/build.gradle

@@ -0,0 +1,51 @@
+plugins {
+    id 'io.nextflow.nextflow-plugin' version '1.0.0-beta.15'
+}
+
+version = '0.1.0'
+
+nextflowPlugin {
+    nextflowVersion = '26.04.6'
+
+    provider = 'recreational.tech'
+    className = 'recreationaltech.plugin.K8sPlugin'
+    useDefaultDependencies = true
+    generateSpec = false
+    extensionPoints = [
+            'recreationaltech.plugin.K8sConfig',
+            'recreationaltech.plugin.K8sExecutor',
+            'recreationaltech.plugin.cli.KubeCommandImpl',
+    ]
+}
+
+sourceSets {
+    main.java.srcDirs = []
+    main.groovy.srcDirs = ['src/main/groovy']
+    main.resources.srcDirs = ['src/resources']
+    test.groovy.srcDirs = ['src/test/groovy']
+    test.java.srcDirs = []
+    test.resources.srcDirs = []
+}
+
+configurations {
+    // see https://docs.gradle.org/4.1/userguide/dependency_management.html#sub:exclude_transitive_dependencies
+    runtimeClasspath.exclude group: 'org.slf4j', module: 'slf4j-api'
+}
+
+dependencies {
+    //compileOnly project(':nextflow')
+    compileOnly 'org.slf4j:slf4j-api:2.0.17'
+    compileOnly 'org.pf4j:pf4j:3.14.1'
+    compileOnly 'dev.failsafe:failsafe:3.3.2'
+
+    implementation 'org.bouncycastle:bcprov-ext-jdk18on:1.78.1'
+    implementation 'org.bouncycastle:bcpkix-jdk18on:1.84'
+
+    //testImplementation(testFixtures(project(":nextflow")))
+    testImplementation "org.apache.groovy:groovy:4.0.31"
+    testImplementation "org.apache.groovy:groovy-nio:4.0.31"
+}
+
+test {
+    useJUnitPlatform()
+}

k8s-dvfs/gradle/wrapper/gradle-wrapper.properties

@@ -1,6 +1,6 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-9.3.1-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.14-bin.zip
 networkTimeout=10000
 validateDistributionUrl=true
 zipStoreBase=GRADLE_USER_HOME

k8s-dvfs/gradlew

@@ -15,8 +15,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
-# SPDX-License-Identifier: Apache-2.0
-#
 
 ##############################################################################
 #
@@ -57,7 +55,7 @@
 #       Darwin, MinGW, and NonStop.
 #
 #   (3) This script is generated from the Groovy template
-#       https://github.com/gradle/gradle/blob/HEAD/platforms/jvm/plugins-application/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt
+#       https://github.com/gradle/gradle/blob/HEAD/subprojects/plugins/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt
 #       within the Gradle project.
 #
 #       You can find Gradle at https://github.com/gradle/gradle/.
@@ -86,7 +84,7 @@ done
 # shellcheck disable=SC2034
 APP_BASE_NAME=${0##*/}
 # Discard cd standard output in case $CDPATH is set (https://github.com/gradle/gradle/issues/25036)
-APP_HOME=$( cd -P "${APP_HOME:-./}" > /dev/null && printf '%s\n' "$PWD" ) || exit
+APP_HOME=$( cd "${APP_HOME:-./}" > /dev/null && pwd -P ) || exit
 
 # Use the maximum available, or set MAX_FD != -1 to use that value.
 MAX_FD=maximum
@@ -114,7 +112,7 @@ case "$( uname )" in                #(
   NONSTOP* )        nonstop=true ;;
 esac
 
-CLASSPATH="\\\"\\\""
+CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
 
 
 # Determine the Java command to use to start the JVM.
@@ -205,7 +203,7 @@ fi
 DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
 
 # Collect all arguments for the java command:
-#   * DEFAULT_JVM_OPTS, JAVA_OPTS, and optsEnvironmentVar are not allowed to contain shell fragments,
+#   * DEFAULT_JVM_OPTS, JAVA_OPTS, JAVA_OPTS, and optsEnvironmentVar are not allowed to contain shell fragments,
 #     and any embedded shellness will be escaped.
 #   * For example: A user cannot expect ${Hostname} to be expanded, as it is an environment variable and will be
 #     treated as '${Hostname}' itself on the command line.
@@ -213,7 +211,7 @@ DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
 set -- \
         "-Dorg.gradle.appname=$APP_BASE_NAME" \
         -classpath "$CLASSPATH" \
-        -jar "$APP_HOME/gradle/wrapper/gradle-wrapper.jar" \
+        org.gradle.wrapper.GradleWrapperMain \
         "$@"
 
 # Stop when "xargs" is not available.

k8s-dvfs/settings.gradle

@@ -0,0 +1 @@
+rootProject.name = 'k8s-dvfs'

k8s-dvfs/src/main/groovy/recreationaltech/plugin/K8sConfig.groovy

@@ -14,10 +14,10 @@
  * limitations under the License.
  */
 
-package nextflow.k8s
+package recreationaltech.plugin
 
 import nextflow.config.scopes.Config
-import nextflow.k8s.client.K8sRetryConfig
+import recreationaltech.plugin.client.K8sRetryConfig
 
 import javax.annotation.Nullable
 
@@ -31,13 +31,13 @@ import nextflow.config.spec.ScopeName
 import nextflow.container.ContainerHelper
 import nextflow.script.dsl.Description
 import nextflow.exception.AbortOperationException
-import nextflow.k8s.client.ClientConfig
-import nextflow.k8s.client.K8sClient
-import nextflow.k8s.client.K8sResponseException
-import nextflow.k8s.model.PodOptions
-import nextflow.k8s.model.PodSecurityContext
-import nextflow.k8s.model.PodVolumeClaim
-import nextflow.k8s.model.ResourceType
+import recreationaltech.plugin.client.ClientConfig
+import recreationaltech.plugin.client.K8sClient
+import recreationaltech.plugin.client.K8sResponseException
+import recreationaltech.plugin.model.PodOptions
+import recreationaltech.plugin.model.PodSecurityContext
+import recreationaltech.plugin.model.PodVolumeClaim
+import recreationaltech.plugin.model.ResourceType
 import nextflow.util.Duration
 
 import java.util.concurrent.TimeUnit
@@ -260,6 +260,24 @@ class K8sConfig implements ConfigScope {
     """)
     final Duration noiseRuntimeEstimatorNoiseMagnitude
 
+    @ConfigOption
+    @Description("""
+        Max. amount of time two runtime estimates can differ to be considered equal.
+    """)
+    final Duration runtimeComparisonEpsilon
+
+    @ConfigOption
+    @Description("""
+        Number of saved top runtimes used to classify a task as critical.
+    """)
+    final int dvfsSchedulingNumTopRuntimes
+
+    @ConfigOption
+    @Description("""
+        If not empty, only nodes with the given label will be used.
+    """)
+    final String nodeLabel
+
     /* required by extension point -- do not remove */
     K8sConfig() {
         this(Collections.emptyMap())
@@ -300,7 +318,12 @@ class K8sConfig implements ConfigScope {
 
         schedulingStrategy = opts.schedulingStrategy as String ?: "Hash"
         runtimeEstimator = opts.runtimeEstimator as String ?: "LinearFit"
-        noiseRuntimeEstimatorNoiseMagnitude = opts.noiseRuntimeEstimatorNoiseMagnitude as Duration ?: new Duration(10, TimeUnit.SECONDS)
+        noiseRuntimeEstimatorNoiseMagnitude = opts.noiseRuntimeEstimatorNoiseMagnitude as Duration ?: new Duration(30, TimeUnit.SECONDS)
+        runtimeComparisonEpsilon = opts.runtimeComparisonEpsilon as Duration ?: new Duration(10, TimeUnit.SECONDS)
+        def numTop = opts.dvfsSchedulingNumTopRuntimes
+        dvfsSchedulingNumTopRuntimes = numTop != null && numTop.toString().trim() != '' ? numTop as int : 3
+
+        nodeLabel = opts.nodeLabel as String ?: ""
 
         // -- shortcut to pod image pull-policy
         if( imagePullPolicy )
@@ -362,6 +385,12 @@ class K8sConfig implements ConfigScope {
         return DEFAULT_FUSE_PLUGIN
     }
 
+    String[] getNodeLabelFilter() {
+        if (nodeLabel.empty)
+            return null
+        return nodeLabel.split('=', 2)
+    }
+
     /**
      * Whenever the pod should honour the entrypoint defined by the image (default: false)
      *

k8s-dvfs/src/main/groovy/recreationaltech/plugin/K8sDVFSClient.groovy

@@ -1,4 +1,4 @@
-package nextflow.k8s
+package recreationaltech.plugin
 
 import groovy.util.logging.Slf4j
 

k8s-dvfs/src/main/groovy/recreationaltech/plugin/K8sDriverLauncher.groovy

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package nextflow.k8s
+package recreationaltech.plugin
 
 import groovy.transform.MapConstructor
 
@@ -32,12 +32,12 @@ import nextflow.cli.CmdRun
 import nextflow.config.ConfigBuilder
 import nextflow.exception.AbortOperationException
 import nextflow.file.FileHelper
-import nextflow.k8s.client.K8sClient
-import nextflow.k8s.client.K8sResponseException
-import nextflow.k8s.model.PodEnv
-import nextflow.k8s.model.PodMountConfig
-import nextflow.k8s.model.PodSpecBuilder
-import nextflow.k8s.model.ResourceType
+import recreationaltech.plugin.client.K8sClient
+import recreationaltech.plugin.client.K8sResponseException
+import recreationaltech.plugin.model.PodEnv
+import recreationaltech.plugin.model.PodMountConfig
+import recreationaltech.plugin.model.PodSpecBuilder
+import recreationaltech.plugin.model.ResourceType
 import nextflow.scm.AssetManager
 import nextflow.scm.ProviderConfig
 import nextflow.util.ConfigHelper
@@ -132,8 +132,6 @@ class K8sDriverLauncher {
      */
     private String plugins
 
-    private K8sNodeInitDeployer initDeployer
-
     /**
      * Launcher entry point. Set-up the environment and create a pod that run the Nextflow
      * application (which in turns executed each task as a pod)
@@ -155,7 +153,6 @@ class K8sDriverLauncher {
 
         createK8sConfigMap()
 
-        initDeployer.deploy()
         createK8sLauncherPod()
         waitPodStart()
         // login into container session
@@ -570,7 +567,7 @@ class K8sDriverLauncher {
 
     /**
      * Creates and executes the nextflow driver pod
-     * @return A {@link nextflow.k8s.client.K8sResponseJson} response object
+     * @return A {@link recreationaltech.plugin.client.K8sResponseJson} response object
      */
     protected createK8sLauncherPod() {
         final spec = makeLauncherSpec()

k8s-dvfs/src/main/groovy/recreationaltech/plugin/K8sExecutor.groovy

@@ -14,11 +14,12 @@
  * limitations under the License.
  */
 
-package nextflow.k8s
+package recreationaltech.plugin
 
 import groovy.transform.CompileDynamic
-import nextflow.k8s.strategies.K8sDVFSSchedulingStrategy
-import nextflow.k8s.strategies.K8sHashSchedulingStrategy
+import recreationaltech.plugin.strategies.K8sDVFSFrequencyBandsSchedulingStrategy
+import recreationaltech.plugin.strategies.K8sDVFSSchedulingStrategy
+import recreationaltech.plugin.strategies.K8sHashSchedulingStrategy
 
 import java.util.concurrent.TimeUnit
 
@@ -29,7 +30,7 @@ import groovy.transform.Memoized
 import groovy.util.logging.Slf4j
 import nextflow.executor.Executor
 import nextflow.fusion.FusionHelper
-import nextflow.k8s.client.K8sClient
+import recreationaltech.plugin.client.K8sClient
 import nextflow.processor.TaskHandler
 import nextflow.processor.TaskMonitor
 import nextflow.processor.TaskPollingMonitor
@@ -45,7 +46,7 @@ import org.pf4j.ExtensionPoint
  */
 @Slf4j
 @CompileStatic
-@ServiceName('k8s')
+@ServiceName('k8s-dvfs')
 class K8sExecutor extends Executor implements ExtensionPoint {
 
     /**
@@ -57,6 +58,8 @@ class K8sExecutor extends Executor implements ExtensionPoint {
     private K8sTaskScheduler taskScheduler
     private Thread schedulerThread
 
+    private K8sNodeInitDeployer initDeployer
+
     K8sRuntimeRecorder runtimeRecorder
     K8sRuntimeEstimator runtimeEstimator
 
@@ -96,6 +99,9 @@ class K8sExecutor extends Executor implements ExtensionPoint {
 
         log.debug "[K8s] config=$k8sConfig; API client config=$client.config"
 
+        this.initDeployer = new K8sNodeInitDeployer(client, k8sConfig)
+        initDeployer.deploy()
+
         this.runtimeRecorder = new K8sRuntimeRecorder(k8sConfig.recordTaskRuntimes, k8sConfig.runtimeRecordPath)
 
         if (k8sConfig.runtimeEstimator == "LinearFit") {
@@ -112,26 +118,31 @@ class K8sExecutor extends Executor implements ExtensionPoint {
         K8sSchedulingStrategy strategy = null
         if (k8sConfig.schedulingStrategy == "Hash") {
             strategy = new K8sHashSchedulingStrategy()
-        } else if (k8sConfig.schedulingStrategy == "DVFS") {
+        } else if (k8sConfig.schedulingStrategy == "DVFS" || k8sConfig.schedulingStrategy == "DVFS-SPEED") {
             String[] ips = new String[nodes.length]
             for (int i = 0; i < nodes.length; i++) {
-                ips[i] = client.getPodIpAddress(K8sNodeInitDeployer.buildPodName(nodes[i]))
+                // Use node external IP since pods use hostNetwork
+                ips[i] = client.getNodeExternalIp(nodes[i])
                 log.info "[K8s] node ${nodes[i]} -> ${ips[i]}"
             }
             strategy = new K8sDVFSSchedulingStrategy(this.runtimeEstimator,
                 new K8sDVFSClient(nodes, ips),
-                () -> getClient())
-            strategy.fullSpeedMode = false
-        } else if (k8sConfig.schedulingStrategy == "DVFS-SPEED") {
+                () -> getClient(),
+                k8sConfig.runtimeComparisonEpsilon,
+                k8sConfig.dvfsSchedulingNumTopRuntimes)
+            strategy.fullSpeedMode = k8sConfig.schedulingStrategy == "DVFS-SPEED"
+        } else if (k8sConfig.schedulingStrategy == "DVFS-BAND") {
             String[] ips = new String[nodes.length]
             for (int i = 0; i < nodes.length; i++) {
-                ips[i] = client.getPodIpAddress(K8sNodeInitDeployer.buildPodName(nodes[i]))
+                // Use node external IP since pods use hostNetwork
+                ips[i] = client.getNodeExternalIp(nodes[i])
                 log.info "[K8s] node ${nodes[i]} -> ${ips[i]}"
             }
-            strategy = new K8sDVFSSchedulingStrategy(this.runtimeEstimator,
-                new K8sDVFSClient(nodes, ips),
-                () -> getClient())
-            strategy.fullSpeedMode = true
+            strategy = new K8sDVFSFrequencyBandsSchedulingStrategy(this.runtimeEstimator,
+                    new K8sDVFSClient(nodes, ips),
+                    () -> getClient(),
+                    k8sConfig.runtimeComparisonEpsilon,
+                    k8sConfig.dvfsSchedulingNumTopRuntimes)
         } else {
             log.error "[K8s] invalid scheduling strategy $k8sConfig.schedulingStrategy, falling back on \"Hash\""
             strategy = new K8sHashSchedulingStrategy()
@@ -144,10 +155,19 @@ class K8sExecutor extends Executor implements ExtensionPoint {
 
     @CompileDynamic
     private String[] getNodeList() {
-        final resp = getClient().nodeList()
+        final resp = client.nodeList()
         ArrayList<String> nodes = new ArrayList<String>()
-        for ( Map item : resp.items ) {
-            nodes.add(item.metadata.name as String)
+        String[] filter = getK8sConfig().getNodeLabelFilter()
+        if (filter == null) {
+            for (Map item : resp.items) {
+                nodes.add(item.metadata.name as String)
+            }
+        } else {
+            for (Map item : resp.items) {
+                Map<String, String> labels = item.metadata.labels as Map<String, String>
+                if (labels.get(filter[0]) == filter[1])
+                    nodes.add(item.metadata.name as String)
+            }
         }
         return nodes.toArray()
     }
@@ -157,6 +177,7 @@ class K8sExecutor extends Executor implements ExtensionPoint {
         this.runtimeRecorder.write()
         this.taskScheduler.stop()
         this.schedulerThread.join()
+        this.initDeployer.cleanup()
     }
 
     /**

k8s-dvfs/src/main/groovy/recreationaltech/plugin/K8sLinearFitRuntimeEstimator.groovy

@@ -1,4 +1,4 @@
-package nextflow.k8s
+package recreationaltech.plugin
 
 import groovy.util.logging.Slf4j
 

k8s-dvfs/src/main/groovy/recreationaltech/plugin/K8sNodeInitConfig.groovy

@@ -1,4 +1,4 @@
-package nextflow.k8s
+package recreationaltech.plugin
 
 import groovy.util.logging.Slf4j
 import nextflow.config.scopes.Config

k8s-dvfs/src/main/groovy/recreationaltech/plugin/K8sNodeInitDeployer.groovy

@@ -1,9 +1,9 @@
-package nextflow.k8s
+package recreationaltech.plugin
 
 import groovy.util.logging.Slf4j
-import nextflow.k8s.client.K8sClient
-import nextflow.k8s.model.PodHostMount
-import nextflow.k8s.model.PodSpecBuilder
+import recreationaltech.plugin.client.K8sClient
+import recreationaltech.plugin.model.PodHostMount
+import recreationaltech.plugin.model.PodSpecBuilder
 
 @Slf4j
 class K8sNodeInitDeployer {
@@ -19,13 +19,14 @@ class K8sNodeInitDeployer {
         final init = config.nodeInit
         if ( !init?.enabled )
             return
+        final namespace = config.namespace
 
         log.info("deploying init pods")
 
         final nodes = getNodes()
         for ( String nodeName : nodes ) {
             log.info(" ... deploying to " + nodeName)
-            final spec = makePodSpec(init, nodeName)
+            final spec = makePodSpec(init, nodeName, namespace)
             client.podCreate(spec)
         }
 
@@ -108,8 +109,17 @@ exit 0
     private List<String> getNodes() {
         final resp = client.nodeList()
         ArrayList<String> nodes = new ArrayList<String>()
-        for ( Map item: resp.items ) {
-            nodes.add(item.metadata.name as String)
+        String[] filter = config.getNodeLabelFilter()
+        if (filter == null) {
+            for (Map item : resp.items) {
+                nodes.add(item.metadata.name as String)
+            }
+        } else {
+            for (Map item : resp.items) {
+                Map<String, String> labels = item.metadata.labels as Map<String, String>
+                if (labels.get(filter[0]) == filter[1])
+                    nodes.add(item.metadata.name as String)
+            }
         }
         return nodes
     }
@@ -123,7 +133,7 @@ exit 0
         return name
     }
 
-    private Map makePodSpec(K8sNodeInitConfig config, String nodeName) {
+    private Map makePodSpec(K8sNodeInitConfig config, String nodeName, String namespace) {
         ArrayList<PodHostMount> mounts = new ArrayList<PodHostMount>()
         mounts.add(new PodHostMount("/sys", "/sys"))
         mounts.add(new PodHostMount("/dev", "/dev"))
@@ -137,6 +147,8 @@ exit 0
             .withHostMounts(mounts)
             .withPodName(buildPodName(nodeName))
             .withPort(8080)
+            .withHostNetwork(true)
+            .withNamespace(namespace)
             .build()
     }
 

k8s-dvfs/src/main/groovy/recreationaltech/plugin/K8sNoiseRuntimeEstimator.groovy

@@ -1,4 +1,4 @@
-package nextflow.k8s
+package recreationaltech.plugin
 
 import nextflow.util.Duration
 

k8s-dvfs/src/main/groovy/recreationaltech/plugin/K8sPlugin.groovy

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package nextflow.k8s
+package recreationaltech.plugin
 
 import groovy.transform.CompileStatic
 import nextflow.plugin.BasePlugin

k8s-dvfs/src/main/groovy/recreationaltech/plugin/K8sRuntimeEstimator.groovy

@@ -1,4 +1,4 @@
-package nextflow.k8s
+package recreationaltech.plugin
 
 import groovy.util.logging.Slf4j
 

k8s-dvfs/src/main/groovy/recreationaltech/plugin/K8sRuntimeRecord.groovy

@@ -1,4 +1,4 @@
-package nextflow.k8s
+package recreationaltech.plugin
 
 record K8sRuntimeRecord(
     String taskName,

k8s-dvfs/src/main/groovy/recreationaltech/plugin/K8sRuntimeRecorder.groovy

@@ -1,4 +1,4 @@
-package nextflow.k8s
+package recreationaltech.plugin
 
 import groovy.util.logging.Slf4j
 

k8s-dvfs/src/main/groovy/recreationaltech/plugin/K8sSchedulingDecision.groovy

@@ -1,4 +1,4 @@
-package nextflow.k8s
+package recreationaltech.plugin
 
 import groovy.transform.CompileStatic
 

k8s-dvfs/src/main/groovy/recreationaltech/plugin/K8sSchedulingRequest.groovy

@@ -1,4 +1,4 @@
-package nextflow.k8s
+package recreationaltech.plugin
 
 import groovy.transform.CompileStatic
 import nextflow.processor.TaskRun

k8s-dvfs/src/main/groovy/recreationaltech/plugin/K8sSchedulingStrategy.groovy

@@ -1,4 +1,4 @@
-package nextflow.k8s
+package recreationaltech.plugin
 
 interface K8sSchedulingStrategy {
     /**

k8s-dvfs/src/main/groovy/recreationaltech/plugin/K8sTaskHandler.groovy

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package nextflow.k8s
+package recreationaltech.plugin
 
 import java.nio.file.FileAlreadyExistsException
 import java.nio.file.Files
@@ -29,16 +29,16 @@ import nextflow.SysEnv
 import nextflow.container.ContainerHelper
 import nextflow.container.DockerBuilder
 import nextflow.exception.NodeTerminationException
-import nextflow.k8s.client.PodUnschedulableException
+import recreationaltech.plugin.client.PodUnschedulableException
 import nextflow.exception.ProcessSubmitException
 import nextflow.executor.BashWrapperBuilder
 import nextflow.fusion.FusionAwareTask
-import nextflow.k8s.client.K8sClient
-import nextflow.k8s.client.K8sResponseException
-import nextflow.k8s.model.PodEnv
-import nextflow.k8s.model.PodOptions
-import nextflow.k8s.model.PodSpecBuilder
-import nextflow.k8s.model.ResourceType
+import recreationaltech.plugin.client.K8sClient
+import recreationaltech.plugin.client.K8sResponseException
+import recreationaltech.plugin.model.PodEnv
+import recreationaltech.plugin.model.PodOptions
+import recreationaltech.plugin.model.PodSpecBuilder
+import recreationaltech.plugin.model.ResourceType
 import nextflow.processor.TaskHandler
 import nextflow.processor.TaskRun
 import nextflow.processor.TaskStatus

k8s-dvfs/src/main/groovy/recreationaltech/plugin/K8sTaskScheduler.groovy

@@ -1,4 +1,4 @@
-package nextflow.k8s
+package recreationaltech.plugin
 
 
 import groovy.transform.CompileStatic

k8s-dvfs/src/main/groovy/recreationaltech/plugin/K8sWrapperBuilder.groovy

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package nextflow.k8s
+package recreationaltech.plugin
 
 
 import groovy.transform.CompileStatic

k8s-dvfs/src/main/groovy/recreationaltech/plugin/cli/KubeCommandImpl.groovy

@@ -14,11 +14,11 @@
  * limitations under the License.
  */
 
-package nextflow.k8s.cli
+package recreationaltech.plugin.cli
 
 import groovy.transform.CompileStatic
 import nextflow.cli.CmdKubeRun
-import nextflow.k8s.K8sDriverLauncher
+import recreationaltech.plugin.K8sDriverLauncher
 
 /**
  * Kuberun command implementation logic

k8s-dvfs/src/main/groovy/recreationaltech/plugin/client/ClientConfig.groovy

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package nextflow.k8s.client
+package recreationaltech.plugin.client
 
 import groovy.util.logging.Slf4j
 import nextflow.util.Duration

k8s-dvfs/src/main/groovy/recreationaltech/plugin/client/ConfigDiscovery.groovy

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package nextflow.k8s.client
+package recreationaltech.plugin.client
 
 import javax.net.ssl.KeyManager
 import javax.net.ssl.KeyManagerFactory

k8s-dvfs/src/main/groovy/recreationaltech/plugin/client/K8sClient.groovy

@@ -14,13 +14,14 @@
  * limitations under the License.
  */
 
-package nextflow.k8s.client
+package recreationaltech.plugin.client
 
 import dev.failsafe.Failsafe
 import dev.failsafe.FailsafeException
 import dev.failsafe.RetryPolicy
 import dev.failsafe.event.EventListener
 import dev.failsafe.event.ExecutionAttemptedEvent
+import dev.failsafe.function.CheckedPredicate
 import dev.failsafe.function.CheckedSupplier
 import nextflow.exception.K8sOutOfCpuException
 import nextflow.exception.K8sOutOfMemoryException
@@ -371,6 +372,32 @@ class K8sClient {
         (resp?.spec as Map)?.nodeName as String
     }
 
+    /**
+     * Get the external IP address of a node
+     * @param nodeName The node name
+     * @return The external IP address of the node, or internal IP if external is not available
+     */
+    String getNodeExternalIp(String nodeName) {
+        assert nodeName
+        final K8sResponseJson resp = nodeDescribe(nodeName)
+        final status = resp.status as Map
+        final addresses = status?.addresses as List<Map>
+        
+        // Try to find ExternalIP first
+        for (Map address : addresses) {
+            if (address.type == 'ExternalIP') {
+                return address.address as String
+            }
+        }
+        // Fall back to InternalIP
+        for (Map address : addresses) {
+            if (address.type == 'InternalIP') {
+                return address.address as String
+            }
+        }
+        return null
+    }
+
     /**
      * Get pod current state object
      *
@@ -870,10 +897,17 @@ class K8sClient {
             trace('GET', action, resp.text)
             final podList = new K8sResponseJson(resp.text)
             final items = podList.items as List<Map>
-            
+
             long totalAllocated = 0L
             if (items) {
                 for (Map pod : items) {
+                    // Skip terminated/succeeded pods
+                    final status = pod.status as Map
+                    final phase = status?.phase as String
+                    if (phase in ['Succeeded', 'Failed', 'Unknown']) {
+                        continue
+                    }
+
                     final spec = pod.spec as Map
                     if (spec) {
                         final containers = spec.containers as List<Map>
@@ -936,6 +970,13 @@ class K8sClient {
             long totalAllocated = 0L
             if (items) {
                 for (Map pod : items) {
+                    // Skip terminated/succeeded pods
+                    final status = pod.status as Map
+                    final phase = status?.phase as String
+                    if (phase in ['Succeeded', 'Failed', 'Unknown']) {
+                        continue
+                    }
+
                     final spec = pod.spec as Map
                     if (spec) {
                         final containers = spec.containers as List<Map>
@@ -1187,17 +1228,17 @@ class K8sClient {
     }
 
     /**
-     * Creates a retry policy using the configuration specified by {@link nextflow.k8s.client.K8sRetryConfig}
+     * Creates a retry policy using the configuration specified by {@link recreationaltech.plugin.client.K8sRetryConfig}
      *
      * @param cond A predicate that determines when a retry should be triggered
      * @return The {@link dev.failsafe.RetryPolicy} instance
      */
-    protected <T> RetryPolicy<T> retryPolicy(Predicate<? extends Throwable> cond) {
+    protected <T> RetryPolicy<T> retryPolicy(CheckedPredicate<? extends Throwable> cond) {
         final cfg = config.retryConfig
         final listener = new EventListener<ExecutionAttemptedEvent<T>>() {
             @Override
             void accept(ExecutionAttemptedEvent<T> event) throws Throwable {
-                log.debug("K8s response error - attempt: ${event.attemptCount}; reason: ${event.lastFailure.message}")
+                log.debug("K8s response error - attempt: ${event.attemptCount}; reason: ${event.lastException?.message ?: 'unknown'}")
             }
         }
         return RetryPolicy.<T>builder()
@@ -1219,9 +1260,8 @@ class K8sClient {
      */
     protected <T> T apply(CheckedSupplier<T> action) {
         // define the retry condition
-        final cond = new Predicate<? extends Throwable>() {
-            @Override
-            boolean test(Throwable t) {
+        final cond = [
+            test: { Throwable t ->
                 if ( t instanceof K8sResponseException && t.response.code in RETRY_CODES )
                     return true
                 if( t instanceof SocketException || t.cause instanceof SocketException )
@@ -1230,7 +1270,7 @@ class K8sClient {
                     return true
                 return false
             }
-        }
+        ] as CheckedPredicate<Throwable>
         // create the retry policy object
         final policy = retryPolicy(cond)
         // apply the action with and throw the original cause

k8s-dvfs/src/main/groovy/recreationaltech/plugin/client/K8sResponseApi.groovy

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package nextflow.k8s.client
+package recreationaltech.plugin.client
 
 import groovy.transform.CompileStatic
 

k8s-dvfs/src/main/groovy/recreationaltech/plugin/client/K8sResponseException.groovy

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package nextflow.k8s.client
+package recreationaltech.plugin.client
 
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j

k8s-dvfs/src/main/groovy/recreationaltech/plugin/client/K8sResponseJson.groovy

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package nextflow.k8s.client
+package recreationaltech.plugin.client
 
 import groovy.json.JsonOutput
 import groovy.json.JsonSlurper

k8s-dvfs/src/main/groovy/recreationaltech/plugin/client/K8sRetryConfig.groovy

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package nextflow.k8s.client
+package recreationaltech.plugin.client
 
 import groovy.transform.CompileStatic
 import groovy.transform.EqualsAndHashCode

k8s-dvfs/src/main/groovy/recreationaltech/plugin/client/PodUnschedulableException.groovy

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package nextflow.k8s.client
+package recreationaltech.plugin.client
 
 import groovy.transform.CompileStatic
 import nextflow.exception.ProcessException

k8s-dvfs/src/main/groovy/recreationaltech/plugin/client/SSLUtils.java

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package nextflow.k8s.client;
+package recreationaltech.plugin.client;
 
 /**
  * This file is derived from

k8s-dvfs/src/main/groovy/recreationaltech/plugin/model/PodEnv.groovy

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package nextflow.k8s.model
+package recreationaltech.plugin.model
 
 import groovy.transform.CompileStatic
 import groovy.transform.EqualsAndHashCode

k8s-dvfs/src/main/groovy/recreationaltech/plugin/model/PodHostMount.groovy

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package nextflow.k8s.model
+package recreationaltech.plugin.model
 
 import groovy.transform.CompileStatic
 import groovy.transform.EqualsAndHashCode

k8s-dvfs/src/main/groovy/recreationaltech/plugin/model/PodMountConfig.groovy

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package nextflow.k8s.model
+package recreationaltech.plugin.model
 
 import java.nio.file.Paths
 

k8s-dvfs/src/main/groovy/recreationaltech/plugin/model/PodMountCsiEphemeral.groovy

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package nextflow.k8s.model
+package recreationaltech.plugin.model
 
 import java.nio.file.Paths
 

k8s-dvfs/src/main/groovy/recreationaltech/plugin/model/PodMountEmptyDir.groovy

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package nextflow.k8s.model
+package recreationaltech.plugin.model
 
 import groovy.transform.CompileStatic
 import groovy.transform.EqualsAndHashCode

k8s-dvfs/src/main/groovy/recreationaltech/plugin/model/PodMountSecret.groovy

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package nextflow.k8s.model
+package recreationaltech.plugin.model
 
 import java.nio.file.Paths
 

k8s-dvfs/src/main/groovy/recreationaltech/plugin/model/PodNodeSelector.groovy

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package nextflow.k8s.model
+package recreationaltech.plugin.model
 
 import groovy.transform.CompileStatic
 import groovy.transform.EqualsAndHashCode

k8s-dvfs/src/main/groovy/recreationaltech/plugin/model/PodOptions.groovy

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package nextflow.k8s.model
+package recreationaltech.plugin.model
 
 import groovy.transform.CompileStatic
 import groovy.transform.EqualsAndHashCode

k8s-dvfs/src/main/groovy/recreationaltech/plugin/model/PodSecurityContext.groovy

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package nextflow.k8s.model
+package recreationaltech.plugin.model
 
 import groovy.transform.CompileStatic
 import groovy.transform.EqualsAndHashCode

k8s-dvfs/src/main/groovy/recreationaltech/plugin/model/PodSpecBuilder.groovy

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package nextflow.k8s.model
+package recreationaltech.plugin.model
 
 import java.nio.file.Path
 import java.util.concurrent.atomic.AtomicInteger
@@ -130,6 +130,8 @@ class PodSpecBuilder {
 
     Integer port = null
 
+    boolean hostNetwork = false
+
     /**
      * @return A sequential volume unique identifier
      */
@@ -413,6 +415,11 @@ class PodSpecBuilder {
         return this
     }
 
+    PodSpecBuilder withHostNetwork(boolean value) {
+        this.hostNetwork = value
+        return this
+    }
+
     @PackageScope List<Map> createPullSecret() {
         def result = new ArrayList(1)
         def entry = new LinkedHashMap(1)
@@ -519,6 +526,9 @@ class PodSpecBuilder {
         if ( nodeName )
             spec.nodeName = nodeName
 
+        if ( hostNetwork )
+            spec.hostNetwork = true
+
         final pod = [
                 apiVersion: 'v1',
                 kind: 'Pod',

k8s-dvfs/src/main/groovy/recreationaltech/plugin/model/PodVolumeClaim.groovy

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package nextflow.k8s.model
+package recreationaltech.plugin.model
 
 import groovy.transform.CompileStatic
 import groovy.transform.EqualsAndHashCode

k8s-dvfs/src/main/groovy/recreationaltech/plugin/model/ResourceType.groovy

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package nextflow.k8s.model
+package recreationaltech.plugin.model
 
 /**
  * Model the resource type to be used to run nextflow tasks

k8s-dvfs/src/main/groovy/recreationaltech/plugin/strategies/K8sDVFSFrequencyBandsSchedulingStrategy.groovy

@@ -0,0 +1,395 @@
+package recreationaltech.plugin.strategies
+
+import groovy.transform.CompileStatic
+import groovy.util.logging.Slf4j
+import nextflow.processor.TaskRun
+import nextflow.util.Duration
+import recreationaltech.plugin.*
+import recreationaltech.plugin.client.K8sClient
+
+/**
+ * Implements a scheduling strategy utilizing dvfs to reduce the energy consumption
+ * of workflow execution, while attempting to maintain the same makespan.
+ *
+ * This variant divides available nodes into three classes:
+ * - High frequency (100%)
+ * - Middle frequency (66%)
+ * - Low frequency (33%)
+ *
+ * Tasks are assigned to frequency classes according to their
+ * estimated runtime t:
+ * - t is in top-k runtimes => High
+ * - t is at most 1/2 top runtime => Middle
+ * - t is below 1/2 top runtime => Low
+ *
+ * Nodes are assigned to the classes via round robin,
+ * starting with high.
+ */
+@Slf4j
+@CompileStatic
+class K8sDVFSFrequencyBandsSchedulingStrategy implements K8sSchedulingStrategy {
+
+    /** Used for passing K8sExecutor.getClient.
+     * We cannot pass the client directly, becaue it can be refreshed
+     * during workflow execution.
+     */
+    public interface K8sClientGetter {
+        K8sClient getClient()
+    }
+
+    private static long getTaskMemoryRequirment(TaskRun task) {
+        return task.config.getMemory() ? task.config.getMemory().bytes : 64 * 1024 * 1024
+    }
+
+    private static int getTaskCPURequirement(TaskRun task) {
+        return task.config.hasCpus() ? task.config.getCpus() * 1000 : 1000
+    }
+
+    @Slf4j
+    private class WorkerNode {
+        private class AssignedTask {
+            TaskRun task
+
+            AssignedTask(TaskRun t) {
+                this.task = t
+            }
+        }
+
+        String name
+
+        long frequency
+
+        ArrayList<AssignedTask> tasks
+
+        WorkerNode(String name, long frequency, K8sClientGetter clientGetter) {
+            this.name = name
+            this.frequency = frequency
+            this.tasks = new ArrayList<>()
+        }
+
+        /* Return the number of available (unoccupied) bytes */
+        long getAvailableMemory() {
+            def k8sClient = clientGetter.getClient()
+            Long available = k8sClient.getNodeMemoryAvailableBytes(this.name)
+            if (available == null) {
+                log.warn "[K8s] failed to retrieve available memory for node ${name}"
+                // Fallback: try capacity - allocated
+                Long capacity = k8sClient.getNodeMemoryCapacityBytes(this.name)
+                Long allocated = k8sClient.getNodeMemoryAllocatedBytes(this.name)
+                if (capacity != null && allocated != null) {
+                    return capacity - allocated
+                }
+                return 0
+            }
+            return available
+        }
+
+        /* Return the number of available (unoccupied) cpu cores */
+        long getAvailableCPUs() {
+            def k8sClient = clientGetter.getClient()
+            Long available = k8sClient.getNodeCpuAvailableMillis(this.name)
+            if (available == null) {
+                log.warn "[K8s] failed to retrieve available CPU for node ${name}"
+                // Fallback: try capacity - allocated
+                Long capacity = k8sClient.getNodeCpuCapacityMillis(this.name)
+                Long allocated = k8sClient.getNodeCpuAllocatedMillis(this.name)
+                if (capacity != null && allocated != null) {
+                    return capacity - allocated
+                }
+                return 0
+            }
+            return available
+        }
+
+        /* Return the total amount of installed memory */
+        long getMemoryAmount() {
+            def k8sClient = clientGetter.getClient()
+            Long capacity = k8sClient.getNodeMemoryCapacityBytes(this.name)
+            return capacity != null ? capacity.longValue() : 0
+        }
+
+        /* Return the total number of installed cpu cores */
+        long getCPUCount() {
+            def k8sClient = clientGetter.getClient()
+            Long capacity = k8sClient.getNodeCpuCapacityMillis(this.name)
+            return capacity != null ? capacity.longValue(): 0
+        }
+
+        // Resets the frequency
+        private void updateFrequency(K8sDVFSClient dvfsClient) {
+            if (tasks.size() == 0)
+                return
+            long maxFrequency = dvfsClient.getNodeMaxFrequency(this.name).orElse(this.frequency)
+            log.info "[K8s] node ${name} running at ${frequency} Hz / ${maxFrequency} Hz ${((double)frequency/(double)maxFrequency) * 100.0}%"
+            dvfsClient.setNodeFrequency(name, (int)frequency)
+        }
+
+        void assignTask(TaskRun task, K8sDVFSClient dvfsClient) {
+            log.info "[K8s] node ${name}: task ${task.name} assigned with ${this.frequency}"
+            this.tasks.add(new AssignedTask(task))
+            updateFrequency(dvfsClient)
+        }
+
+        void taskFinished(TaskRun task, K8sDVFSClient dvfsClient) {
+            log.info "[K8s] node ${name}: task ${task.name} finished"
+            this.tasks.removeIf {it.task == task}
+            updateFrequency(dvfsClient)
+        }
+    }
+
+    class SchedulingRequestComparator implements Comparator<K8sSchedulingRequest> {
+        K8sRuntimeEstimator runtimeEstimator
+        long currentTime
+        double epsilon
+
+        @Override
+        int compare(K8sSchedulingRequest o1, K8sSchedulingRequest o2) {
+            // First, check if one of the tasks is (estimated to be) on the critical path
+            double t1 = runtimeEstimator.estimate(o1.handler)
+            double t2 = runtimeEstimator.estimate(o2.handler)
+
+            if (t1 > t2 + epsilon)
+                return -1
+            else if (t2 > t1 + epsilon)
+                return 1
+
+            // Both are not on the critical path. Sort based on the time they spent in the queue
+            long w1 = currentTime - o1.submitTimeMillis
+            long w2 = currentTime - o2.submitTimeMillis
+            if (w1 > w2)
+                return -1
+            else if (w2 > w1)
+                return 1
+            return 0
+        }
+    }
+
+    private K8sRuntimeEstimator runtimeEstimator
+    private K8sDVFSClient dvfsClient
+
+    private ArrayList<WorkerNode> nodes
+    private HashMap<String, WorkerNode> taskToNode
+    private long globalMaxFrequency
+    private long globalMinFrequency
+    private long[] frequencies
+
+    private K8sClientGetter clientGetter
+
+    private double comparisonEpsilonMillis
+
+    private double[] topRuntimes
+    private double averageRuntime
+    private double finishedTaskCount
+
+    K8sDVFSFrequencyBandsSchedulingStrategy(K8sRuntimeEstimator runtimeEstimator,
+                                            K8sDVFSClient dvfsClient,
+                                            K8sClientGetter clientGetter,
+                                            Duration runtimeComparisonEpsilon,
+                                            int topRuntimeCount) {
+        this.runtimeEstimator = runtimeEstimator
+        this.dvfsClient = dvfsClient
+        this.nodes = new ArrayList<>()
+        this.taskToNode = new HashMap<>();
+        this.clientGetter = clientGetter
+        this.comparisonEpsilonMillis = (double)runtimeComparisonEpsilon.toMillis()
+        this.topRuntimes = new double[topRuntimeCount]
+        for (int i = 0; i < topRuntimeCount; i++) {
+            this.topRuntimes[i] = 0.0
+        }
+        this.averageRuntime = 0.0
+        this.finishedTaskCount = 0.0
+    }
+
+    private boolean isInTopRuntimes(double rt) {
+        for (int i = 0; i < topRuntimes.size(); i++) {
+            if (rt >= topRuntimes[i])
+                return true
+        }
+        return false
+    }
+
+    private void updateTopRuntimes(double rt) {
+        for (int i = 0; i < topRuntimes.size(); i++) {
+            if (rt > topRuntimes[i]) {
+                /* Move all one down */
+                for (int j = topRuntimes.size() - 1; j > i; j--) {
+                    topRuntimes[j] = topRuntimes[j - 1];
+                }
+                topRuntimes[i] = rt
+                break
+            }
+        }
+    }
+
+    @Override
+    K8sSchedulingDecision schedule(K8sTaskScheduler scheduler, List<K8sSchedulingRequest> queue) {
+        if (nodes.isEmpty()) {
+            if (!initNodes(scheduler))
+                return null
+        }
+
+        /* Step 1: Sort by task priority. We will attempt to schedule tasks "in order", so that the
+         * highest priority tasks are assigned to nodes as soon as possible.
+         *
+         * Priority is based on a) the tasks estimated runtime and b) the wait time of the task.
+         */
+        SchedulingRequestComparator comparator = new SchedulingRequestComparator()
+        comparator.runtimeEstimator = runtimeEstimator
+        comparator.epsilon = comparisonEpsilonMillis
+        comparator.currentTime = System.currentTimeMillis()
+        queue.sort(comparator)
+
+        /* Step 2: For each task attempt to schedule it onto a node */
+        for (K8sSchedulingRequest req : queue) {
+            /* Step 2.1: Determine if the task is on the critical path.
+             * If yes, we just schedule it at max frequency on the node with the highest available
+             * frequency. If not, we determine a frequency (see below).
+             */
+            final double taskEstimation = runtimeEstimator.estimate(req.handler)
+            final boolean isCriticalPath = isInTopRuntimes(taskEstimation)
+            long frequency = this.frequencies[0]
+            if (!isCriticalPath) {
+                if (taskEstimation >= topRuntimes[0] * .5)
+                    frequency = this.frequencies[1]
+                else
+                    frequency = this.frequencies[2]
+            }
+
+            /* Step 2.2: Filter nodes based on task requirements */
+            ArrayList<WorkerNode> suitableNodes = filterNodes(req.task)
+            if (suitableNodes.size() == 0) {
+                if (!anyNode(req.task)) {
+                    log.error "[K8s] unable to schedule task ${req.task} - no node satisfies resource requirements ${getTaskMemoryRequirment(req.task)} bytes ${getTaskCPURequirement(req.task)} cpus"
+                    return null
+                }
+                /* No node can currently execute this task, but it should be possible in the future */
+                /* log.info "[K8s] ${req.task} can not be scheduled: ${getTaskMemoryRequirment(req.task)} bytes ${getTaskCPURequirement(req.task)} CPUs"
+                for (WorkerNode n : this.nodes) {
+                    log.info "[K8s] node ${n.name} - ${n.availableMemory}, ${n.availableCPUs}"
+                } */
+                continue
+            }
+
+            /* Step 2.3: Assign to node based on "best fit" - current node frequency is closest to determined frequency */
+            long minDist = Math.abs(suitableNodes[0].frequency - frequency)
+            WorkerNode closest = suitableNodes[0]
+            for (WorkerNode node : suitableNodes) {
+                long dist = Math.abs(node.frequency - frequency)
+                if (dist < minDist) {
+                    closest = node
+                    minDist = dist
+                }
+            }
+
+            closest.assignTask(req.task, dvfsClient)
+            taskToNode.put(req.task.hash.toString(), closest)
+            log.info "[K8s] DVFS: Assigned task ${req.task} to node ${closest.name} - ${taskToNode.size()} assigned tasks"
+            return new K8sSchedulingDecision(req, closest.name)
+        }
+
+        log.info "[K8s] unable to schedule any task. The queue contains ${queue.size()} tasks."
+        return null
+    }
+
+    @Override
+    boolean scheduleImmediately(K8sTaskScheduler scheduler, List<K8sSchedulingRequest> queue) {
+        if (nodes.isEmpty()) {
+            if (!initNodes(scheduler))
+                return false
+        }
+        /* We want to schedule immediately if there are unoccupied nodes */
+        boolean doIt = queue != null && queue.size() > 0 && taskToNode.size() < nodes.size()
+        log.info "[K8s] scheduleImmediately: ${queue.size()} tasks in queue, ${taskToNode.size()} tasks running on ${nodes.size()} nodes: ${doIt}"
+        return doIt
+    }
+
+    @Override
+    synchronized void taskFinished(K8sTaskHandler task) {
+        /* TODO: This just uses elapsed wall-clock time, regardless of the frequency used to execute the task.
+         * This will skew the average towards longer runtimes, which is undesirable, because it will lead to more
+         * tasks classified as "critical path".
+         * A simple (rough) solution could be to keep track of the tasks "relative" frequency and just scale the
+         * elapsed time based on that.
+         */
+        double runtime = (double)(task.getCompleteTimeMillis() - task.getStartTimeMillis())
+        averageRuntime = (runtime + finishedTaskCount * averageRuntime) / (finishedTaskCount + 1.0)
+        finishedTaskCount += 1.0
+        updateTopRuntimes(runtime)
+
+        /* Free resources allocated by this task */
+        WorkerNode node = taskToNode.get(task.task.hash.toString())
+        if (node != null) {
+            node.taskFinished(task.task, dvfsClient)
+            taskToNode.remove(task.task.hash.toString())
+        } else {
+            log.warn "[K8s] no node recorded for task ${task.toString()}"
+        }
+
+        log.info "[K8s] task ${task.toString()} finished - ${taskToNode.size()} tasks running"
+        if (node != null) {
+            log.info "[K8s] task ran on node ${node.name} - ${node.availableMemory} bytes ${node.availableCPUs}"
+        }
+    }
+
+    private synchronized boolean initNodes(K8sTaskScheduler scheduler) {
+        this.globalMaxFrequency = Long.MAX_VALUE
+        this.globalMinFrequency = Long.MIN_VALUE
+        final nodes = scheduler.getNodes()
+
+        for (String node : nodes) {
+            final min = dvfsClient.getNodeMinFrequency(node)
+            final max = dvfsClient.getNodeMaxFrequency(node)
+
+            if (min.empty || max.empty) {
+                log.error "[K8s] failed to query node $node information"
+                continue
+            }
+            globalMaxFrequency = Long.min(globalMaxFrequency, max.asLong)
+            globalMinFrequency = Long.max(globalMinFrequency, min.asLong)
+
+            log.info "[K8s] node ${node}: ${min.asLong} Hz - ${max.asLong} Hz"
+        }
+
+        long diff = globalMaxFrequency - globalMinFrequency
+        long diff3 = diff.intdiv(3)
+        this.frequencies = [
+            globalMaxFrequency,
+            globalMinFrequency + diff3 * 2,
+            globalMinFrequency + diff3,
+        ]
+
+        int next = 0
+        for (String node : nodes) {
+            this.nodes.add(new WorkerNode(node, this.frequencies[next], this.clientGetter))
+            log.info "[K8s] node ${node}: set to ${this.frequencies[next]} Hz"
+            next = (next + 1) % this.frequencies.length
+        }
+
+        return !this.nodes.isEmpty()
+    }
+
+    /* Returns a list of nodes that fulfill the tasks resource requirements
+     */
+    private ArrayList<WorkerNode> filterNodes(TaskRun task) {
+        final long reqBytes = getTaskMemoryRequirment(task)
+        final int reqCPUs = getTaskCPURequirement(task)
+        ArrayList<WorkerNode> suitableNodes = new ArrayList<>()
+        for (WorkerNode n : nodes) {
+            if (n.availableMemory >= reqBytes && n.availableCPUs >= reqCPUs) {
+                log.info "[K8s] task ${task.name}: ${reqBytes} bytes ${reqCPUs} cpus: node ${n.name} has ${n.availableMemory} bytes, ${n.availableCPUs} cpus"
+                suitableNodes.add(n)
+            }
+        }
+        return suitableNodes
+    }
+
+    private boolean anyNode(TaskRun task) {
+        final long reqBytes = getTaskMemoryRequirment(task)
+        final int reqCPUs = getTaskCPURequirement(task)
+        for (WorkerNode n : nodes) {
+            if (n.memoryAmount >= reqBytes && n.CPUCount >= reqCPUs)
+                return true
+        }
+        return false
+    }
+}

k8s-dvfs/src/main/groovy/recreationaltech/plugin/strategies/K8sDVFSSchedulingStrategy.groovy

@@ -1,17 +1,17 @@
-package nextflow.k8s.strategies
+package recreationaltech.plugin.strategies
 
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
-import nextflow.k8s.K8sDVFSClient
-import nextflow.k8s.K8sRuntimeEstimator
-import nextflow.k8s.K8sSchedulingDecision
-import nextflow.k8s.K8sSchedulingRequest
-import nextflow.k8s.K8sSchedulingStrategy
-import nextflow.k8s.K8sTaskHandler
-import nextflow.k8s.K8sTaskScheduler
-import nextflow.k8s.client.K8sClient
+import recreationaltech.plugin.K8sDVFSClient
+import recreationaltech.plugin.K8sRuntimeEstimator
+import recreationaltech.plugin.K8sSchedulingDecision
+import recreationaltech.plugin.K8sSchedulingRequest
+import recreationaltech.plugin.K8sSchedulingStrategy
+import recreationaltech.plugin.K8sTaskHandler
+import recreationaltech.plugin.K8sTaskScheduler
+import recreationaltech.plugin.client.K8sClient
 import nextflow.processor.TaskRun
-import nextflow.util.ArrayTuple
+import nextflow.util.Duration
 
 /**
  * Implements a scheduling strategy utilizing dvfs to reduce the energy consumption
@@ -132,26 +132,34 @@ class K8sDVFSSchedulingStrategy implements K8sSchedulingStrategy {
             updateFrequency(dvfsClient)
         }
 
-        void taskFinished(TaskRun task, K8sDVFSClient dvfsClient) {
+        // Returns the frequency that was assigned to the task
+        long taskFinished(TaskRun task, K8sDVFSClient dvfsClient) {
+            long f = Long.MAX_VALUE
             log.info "[K8s] node ${name}: task ${task.name} finished"
-            this.tasks.removeIf {it.task == task}
-            updateFrequency(dvfsClient)
+            AssignedTask t = this.tasks.find { it.task == task }
+            if (t != null) {
+                f = t.frequency
+                this.tasks.remove(t)
+                updateFrequency(dvfsClient)
+            }
+            return f
         }
     }
 
     class SchedulingRequestComparator implements Comparator<K8sSchedulingRequest> {
         K8sRuntimeEstimator runtimeEstimator
         long currentTime
-        double avgRuntime
+        double epsilon
 
         @Override
         int compare(K8sSchedulingRequest o1, K8sSchedulingRequest o2) {
             // First, check if one of the tasks is (estimated to be) on the critical path
             double t1 = runtimeEstimator.estimate(o1.handler)
             double t2 = runtimeEstimator.estimate(o2.handler)
-            if (t1 > avgRuntime && t2 <= avgRuntime)
+
+            if (t1 > t2 + epsilon)
                 return -1
-            else if (t1 < avgRuntime && t2 > avgRuntime)
+            else if (t2 > t1 + epsilon)
                 return 1
 
             // Both are not on the critical path. Sort based on the time they spent in the queue
@@ -170,23 +178,57 @@ class K8sDVFSSchedulingStrategy implements K8sSchedulingStrategy {
 
     private ArrayList<WorkerNode> nodes
     private HashMap<String, WorkerNode> taskToNode
-
-    private double averageRuntime
-    private long finishedTaskCount
-
     private long globalMaxFrequency
     private long globalMinFrequency
 
     private K8sClientGetter clientGetter
 
+    private double comparisonEpsilonMillis
+
+    private double[] topRuntimes
+    private double averageRuntime
+    private double finishedTaskCount
+
     boolean fullSpeedMode
 
-    K8sDVFSSchedulingStrategy(K8sRuntimeEstimator runtimeEstimator, K8sDVFSClient dvfsClient, K8sClientGetter clientGetter) {
+    K8sDVFSSchedulingStrategy(K8sRuntimeEstimator runtimeEstimator,
+                              K8sDVFSClient dvfsClient,
+                              K8sClientGetter clientGetter,
+                              Duration runtimeComparisonEpsilon,
+                              int topRuntimeCount) {
         this.runtimeEstimator = runtimeEstimator
         this.dvfsClient = dvfsClient
         this.nodes = new ArrayList<>()
         this.taskToNode = new HashMap<>();
         this.clientGetter = clientGetter
+        this.comparisonEpsilonMillis = (double)runtimeComparisonEpsilon.toMillis()
+        this.topRuntimes = new double[topRuntimeCount]
+        for (int i = 0; i < topRuntimeCount; i++) {
+            this.topRuntimes[i] = 0.0
+        }
+        this.averageRuntime = 0.0
+        this.finishedTaskCount = 0.0
+    }
+
+    private boolean isInTopRuntimes(double rt) {
+        for (int i = 0; i < topRuntimes.size(); i++) {
+            if (rt >= topRuntimes[i])
+                return true
+        }
+        return false
+    }
+
+    private void updateTopRuntimes(double rt) {
+        for (int i = 0; i < topRuntimes.size(); i++) {
+            if (rt > topRuntimes[i]) {
+                /* Move all one down */
+                for (int j = topRuntimes.size() - 1; j > i; j--) {
+                    topRuntimes[j] = topRuntimes[j - 1];
+                }
+                topRuntimes[i] = rt
+                break
+            }
+        }
     }
 
     @Override
@@ -199,11 +241,11 @@ class K8sDVFSSchedulingStrategy implements K8sSchedulingStrategy {
         /* Step 1: Sort by task priority. We will attempt to schedule tasks "in order", so that the
          * highest priority tasks are assigned to nodes as soon as possible.
          *
-         * Priority is based on a) an estimation if the task is on the critical path and b) the wait time of the task.
+         * Priority is based on a) the tasks estimated runtime and b) the wait time of the task.
          */
         SchedulingRequestComparator comparator = new SchedulingRequestComparator()
         comparator.runtimeEstimator = runtimeEstimator
-        comparator.avgRuntime = averageRuntime
+        comparator.epsilon = comparisonEpsilonMillis
         comparator.currentTime = System.currentTimeMillis()
         queue.sort(comparator)
 
@@ -214,7 +256,7 @@ class K8sDVFSSchedulingStrategy implements K8sSchedulingStrategy {
              * frequency. If not, we determine a frequency (see below).
              */
             final double taskEstimation = runtimeEstimator.estimate(req.handler)
-            final boolean isCriticalPath = taskEstimation > averageRuntime
+            final boolean isCriticalPath = isInTopRuntimes(taskEstimation)
             long frequency = globalMaxFrequency
             if (!isCriticalPath && !fullSpeedMode) {
                 /* Set frequency so that we expect the runtime to be close to the mean runtime. */
@@ -231,10 +273,10 @@ class K8sDVFSSchedulingStrategy implements K8sSchedulingStrategy {
                     return null
                 }
                 /* No node can currently execute this task, but it should be possible in the future */
-                /* log.info "[K8s] ${req.task} can not be scheduled: ${getTaskMemoryRequirment(req.task)} bytes ${getTaskCPURequirement(req.task)} CPUs"
+                log.info "[K8s] ${req.task} can not be scheduled: ${getTaskMemoryRequirment(req.task)} bytes ${getTaskCPURequirement(req.task)} CPUs"
                 for (WorkerNode n : this.nodes) {
                     log.info "[K8s] node ${n.name} - ${n.availableMemory}, ${n.availableCPUs}"
-                } */
+                }
                 continue
             }
 
@@ -273,20 +315,11 @@ class K8sDVFSSchedulingStrategy implements K8sSchedulingStrategy {
 
     @Override
     synchronized void taskFinished(K8sTaskHandler task) {
-        /* TODO: This just uses elapsed wall-clock time, regardless of the frequency used to execute the task.
-         * This will skew the average towards longer runtimes, which is undesirable, because it will lead to more
-         * tasks classified as "critical path".
-         * A simple (rough) solution could be to keep track of the tasks "relative" frequency and just scale the
-         * elapsed time based on that.
-         */
-        double runtime = (double)(task.getCompleteTimeMillis() - task.getStartTimeMillis())
-        averageRuntime = (runtime + finishedTaskCount * averageRuntime) / (finishedTaskCount + 1)
-        finishedTaskCount += 1
-
+        long freq = globalMaxFrequency
         /* Free resources allocated by this task */
         WorkerNode node = taskToNode.get(task.task.hash.toString())
         if (node != null) {
-            node.taskFinished(task.task, dvfsClient)
+            freq = node.taskFinished(task.task, dvfsClient)
             taskToNode.remove(task.task.hash.toString())
         } else {
             log.warn "[K8s] no node recorded for task ${task.toString()}"
@@ -294,8 +327,17 @@ class K8sDVFSSchedulingStrategy implements K8sSchedulingStrategy {
 
         log.info "[K8s] task ${task.toString()} finished - ${taskToNode.size()} tasks running"
         if (node != null) {
-            log.info "[K8s] task ran on node ${node.name} - ${node.availableMemory} bytes ${node.availableCPUs}"
+            log.info "[K8s] task ran on node ${node.name} - ${node.availableMemory} bytes ${node.availableCPUs} at ${freq}/${globalMaxFrequency} Hz (${(double)freq / (double)globalMaxFrequency}%)"
         }
+
+        /* We scale the runtime by the tasks relative frequency to avoid skewing the average runtime towards
+         * longer runtimes. This is obviously only a rough approximation.
+         */
+        double runtime = (double)(task.getCompleteTimeMillis() - task.getStartTimeMillis())
+        runtime *= (double)freq / (double)globalMaxFrequency
+        averageRuntime = (runtime + finishedTaskCount * averageRuntime) / (finishedTaskCount + 1.0)
+        finishedTaskCount += 1.0
+        updateTopRuntimes(runtime)
     }
 
     private synchronized boolean initNodes(K8sTaskScheduler scheduler) {

k8s-dvfs/src/main/groovy/recreationaltech/plugin/strategies/K8sHashSchedulingStrategy.groovy

@@ -1,11 +1,11 @@
-package nextflow.k8s.strategies
+package recreationaltech.plugin.strategies
 
 import groovy.transform.CompileStatic
-import nextflow.k8s.K8sSchedulingDecision
-import nextflow.k8s.K8sSchedulingRequest
-import nextflow.k8s.K8sSchedulingStrategy
-import nextflow.k8s.K8sTaskHandler
-import nextflow.k8s.K8sTaskScheduler
+import recreationaltech.plugin.K8sSchedulingDecision
+import recreationaltech.plugin.K8sSchedulingRequest
+import recreationaltech.plugin.K8sSchedulingStrategy
+import recreationaltech.plugin.K8sTaskHandler
+import recreationaltech.plugin.K8sTaskScheduler
 
 @CompileStatic
 class K8sHashSchedulingStrategy implements K8sSchedulingStrategy {

k8s-dvfs/src/test/groovy/recreationaltech/plugin/K8sConfigTest.groovy

@@ -14,14 +14,14 @@
  * limitations under the License.
  */
 
-package nextflow.k8s
+package recreationaltech.plugin
 
 import nextflow.BuildInfo
 import nextflow.SysEnv
-import nextflow.k8s.client.ClientConfig
-import nextflow.k8s.model.PodEnv
-import nextflow.k8s.model.PodSecurityContext
-import nextflow.k8s.model.PodVolumeClaim
+import recreationaltech.plugin.client.ClientConfig
+import recreationaltech.plugin.model.PodEnv
+import recreationaltech.plugin.model.PodSecurityContext
+import recreationaltech.plugin.model.PodVolumeClaim
 import nextflow.util.Duration
 import spock.lang.Specification
 import spock.lang.Unroll

k8s-dvfs/src/test/groovy/recreationaltech/plugin/K8sDriverLauncherTest.groovy

@@ -14,19 +14,19 @@
  * limitations under the License.
  */
 
-package nextflow.k8s
+package recreationaltech.plugin
 
 import java.nio.file.Files
 
 import nextflow.cli.CliOptions
 import nextflow.cli.CmdKubeRun
 import nextflow.cli.Launcher
-import nextflow.k8s.client.ClientConfig
-import nextflow.k8s.client.K8sClient
-import nextflow.k8s.model.PodMountConfig
-import nextflow.k8s.model.PodOptions
-import nextflow.k8s.model.PodSpecBuilder
-import nextflow.k8s.model.PodVolumeClaim
+import recreationaltech.plugin.client.ClientConfig
+import recreationaltech.plugin.client.K8sClient
+import recreationaltech.plugin.model.PodMountConfig
+import recreationaltech.plugin.model.PodOptions
+import recreationaltech.plugin.model.PodSpecBuilder
+import recreationaltech.plugin.model.PodVolumeClaim
 import spock.lang.Specification
 import spock.lang.Unroll
 /**

k8s-dvfs/src/test/groovy/recreationaltech/plugin/K8sExecutorTest.groovy

@@ -14,13 +14,13 @@
  * limitations under the License.
  */
 
-package nextflow.k8s
+package recreationaltech.plugin
 
 import java.util.concurrent.TimeUnit
 
 import com.google.common.cache.CacheBuilder
-import nextflow.k8s.client.ClientConfig
-import nextflow.k8s.client.K8sClient
+import recreationaltech.plugin.client.ClientConfig
+import recreationaltech.plugin.client.K8sClient
 import spock.lang.Specification
 
 /**

k8s-dvfs/src/test/groovy/recreationaltech/plugin/K8sNodeInitDeployerTest.groovy

@@ -1,7 +1,7 @@
-package nextflow.k8s
+package recreationaltech.plugin
 
-import nextflow.k8s.client.K8sClient
-import nextflow.k8s.model.PodSpecBuilder
+import recreationaltech.plugin.client.K8sClient
+import recreationaltech.plugin.model.PodSpecBuilder
 import spock.lang.Specification
 
 class K8sNodeInitDeployerTest extends Specification {
@@ -52,6 +52,7 @@ class K8sNodeInitDeployerTest extends Specification {
             spec.metadata.namespace == 'default'
             spec.spec.nodeName == 'node-a'
             spec.spec.restartPolicy == 'Never'
+            spec.spec.hostNetwork == true
 
             def container = spec.spec.containers[0]
             container.name == 'nf-init-node-a'

k8s-dvfs/src/test/groovy/recreationaltech/plugin/K8sSchedulingRequestTest.groovy

@@ -1,4 +1,4 @@
-package nextflow.k8s
+package recreationaltech.plugin
 
 import nextflow.processor.TaskRun
 import spock.lang.Specification

k8s-dvfs/src/test/groovy/recreationaltech/plugin/K8sTaskHandlerTest.groovy

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package nextflow.k8s
+package recreationaltech.plugin
 
 import java.nio.file.Files
 import java.nio.file.Path
@@ -26,18 +26,18 @@ import nextflow.exception.NodeTerminationException
 import nextflow.file.http.XPath
 import nextflow.fusion.FusionConfig
 import nextflow.fusion.FusionScriptLauncher
-import nextflow.k8s.client.ClientConfig
-import nextflow.k8s.client.K8sClient
-import nextflow.k8s.client.K8sResponseException
-import nextflow.k8s.client.K8sResponseJson
-import nextflow.k8s.client.PodUnschedulableException
-import nextflow.k8s.model.PodEnv
-import nextflow.k8s.model.PodHostMount
-import nextflow.k8s.model.PodMountConfig
-import nextflow.k8s.model.PodMountSecret
-import nextflow.k8s.model.PodOptions
-import nextflow.k8s.model.PodSpecBuilder
-import nextflow.k8s.model.PodVolumeClaim
+import recreationaltech.plugin.client.ClientConfig
+import recreationaltech.plugin.client.K8sClient
+import recreationaltech.plugin.client.K8sResponseException
+import recreationaltech.plugin.client.K8sResponseJson
+import recreationaltech.plugin.client.PodUnschedulableException
+import recreationaltech.plugin.model.PodEnv
+import recreationaltech.plugin.model.PodHostMount
+import recreationaltech.plugin.model.PodMountConfig
+import recreationaltech.plugin.model.PodMountSecret
+import recreationaltech.plugin.model.PodOptions
+import recreationaltech.plugin.model.PodSpecBuilder
+import recreationaltech.plugin.model.PodVolumeClaim
 import nextflow.processor.TaskBean
 import nextflow.processor.TaskConfig
 import nextflow.processor.TaskProcessor

k8s-dvfs/src/test/groovy/recreationaltech/plugin/K8sWrapperBuilderTest.groovy

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package nextflow.k8s
+package recreationaltech.plugin
 
 import java.nio.file.Files
 

k8s-dvfs/src/test/groovy/recreationaltech/plugin/client/ClientConfigTest.groovy

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package nextflow.k8s.client
+package recreationaltech.plugin.client
 
 import java.nio.file.Files
 

k8s-dvfs/src/test/groovy/recreationaltech/plugin/client/ConfigDiscoveryTest.groovy

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package nextflow.k8s.client
+package recreationaltech.plugin.client
 import javax.net.ssl.KeyManager
 import java.nio.file.Files
 

k8s-dvfs/src/test/groovy/recreationaltech/plugin/client/K8sClientTest.groovy

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package nextflow.k8s.client
+package recreationaltech.plugin.client
 
 import nextflow.exception.K8sOutOfCpuException
 import nextflow.exception.K8sOutOfMemoryException
@@ -1139,6 +1139,61 @@ class K8sClientTest extends Specification {
         result.metadata.name == 'test-node'
     }
 
+    def 'should get node external IP with ExternalIP address' () {
+        given:
+        def JSON = '''
+            {
+                "kind": "Node",
+                "apiVersion": "v1",
+                "metadata": {
+                    "name": "test-node"
+                },
+                "status": {
+                    "addresses": [
+                        {"type": "InternalIP", "address": "192.168.1.100"},
+                        {"type": "ExternalIP", "address": "203.0.113.10"}
+                    ]
+                }
+            }
+        '''
+
+        def client = Spy(K8sClient)
+        final NODE_NAME = 'test-node'
+
+        when:
+        def result = client.getNodeExternalIp(NODE_NAME)
+        then:
+        1 * client.nodeDescribe(NODE_NAME) >> new K8sResponseJson(JSON)
+        result == '203.0.113.10'
+    }
+
+    def 'should get node external IP fallback to InternalIP' () {
+        given:
+        def JSON = '''
+            {
+                "kind": "Node",
+                "apiVersion": "v1",
+                "metadata": {
+                    "name": "test-node"
+                },
+                "status": {
+                    "addresses": [
+                        {"type": "InternalIP", "address": "192.168.1.100"}
+                    ]
+                }
+            }
+        '''
+
+        def client = Spy(K8sClient)
+        final NODE_NAME = 'test-node'
+
+        when:
+        def result = client.getNodeExternalIp(NODE_NAME)
+        then:
+        1 * client.nodeDescribe(NODE_NAME) >> new K8sResponseJson(JSON)
+        result == '192.168.1.100'
+    }
+
     def 'should get node CPU capacity' () {
         given:
         def JSON = '''

k8s-dvfs/src/test/groovy/recreationaltech/plugin/client/K8sResponseExceptionTest.groovy

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package nextflow.k8s.client
+package recreationaltech.plugin.client
 
 import spock.lang.Specification
 

k8s-dvfs/src/test/groovy/recreationaltech/plugin/client/K8sResponseJsonTest.groovy

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package nextflow.k8s.client
+package recreationaltech.plugin.client
 
 import spock.lang.Specification
 

k8s-dvfs/src/test/groovy/recreationaltech/plugin/model/PodEnvTest.groovy

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package nextflow.k8s.model
+package recreationaltech.plugin.model
 
 import spock.lang.Specification
 

k8s-dvfs/src/test/groovy/recreationaltech/plugin/model/PodMountConfigTest.groovy

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package nextflow.k8s.model
+package recreationaltech.plugin.model
 
 import spock.lang.Specification
 

k8s-dvfs/src/test/groovy/recreationaltech/plugin/model/PodMountSecretTest.groovy

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package nextflow.k8s.model
+package recreationaltech.plugin.model
 
 import spock.lang.Specification
 

k8s-dvfs/src/test/groovy/recreationaltech/plugin/model/PodNodeSelectorTest.groovy

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package nextflow.k8s.model
+package recreationaltech.plugin.model
 
 import spock.lang.Specification
 

k8s-dvfs/src/test/groovy/recreationaltech/plugin/model/PodOptionsTest.groovy

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package nextflow.k8s.model
+package recreationaltech.plugin.model
 
 import spock.lang.Specification
 

k8s-dvfs/src/test/groovy/recreationaltech/plugin/model/PodSpecBuilderTest.groovy

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package nextflow.k8s.model
+package recreationaltech.plugin.model
 
 import nextflow.executor.res.AcceleratorResource
 import nextflow.util.MemoryUnit

k8s-dvfs/src/test/groovy/recreationaltech/plugin/model/PodVolumeClaimTest.groovy

@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-package nextflow.k8s.model
+package recreationaltech.plugin.model
 
 import spock.lang.Specification
 /**

nextflow/.claude/commands/speckit.analyze.md

@@ -1,184 +0,0 @@
----
-description: Perform a non-destructive cross-artifact consistency and quality analysis across spec.md, plan.md, and tasks.md after task generation.
----
-
-## User Input
-
-```text
-$ARGUMENTS
-```
-
-You **MUST** consider the user input before proceeding (if not empty).
-
-## Goal
-
-Identify inconsistencies, duplications, ambiguities, and underspecified items across the three core artifacts (`spec.md`, `plan.md`, `tasks.md`) before implementation. This command MUST run only after `/speckit.tasks` has successfully produced a complete `tasks.md`.
-
-## Operating Constraints
-
-**STRICTLY READ-ONLY**: Do **not** modify any files. Output a structured analysis report. Offer an optional remediation plan (user must explicitly approve before any follow-up editing commands would be invoked manually).
-
-**Constitution Authority**: The project constitution (`.specify/memory/constitution.md`) is **non-negotiable** within this analysis scope. Constitution conflicts are automatically CRITICAL and require adjustment of the spec, plan, or tasks—not dilution, reinterpretation, or silent ignoring of the principle. If a principle itself needs to change, that must occur in a separate, explicit constitution update outside `/speckit.analyze`.
-
-## Execution Steps
-
-### 1. Initialize Analysis Context
-
-Run `.specify/scripts/bash/check-prerequisites.sh --json --require-tasks --include-tasks` once from repo root and parse JSON for FEATURE_DIR and AVAILABLE_DOCS. Derive absolute paths:
-
-- SPEC = FEATURE_DIR/spec.md
-- PLAN = FEATURE_DIR/plan.md
-- TASKS = FEATURE_DIR/tasks.md
-
-Abort with an error message if any required file is missing (instruct the user to run missing prerequisite command).
-For single quotes in args like "I'm Groot", use escape syntax: e.g 'I'\''m Groot' (or double-quote if possible: "I'm Groot").
-
-### 2. Load Artifacts (Progressive Disclosure)
-
-Load only the minimal necessary context from each artifact:
-
-**From spec.md:**
-
-- Overview/Context
-- Functional Requirements
-- Non-Functional Requirements
-- User Stories
-- Edge Cases (if present)
-
-**From plan.md:**
-
-- Architecture/stack choices
-- Data Model references
-- Phases
-- Technical constraints
-
-**From tasks.md:**
-
-- Task IDs
-- Descriptions
-- Phase grouping
-- Parallel markers [P]
-- Referenced file paths
-
-**From constitution:**
-
-- Load `.specify/memory/constitution.md` for principle validation
-
-### 3. Build Semantic Models
-
-Create internal representations (do not include raw artifacts in output):
-
-- **Requirements inventory**: Each functional + non-functional requirement with a stable key (derive slug based on imperative phrase; e.g., "User can upload file" → `user-can-upload-file`)
-- **User story/action inventory**: Discrete user actions with acceptance criteria
-- **Task coverage mapping**: Map each task to one or more requirements or stories (inference by keyword / explicit reference patterns like IDs or key phrases)
-- **Constitution rule set**: Extract principle names and MUST/SHOULD normative statements
-
-### 4. Detection Passes (Token-Efficient Analysis)
-
-Focus on high-signal findings. Limit to 50 findings total; aggregate remainder in overflow summary.
-
-#### A. Duplication Detection
-
-- Identify near-duplicate requirements
-- Mark lower-quality phrasing for consolidation
-
-#### B. Ambiguity Detection
-
-- Flag vague adjectives (fast, scalable, secure, intuitive, robust) lacking measurable criteria
-- Flag unresolved placeholders (TODO, TKTK, ???, `<placeholder>`, etc.)
-
-#### C. Underspecification
-
-- Requirements with verbs but missing object or measurable outcome
-- User stories missing acceptance criteria alignment
-- Tasks referencing files or components not defined in spec/plan
-
-#### D. Constitution Alignment
-
-- Any requirement or plan element conflicting with a MUST principle
-- Missing mandated sections or quality gates from constitution
-
-#### E. Coverage Gaps
-
-- Requirements with zero associated tasks
-- Tasks with no mapped requirement/story
-- Non-functional requirements not reflected in tasks (e.g., performance, security)
-
-#### F. Inconsistency
-
-- Terminology drift (same concept named differently across files)
-- Data entities referenced in plan but absent in spec (or vice versa)
-- Task ordering contradictions (e.g., integration tasks before foundational setup tasks without dependency note)
-- Conflicting requirements (e.g., one requires Next.js while other specifies Vue)
-
-### 5. Severity Assignment
-
-Use this heuristic to prioritize findings:
-
-- **CRITICAL**: Violates constitution MUST, missing core spec artifact, or requirement with zero coverage that blocks baseline functionality
-- **HIGH**: Duplicate or conflicting requirement, ambiguous security/performance attribute, untestable acceptance criterion
-- **MEDIUM**: Terminology drift, missing non-functional task coverage, underspecified edge case
-- **LOW**: Style/wording improvements, minor redundancy not affecting execution order
-
-### 6. Produce Compact Analysis Report
-
-Output a Markdown report (no file writes) with the following structure:
-
-## Specification Analysis Report
-
-| ID | Category | Severity | Location(s) | Summary | Recommendation |
-|----|----------|----------|-------------|---------|----------------|
-| A1 | Duplication | HIGH | spec.md:L120-134 | Two similar requirements ... | Merge phrasing; keep clearer version |
-
-(Add one row per finding; generate stable IDs prefixed by category initial.)
-
-**Coverage Summary Table:**
-
-| Requirement Key | Has Task? | Task IDs | Notes |
-|-----------------|-----------|----------|-------|
-
-**Constitution Alignment Issues:** (if any)
-
-**Unmapped Tasks:** (if any)
-
-**Metrics:**
-
-- Total Requirements
-- Total Tasks
-- Coverage % (requirements with >=1 task)
-- Ambiguity Count
-- Duplication Count
-- Critical Issues Count
-
-### 7. Provide Next Actions
-
-At end of report, output a concise Next Actions block:
-
-- If CRITICAL issues exist: Recommend resolving before `/speckit.implement`
-- If only LOW/MEDIUM: User may proceed, but provide improvement suggestions
-- Provide explicit command suggestions: e.g., "Run /speckit.specify with refinement", "Run /speckit.plan to adjust architecture", "Manually edit tasks.md to add coverage for 'performance-metrics'"
-
-### 8. Offer Remediation
-
-Ask the user: "Would you like me to suggest concrete remediation edits for the top N issues?" (Do NOT apply them automatically.)
-
-## Operating Principles
-
-### Context Efficiency
-
-- **Minimal high-signal tokens**: Focus on actionable findings, not exhaustive documentation
-- **Progressive disclosure**: Load artifacts incrementally; don't dump all content into analysis
-- **Token-efficient output**: Limit findings table to 50 rows; summarize overflow
-- **Deterministic results**: Rerunning without changes should produce consistent IDs and counts
-
-### Analysis Guidelines
-
-- **NEVER modify files** (this is read-only analysis)
-- **NEVER hallucinate missing sections** (if absent, report them accurately)
-- **Prioritize constitution violations** (these are always CRITICAL)
-- **Use examples over exhaustive rules** (cite specific instances, not generic patterns)
-- **Report zero issues gracefully** (emit success report with coverage statistics)
-
-## Context
-
-$ARGUMENTS

nextflow/.claude/commands/speckit.checklist.md

@@ -1,294 +0,0 @@
----
-description: Generate a custom checklist for the current feature based on user requirements.
----
-
-## Checklist Purpose: "Unit Tests for English"
-
-**CRITICAL CONCEPT**: Checklists are **UNIT TESTS FOR REQUIREMENTS WRITING** - they validate the quality, clarity, and completeness of requirements in a given domain.
-
-**NOT for verification/testing**:
-
-- ❌ NOT "Verify the button clicks correctly"
-- ❌ NOT "Test error handling works"
-- ❌ NOT "Confirm the API returns 200"
-- ❌ NOT checking if code/implementation matches the spec
-
-**FOR requirements quality validation**:
-
-- ✅ "Are visual hierarchy requirements defined for all card types?" (completeness)
-- ✅ "Is 'prominent display' quantified with specific sizing/positioning?" (clarity)
-- ✅ "Are hover state requirements consistent across all interactive elements?" (consistency)
-- ✅ "Are accessibility requirements defined for keyboard navigation?" (coverage)
-- ✅ "Does the spec define what happens when logo image fails to load?" (edge cases)
-
-**Metaphor**: If your spec is code written in English, the checklist is its unit test suite. You're testing whether the requirements are well-written, complete, unambiguous, and ready for implementation - NOT whether the implementation works.
-
-## User Input
-
-```text
-$ARGUMENTS
-```
-
-You **MUST** consider the user input before proceeding (if not empty).
-
-## Execution Steps
-
-1. **Setup**: Run `.specify/scripts/bash/check-prerequisites.sh --json` from repo root and parse JSON for FEATURE_DIR and AVAILABLE_DOCS list.
-   - All file paths must be absolute.
-   - For single quotes in args like "I'm Groot", use escape syntax: e.g 'I'\''m Groot' (or double-quote if possible: "I'm Groot").
-
-2. **Clarify intent (dynamic)**: Derive up to THREE initial contextual clarifying questions (no pre-baked catalog). They MUST:
-   - Be generated from the user's phrasing + extracted signals from spec/plan/tasks
-   - Only ask about information that materially changes checklist content
-   - Be skipped individually if already unambiguous in `$ARGUMENTS`
-   - Prefer precision over breadth
-
-   Generation algorithm:
-   1. Extract signals: feature domain keywords (e.g., auth, latency, UX, API), risk indicators ("critical", "must", "compliance"), stakeholder hints ("QA", "review", "security team"), and explicit deliverables ("a11y", "rollback", "contracts").
-   2. Cluster signals into candidate focus areas (max 4) ranked by relevance.
-   3. Identify probable audience & timing (author, reviewer, QA, release) if not explicit.
-   4. Detect missing dimensions: scope breadth, depth/rigor, risk emphasis, exclusion boundaries, measurable acceptance criteria.
-   5. Formulate questions chosen from these archetypes:
-      - Scope refinement (e.g., "Should this include integration touchpoints with X and Y or stay limited to local module correctness?")
-      - Risk prioritization (e.g., "Which of these potential risk areas should receive mandatory gating checks?")
-      - Depth calibration (e.g., "Is this a lightweight pre-commit sanity list or a formal release gate?")
-      - Audience framing (e.g., "Will this be used by the author only or peers during PR review?")
-      - Boundary exclusion (e.g., "Should we explicitly exclude performance tuning items this round?")
-      - Scenario class gap (e.g., "No recovery flows detected—are rollback / partial failure paths in scope?")
-
-   Question formatting rules:
-   - If presenting options, generate a compact table with columns: Option | Candidate | Why It Matters
-   - Limit to A–E options maximum; omit table if a free-form answer is clearer
-   - Never ask the user to restate what they already said
-   - Avoid speculative categories (no hallucination). If uncertain, ask explicitly: "Confirm whether X belongs in scope."
-
-   Defaults when interaction impossible:
-   - Depth: Standard
-   - Audience: Reviewer (PR) if code-related; Author otherwise
-   - Focus: Top 2 relevance clusters
-
-   Output the questions (label Q1/Q2/Q3). After answers: if ≥2 scenario classes (Alternate / Exception / Recovery / Non-Functional domain) remain unclear, you MAY ask up to TWO more targeted follow‑ups (Q4/Q5) with a one-line justification each (e.g., "Unresolved recovery path risk"). Do not exceed five total questions. Skip escalation if user explicitly declines more.
-
-3. **Understand user request**: Combine `$ARGUMENTS` + clarifying answers:
-   - Derive checklist theme (e.g., security, review, deploy, ux)
-   - Consolidate explicit must-have items mentioned by user
-   - Map focus selections to category scaffolding
-   - Infer any missing context from spec/plan/tasks (do NOT hallucinate)
-
-4. **Load feature context**: Read from FEATURE_DIR:
-   - spec.md: Feature requirements and scope
-   - plan.md (if exists): Technical details, dependencies
-   - tasks.md (if exists): Implementation tasks
-
-   **Context Loading Strategy**:
-   - Load only necessary portions relevant to active focus areas (avoid full-file dumping)
-   - Prefer summarizing long sections into concise scenario/requirement bullets
-   - Use progressive disclosure: add follow-on retrieval only if gaps detected
-   - If source docs are large, generate interim summary items instead of embedding raw text
-
-5. **Generate checklist** - Create "Unit Tests for Requirements":
-   - Create `FEATURE_DIR/checklists/` directory if it doesn't exist
-   - Generate unique checklist filename:
-     - Use short, descriptive name based on domain (e.g., `ux.md`, `api.md`, `security.md`)
-     - Format: `[domain].md`
-     - If file exists, append to existing file
-   - Number items sequentially starting from CHK001
-   - Each `/speckit.checklist` run creates a NEW file (never overwrites existing checklists)
-
-   **CORE PRINCIPLE - Test the Requirements, Not the Implementation**:
-   Every checklist item MUST evaluate the REQUIREMENTS THEMSELVES for:
-   - **Completeness**: Are all necessary requirements present?
-   - **Clarity**: Are requirements unambiguous and specific?
-   - **Consistency**: Do requirements align with each other?
-   - **Measurability**: Can requirements be objectively verified?
-   - **Coverage**: Are all scenarios/edge cases addressed?
-
-   **Category Structure** - Group items by requirement quality dimensions:
-   - **Requirement Completeness** (Are all necessary requirements documented?)
-   - **Requirement Clarity** (Are requirements specific and unambiguous?)
-   - **Requirement Consistency** (Do requirements align without conflicts?)
-   - **Acceptance Criteria Quality** (Are success criteria measurable?)
-   - **Scenario Coverage** (Are all flows/cases addressed?)
-   - **Edge Case Coverage** (Are boundary conditions defined?)
-   - **Non-Functional Requirements** (Performance, Security, Accessibility, etc. - are they specified?)
-   - **Dependencies & Assumptions** (Are they documented and validated?)
-   - **Ambiguities & Conflicts** (What needs clarification?)
-
-   **HOW TO WRITE CHECKLIST ITEMS - "Unit Tests for English"**:
-
-   ❌ **WRONG** (Testing implementation):
-   - "Verify landing page displays 3 episode cards"
-   - "Test hover states work on desktop"
-   - "Confirm logo click navigates home"
-
-   ✅ **CORRECT** (Testing requirements quality):
-   - "Are the exact number and layout of featured episodes specified?" [Completeness]
-   - "Is 'prominent display' quantified with specific sizing/positioning?" [Clarity]
-   - "Are hover state requirements consistent across all interactive elements?" [Consistency]
-   - "Are keyboard navigation requirements defined for all interactive UI?" [Coverage]
-   - "Is the fallback behavior specified when logo image fails to load?" [Edge Cases]
-   - "Are loading states defined for asynchronous episode data?" [Completeness]
-   - "Does the spec define visual hierarchy for competing UI elements?" [Clarity]
-
-   **ITEM STRUCTURE**:
-   Each item should follow this pattern:
-   - Question format asking about requirement quality
-   - Focus on what's WRITTEN (or not written) in the spec/plan
-   - Include quality dimension in brackets [Completeness/Clarity/Consistency/etc.]
-   - Reference spec section `[Spec §X.Y]` when checking existing requirements
-   - Use `[Gap]` marker when checking for missing requirements
-
-   **EXAMPLES BY QUALITY DIMENSION**:
-
-   Completeness:
-   - "Are error handling requirements defined for all API failure modes? [Gap]"
-   - "Are accessibility requirements specified for all interactive elements? [Completeness]"
-   - "Are mobile breakpoint requirements defined for responsive layouts? [Gap]"
-
-   Clarity:
-   - "Is 'fast loading' quantified with specific timing thresholds? [Clarity, Spec §NFR-2]"
-   - "Are 'related episodes' selection criteria explicitly defined? [Clarity, Spec §FR-5]"
-   - "Is 'prominent' defined with measurable visual properties? [Ambiguity, Spec §FR-4]"
-
-   Consistency:
-   - "Do navigation requirements align across all pages? [Consistency, Spec §FR-10]"
-   - "Are card component requirements consistent between landing and detail pages? [Consistency]"
-
-   Coverage:
-   - "Are requirements defined for zero-state scenarios (no episodes)? [Coverage, Edge Case]"
-   - "Are concurrent user interaction scenarios addressed? [Coverage, Gap]"
-   - "Are requirements specified for partial data loading failures? [Coverage, Exception Flow]"
-
-   Measurability:
-   - "Are visual hierarchy requirements measurable/testable? [Acceptance Criteria, Spec §FR-1]"
-   - "Can 'balanced visual weight' be objectively verified? [Measurability, Spec §FR-2]"
-
-   **Scenario Classification & Coverage** (Requirements Quality Focus):
-   - Check if requirements exist for: Primary, Alternate, Exception/Error, Recovery, Non-Functional scenarios
-   - For each scenario class, ask: "Are [scenario type] requirements complete, clear, and consistent?"
-   - If scenario class missing: "Are [scenario type] requirements intentionally excluded or missing? [Gap]"
-   - Include resilience/rollback when state mutation occurs: "Are rollback requirements defined for migration failures? [Gap]"
-
-   **Traceability Requirements**:
-   - MINIMUM: ≥80% of items MUST include at least one traceability reference
-   - Each item should reference: spec section `[Spec §X.Y]`, or use markers: `[Gap]`, `[Ambiguity]`, `[Conflict]`, `[Assumption]`
-   - If no ID system exists: "Is a requirement & acceptance criteria ID scheme established? [Traceability]"
-
-   **Surface & Resolve Issues** (Requirements Quality Problems):
-   Ask questions about the requirements themselves:
-   - Ambiguities: "Is the term 'fast' quantified with specific metrics? [Ambiguity, Spec §NFR-1]"
-   - Conflicts: "Do navigation requirements conflict between §FR-10 and §FR-10a? [Conflict]"
-   - Assumptions: "Is the assumption of 'always available podcast API' validated? [Assumption]"
-   - Dependencies: "Are external podcast API requirements documented? [Dependency, Gap]"
-   - Missing definitions: "Is 'visual hierarchy' defined with measurable criteria? [Gap]"
-
-   **Content Consolidation**:
-   - Soft cap: If raw candidate items > 40, prioritize by risk/impact
-   - Merge near-duplicates checking the same requirement aspect
-   - If >5 low-impact edge cases, create one item: "Are edge cases X, Y, Z addressed in requirements? [Coverage]"
-
-   **🚫 ABSOLUTELY PROHIBITED** - These make it an implementation test, not a requirements test:
-   - ❌ Any item starting with "Verify", "Test", "Confirm", "Check" + implementation behavior
-   - ❌ References to code execution, user actions, system behavior
-   - ❌ "Displays correctly", "works properly", "functions as expected"
-   - ❌ "Click", "navigate", "render", "load", "execute"
-   - ❌ Test cases, test plans, QA procedures
-   - ❌ Implementation details (frameworks, APIs, algorithms)
-
-   **✅ REQUIRED PATTERNS** - These test requirements quality:
-   - ✅ "Are [requirement type] defined/specified/documented for [scenario]?"
-   - ✅ "Is [vague term] quantified/clarified with specific criteria?"
-   - ✅ "Are requirements consistent between [section A] and [section B]?"
-   - ✅ "Can [requirement] be objectively measured/verified?"
-   - ✅ "Are [edge cases/scenarios] addressed in requirements?"
-   - ✅ "Does the spec define [missing aspect]?"
-
-6. **Structure Reference**: Generate the checklist following the canonical template in `.specify/templates/checklist-template.md` for title, meta section, category headings, and ID formatting. If template is unavailable, use: H1 title, purpose/created meta lines, `##` category sections containing `- [ ] CHK### <requirement item>` lines with globally incrementing IDs starting at CHK001.
-
-7. **Report**: Output full path to created checklist, item count, and remind user that each run creates a new file. Summarize:
-   - Focus areas selected
-   - Depth level
-   - Actor/timing
-   - Any explicit user-specified must-have items incorporated
-
-**Important**: Each `/speckit.checklist` command invocation creates a checklist file using short, descriptive names unless file already exists. This allows:
-
-- Multiple checklists of different types (e.g., `ux.md`, `test.md`, `security.md`)
-- Simple, memorable filenames that indicate checklist purpose
-- Easy identification and navigation in the `checklists/` folder
-
-To avoid clutter, use descriptive types and clean up obsolete checklists when done.
-
-## Example Checklist Types & Sample Items
-
-**UX Requirements Quality:** `ux.md`
-
-Sample items (testing the requirements, NOT the implementation):
-
-- "Are visual hierarchy requirements defined with measurable criteria? [Clarity, Spec §FR-1]"
-- "Is the number and positioning of UI elements explicitly specified? [Completeness, Spec §FR-1]"
-- "Are interaction state requirements (hover, focus, active) consistently defined? [Consistency]"
-- "Are accessibility requirements specified for all interactive elements? [Coverage, Gap]"
-- "Is fallback behavior defined when images fail to load? [Edge Case, Gap]"
-- "Can 'prominent display' be objectively measured? [Measurability, Spec §FR-4]"
-
-**API Requirements Quality:** `api.md`
-
-Sample items:
-
-- "Are error response formats specified for all failure scenarios? [Completeness]"
-- "Are rate limiting requirements quantified with specific thresholds? [Clarity]"
-- "Are authentication requirements consistent across all endpoints? [Consistency]"
-- "Are retry/timeout requirements defined for external dependencies? [Coverage, Gap]"
-- "Is versioning strategy documented in requirements? [Gap]"
-
-**Performance Requirements Quality:** `performance.md`
-
-Sample items:
-
-- "Are performance requirements quantified with specific metrics? [Clarity]"
-- "Are performance targets defined for all critical user journeys? [Coverage]"
-- "Are performance requirements under different load conditions specified? [Completeness]"
-- "Can performance requirements be objectively measured? [Measurability]"
-- "Are degradation requirements defined for high-load scenarios? [Edge Case, Gap]"
-
-**Security Requirements Quality:** `security.md`
-
-Sample items:
-
-- "Are authentication requirements specified for all protected resources? [Coverage]"
-- "Are data protection requirements defined for sensitive information? [Completeness]"
-- "Is the threat model documented and requirements aligned to it? [Traceability]"
-- "Are security requirements consistent with compliance obligations? [Consistency]"
-- "Are security failure/breach response requirements defined? [Gap, Exception Flow]"
-
-## Anti-Examples: What NOT To Do
-
-**❌ WRONG - These test implementation, not requirements:**
-
-```markdown
-- [ ] CHK001 - Verify landing page displays 3 episode cards [Spec §FR-001]
-- [ ] CHK002 - Test hover states work correctly on desktop [Spec §FR-003]
-- [ ] CHK003 - Confirm logo click navigates to home page [Spec §FR-010]
-- [ ] CHK004 - Check that related episodes section shows 3-5 items [Spec §FR-005]
-```
-
-**✅ CORRECT - These test requirements quality:**
-
-```markdown
-- [ ] CHK001 - Are the number and layout of featured episodes explicitly specified? [Completeness, Spec §FR-001]
-- [ ] CHK002 - Are hover state requirements consistently defined for all interactive elements? [Consistency, Spec §FR-003]
-- [ ] CHK003 - Are navigation requirements clear for all clickable brand elements? [Clarity, Spec §FR-010]
-- [ ] CHK004 - Is the selection criteria for related episodes documented? [Gap, Spec §FR-005]
-- [ ] CHK005 - Are loading state requirements defined for asynchronous episode data? [Gap]
-- [ ] CHK006 - Can "visual hierarchy" requirements be objectively measured? [Measurability, Spec §FR-001]
-```
-
-**Key Differences:**
-
-- Wrong: Tests if the system works correctly
-- Correct: Tests if the requirements are written correctly
-- Wrong: Verification of behavior
-- Correct: Validation of requirement quality
-- Wrong: "Does it do X?"
-- Correct: "Is X clearly specified?"

nextflow/.claude/commands/speckit.clarify.md

@@ -1,181 +0,0 @@
----
-description: Identify underspecified areas in the current feature spec by asking up to 5 highly targeted clarification questions and encoding answers back into the spec.
-handoffs: 
-  - label: Build Technical Plan
-    agent: speckit.plan
-    prompt: Create a plan for the spec. I am building with...
----
-
-## User Input
-
-```text
-$ARGUMENTS
-```
-
-You **MUST** consider the user input before proceeding (if not empty).
-
-## Outline
-
-Goal: Detect and reduce ambiguity or missing decision points in the active feature specification and record the clarifications directly in the spec file.
-
-Note: This clarification workflow is expected to run (and be completed) BEFORE invoking `/speckit.plan`. If the user explicitly states they are skipping clarification (e.g., exploratory spike), you may proceed, but must warn that downstream rework risk increases.
-
-Execution steps:
-
-1. Run `.specify/scripts/bash/check-prerequisites.sh --json --paths-only` from repo root **once** (combined `--json --paths-only` mode / `-Json -PathsOnly`). Parse minimal JSON payload fields:
-   - `FEATURE_DIR`
-   - `FEATURE_SPEC`
-   - (Optionally capture `IMPL_PLAN`, `TASKS` for future chained flows.)
-   - If JSON parsing fails, abort and instruct user to re-run `/speckit.specify` or verify feature branch environment.
-   - For single quotes in args like "I'm Groot", use escape syntax: e.g 'I'\''m Groot' (or double-quote if possible: "I'm Groot").
-
-2. Load the current spec file. Perform a structured ambiguity & coverage scan using this taxonomy. For each category, mark status: Clear / Partial / Missing. Produce an internal coverage map used for prioritization (do not output raw map unless no questions will be asked).
-
-   Functional Scope & Behavior:
-   - Core user goals & success criteria
-   - Explicit out-of-scope declarations
-   - User roles / personas differentiation
-
-   Domain & Data Model:
-   - Entities, attributes, relationships
-   - Identity & uniqueness rules
-   - Lifecycle/state transitions
-   - Data volume / scale assumptions
-
-   Interaction & UX Flow:
-   - Critical user journeys / sequences
-   - Error/empty/loading states
-   - Accessibility or localization notes
-
-   Non-Functional Quality Attributes:
-   - Performance (latency, throughput targets)
-   - Scalability (horizontal/vertical, limits)
-   - Reliability & availability (uptime, recovery expectations)
-   - Observability (logging, metrics, tracing signals)
-   - Security & privacy (authN/Z, data protection, threat assumptions)
-   - Compliance / regulatory constraints (if any)
-
-   Integration & External Dependencies:
-   - External services/APIs and failure modes
-   - Data import/export formats
-   - Protocol/versioning assumptions
-
-   Edge Cases & Failure Handling:
-   - Negative scenarios
-   - Rate limiting / throttling
-   - Conflict resolution (e.g., concurrent edits)
-
-   Constraints & Tradeoffs:
-   - Technical constraints (language, storage, hosting)
-   - Explicit tradeoffs or rejected alternatives
-
-   Terminology & Consistency:
-   - Canonical glossary terms
-   - Avoided synonyms / deprecated terms
-
-   Completion Signals:
-   - Acceptance criteria testability
-   - Measurable Definition of Done style indicators
-
-   Misc / Placeholders:
-   - TODO markers / unresolved decisions
-   - Ambiguous adjectives ("robust", "intuitive") lacking quantification
-
-   For each category with Partial or Missing status, add a candidate question opportunity unless:
-   - Clarification would not materially change implementation or validation strategy
-   - Information is better deferred to planning phase (note internally)
-
-3. Generate (internally) a prioritized queue of candidate clarification questions (maximum 5). Do NOT output them all at once. Apply these constraints:
-    - Maximum of 10 total questions across the whole session.
-    - Each question must be answerable with EITHER:
-       - A short multiple‑choice selection (2–5 distinct, mutually exclusive options), OR
-       - A one-word / short‑phrase answer (explicitly constrain: "Answer in <=5 words").
-    - Only include questions whose answers materially impact architecture, data modeling, task decomposition, test design, UX behavior, operational readiness, or compliance validation.
-    - Ensure category coverage balance: attempt to cover the highest impact unresolved categories first; avoid asking two low-impact questions when a single high-impact area (e.g., security posture) is unresolved.
-    - Exclude questions already answered, trivial stylistic preferences, or plan-level execution details (unless blocking correctness).
-    - Favor clarifications that reduce downstream rework risk or prevent misaligned acceptance tests.
-    - If more than 5 categories remain unresolved, select the top 5 by (Impact * Uncertainty) heuristic.
-
-4. Sequential questioning loop (interactive):
-    - Present EXACTLY ONE question at a time.
-    - For multiple‑choice questions:
-       - **Analyze all options** and determine the **most suitable option** based on:
-          - Best practices for the project type
-          - Common patterns in similar implementations
-          - Risk reduction (security, performance, maintainability)
-          - Alignment with any explicit project goals or constraints visible in the spec
-       - Present your **recommended option prominently** at the top with clear reasoning (1-2 sentences explaining why this is the best choice).
-       - Format as: `**Recommended:** Option [X] - <reasoning>`
-       - Then render all options as a Markdown table:
-
-       | Option | Description |
-       |--------|-------------|
-       | A | <Option A description> |
-       | B | <Option B description> |
-       | C | <Option C description> (add D/E as needed up to 5) |
-       | Short | Provide a different short answer (<=5 words) (Include only if free-form alternative is appropriate) |
-
-       - After the table, add: `You can reply with the option letter (e.g., "A"), accept the recommendation by saying "yes" or "recommended", or provide your own short answer.`
-    - For short‑answer style (no meaningful discrete options):
-       - Provide your **suggested answer** based on best practices and context.
-       - Format as: `**Suggested:** <your proposed answer> - <brief reasoning>`
-       - Then output: `Format: Short answer (<=5 words). You can accept the suggestion by saying "yes" or "suggested", or provide your own answer.`
-    - After the user answers:
-       - If the user replies with "yes", "recommended", or "suggested", use your previously stated recommendation/suggestion as the answer.
-       - Otherwise, validate the answer maps to one option or fits the <=5 word constraint.
-       - If ambiguous, ask for a quick disambiguation (count still belongs to same question; do not advance).
-       - Once satisfactory, record it in working memory (do not yet write to disk) and move to the next queued question.
-    - Stop asking further questions when:
-       - All critical ambiguities resolved early (remaining queued items become unnecessary), OR
-       - User signals completion ("done", "good", "no more"), OR
-       - You reach 5 asked questions.
-    - Never reveal future queued questions in advance.
-    - If no valid questions exist at start, immediately report no critical ambiguities.
-
-5. Integration after EACH accepted answer (incremental update approach):
-    - Maintain in-memory representation of the spec (loaded once at start) plus the raw file contents.
-    - For the first integrated answer in this session:
-       - Ensure a `## Clarifications` section exists (create it just after the highest-level contextual/overview section per the spec template if missing).
-       - Under it, create (if not present) a `### Session YYYY-MM-DD` subheading for today.
-    - Append a bullet line immediately after acceptance: `- Q: <question> → A: <final answer>`.
-    - Then immediately apply the clarification to the most appropriate section(s):
-       - Functional ambiguity → Update or add a bullet in Functional Requirements.
-       - User interaction / actor distinction → Update User Stories or Actors subsection (if present) with clarified role, constraint, or scenario.
-       - Data shape / entities → Update Data Model (add fields, types, relationships) preserving ordering; note added constraints succinctly.
-       - Non-functional constraint → Add/modify measurable criteria in Non-Functional / Quality Attributes section (convert vague adjective to metric or explicit target).
-       - Edge case / negative flow → Add a new bullet under Edge Cases / Error Handling (or create such subsection if template provides placeholder for it).
-       - Terminology conflict → Normalize term across spec; retain original only if necessary by adding `(formerly referred to as "X")` once.
-    - If the clarification invalidates an earlier ambiguous statement, replace that statement instead of duplicating; leave no obsolete contradictory text.
-    - Save the spec file AFTER each integration to minimize risk of context loss (atomic overwrite).
-    - Preserve formatting: do not reorder unrelated sections; keep heading hierarchy intact.
-    - Keep each inserted clarification minimal and testable (avoid narrative drift).
-
-6. Validation (performed after EACH write plus final pass):
-   - Clarifications session contains exactly one bullet per accepted answer (no duplicates).
-   - Total asked (accepted) questions ≤ 5.
-   - Updated sections contain no lingering vague placeholders the new answer was meant to resolve.
-   - No contradictory earlier statement remains (scan for now-invalid alternative choices removed).
-   - Markdown structure valid; only allowed new headings: `## Clarifications`, `### Session YYYY-MM-DD`.
-   - Terminology consistency: same canonical term used across all updated sections.
-
-7. Write the updated spec back to `FEATURE_SPEC`.
-
-8. Report completion (after questioning loop ends or early termination):
-   - Number of questions asked & answered.
-   - Path to updated spec.
-   - Sections touched (list names).
-   - Coverage summary table listing each taxonomy category with Status: Resolved (was Partial/Missing and addressed), Deferred (exceeds question quota or better suited for planning), Clear (already sufficient), Outstanding (still Partial/Missing but low impact).
-   - If any Outstanding or Deferred remain, recommend whether to proceed to `/speckit.plan` or run `/speckit.clarify` again later post-plan.
-   - Suggested next command.
-
-Behavior rules:
-
-- If no meaningful ambiguities found (or all potential questions would be low-impact), respond: "No critical ambiguities detected worth formal clarification." and suggest proceeding.
-- If spec file missing, instruct user to run `/speckit.specify` first (do not create a new spec here).
-- Never exceed 5 total asked questions (clarification retries for a single question do not count as new questions).
-- Avoid speculative tech stack questions unless the absence blocks functional clarity.
-- Respect user early termination signals ("stop", "done", "proceed").
-- If no questions asked due to full coverage, output a compact coverage summary (all categories Clear) then suggest advancing.
-- If quota reached with unresolved high-impact categories remaining, explicitly flag them under Deferred with rationale.
-
-Context for prioritization: $ARGUMENTS

nextflow/.claude/commands/speckit.constitution.md

@@ -1,82 +0,0 @@
----
-description: Create or update the project constitution from interactive or provided principle inputs, ensuring all dependent templates stay in sync.
-handoffs: 
-  - label: Build Specification
-    agent: speckit.specify
-    prompt: Implement the feature specification based on the updated constitution. I want to build...
----
-
-## User Input
-
-```text
-$ARGUMENTS
-```
-
-You **MUST** consider the user input before proceeding (if not empty).
-
-## Outline
-
-You are updating the project constitution at `.specify/memory/constitution.md`. This file is a TEMPLATE containing placeholder tokens in square brackets (e.g. `[PROJECT_NAME]`, `[PRINCIPLE_1_NAME]`). Your job is to (a) collect/derive concrete values, (b) fill the template precisely, and (c) propagate any amendments across dependent artifacts.
-
-Follow this execution flow:
-
-1. Load the existing constitution template at `.specify/memory/constitution.md`.
-   - Identify every placeholder token of the form `[ALL_CAPS_IDENTIFIER]`.
-   **IMPORTANT**: The user might require less or more principles than the ones used in the template. If a number is specified, respect that - follow the general template. You will update the doc accordingly.
-
-2. Collect/derive values for placeholders:
-   - If user input (conversation) supplies a value, use it.
-   - Otherwise infer from existing repo context (README, docs, prior constitution versions if embedded).
-   - For governance dates: `RATIFICATION_DATE` is the original adoption date (if unknown ask or mark TODO), `LAST_AMENDED_DATE` is today if changes are made, otherwise keep previous.
-   - `CONSTITUTION_VERSION` must increment according to semantic versioning rules:
-     - MAJOR: Backward incompatible governance/principle removals or redefinitions.
-     - MINOR: New principle/section added or materially expanded guidance.
-     - PATCH: Clarifications, wording, typo fixes, non-semantic refinements.
-   - If version bump type ambiguous, propose reasoning before finalizing.
-
-3. Draft the updated constitution content:
-   - Replace every placeholder with concrete text (no bracketed tokens left except intentionally retained template slots that the project has chosen not to define yet—explicitly justify any left).
-   - Preserve heading hierarchy and comments can be removed once replaced unless they still add clarifying guidance.
-   - Ensure each Principle section: succinct name line, paragraph (or bullet list) capturing non‑negotiable rules, explicit rationale if not obvious.
-   - Ensure Governance section lists amendment procedure, versioning policy, and compliance review expectations.
-
-4. Consistency propagation checklist (convert prior checklist into active validations):
-   - Read `.specify/templates/plan-template.md` and ensure any "Constitution Check" or rules align with updated principles.
-   - Read `.specify/templates/spec-template.md` for scope/requirements alignment—update if constitution adds/removes mandatory sections or constraints.
-   - Read `.specify/templates/tasks-template.md` and ensure task categorization reflects new or removed principle-driven task types (e.g., observability, versioning, testing discipline).
-   - Read each command file in `.specify/templates/commands/*.md` (including this one) to verify no outdated references (agent-specific names like CLAUDE only) remain when generic guidance is required.
-   - Read any runtime guidance docs (e.g., `README.md`, `docs/quickstart.md`, or agent-specific guidance files if present). Update references to principles changed.
-
-5. Produce a Sync Impact Report (prepend as an HTML comment at top of the constitution file after update):
-   - Version change: old → new
-   - List of modified principles (old title → new title if renamed)
-   - Added sections
-   - Removed sections
-   - Templates requiring updates (✅ updated / ⚠ pending) with file paths
-   - Follow-up TODOs if any placeholders intentionally deferred.
-
-6. Validation before final output:
-   - No remaining unexplained bracket tokens.
-   - Version line matches report.
-   - Dates ISO format YYYY-MM-DD.
-   - Principles are declarative, testable, and free of vague language ("should" → replace with MUST/SHOULD rationale where appropriate).
-
-7. Write the completed constitution back to `.specify/memory/constitution.md` (overwrite).
-
-8. Output a final summary to the user with:
-   - New version and bump rationale.
-   - Any files flagged for manual follow-up.
-   - Suggested commit message (e.g., `docs: amend constitution to vX.Y.Z (principle additions + governance update)`).
-
-Formatting & Style Requirements:
-
-- Use Markdown headings exactly as in the template (do not demote/promote levels).
-- Wrap long rationale lines to keep readability (<100 chars ideally) but do not hard enforce with awkward breaks.
-- Keep a single blank line between sections.
-- Avoid trailing whitespace.
-
-If the user supplies partial updates (e.g., only one principle revision), still perform validation and version decision steps.
-
-If critical info missing (e.g., ratification date truly unknown), insert `TODO(<FIELD_NAME>): explanation` and include in the Sync Impact Report under deferred items.
-
-Do not create a new template; always operate on the existing `.specify/memory/constitution.md` file.

nextflow/.claude/commands/speckit.implement.md

@@ -1,135 +0,0 @@
----
-description: Execute the implementation plan by processing and executing all tasks defined in tasks.md
----
-
-## User Input
-
-```text
-$ARGUMENTS
-```
-
-You **MUST** consider the user input before proceeding (if not empty).
-
-## Outline
-
-1. Run `.specify/scripts/bash/check-prerequisites.sh --json --require-tasks --include-tasks` from repo root and parse FEATURE_DIR and AVAILABLE_DOCS list. All paths must be absolute. For single quotes in args like "I'm Groot", use escape syntax: e.g 'I'\''m Groot' (or double-quote if possible: "I'm Groot").
-
-2. **Check checklists status** (if FEATURE_DIR/checklists/ exists):
-   - Scan all checklist files in the checklists/ directory
-   - For each checklist, count:
-     - Total items: All lines matching `- [ ]` or `- [X]` or `- [x]`
-     - Completed items: Lines matching `- [X]` or `- [x]`
-     - Incomplete items: Lines matching `- [ ]`
-   - Create a status table:
-
-     ```text
-     | Checklist | Total | Completed | Incomplete | Status |
-     |-----------|-------|-----------|------------|--------|
-     | ux.md     | 12    | 12        | 0          | ✓ PASS |
-     | test.md   | 8     | 5         | 3          | ✗ FAIL |
-     | security.md | 6   | 6         | 0          | ✓ PASS |
-     ```
-
-   - Calculate overall status:
-     - **PASS**: All checklists have 0 incomplete items
-     - **FAIL**: One or more checklists have incomplete items
-
-   - **If any checklist is incomplete**:
-     - Display the table with incomplete item counts
-     - **STOP** and ask: "Some checklists are incomplete. Do you want to proceed with implementation anyway? (yes/no)"
-     - Wait for user response before continuing
-     - If user says "no" or "wait" or "stop", halt execution
-     - If user says "yes" or "proceed" or "continue", proceed to step 3
-
-   - **If all checklists are complete**:
-     - Display the table showing all checklists passed
-     - Automatically proceed to step 3
-
-3. Load and analyze the implementation context:
-   - **REQUIRED**: Read tasks.md for the complete task list and execution plan
-   - **REQUIRED**: Read plan.md for tech stack, architecture, and file structure
-   - **IF EXISTS**: Read data-model.md for entities and relationships
-   - **IF EXISTS**: Read contracts/ for API specifications and test requirements
-   - **IF EXISTS**: Read research.md for technical decisions and constraints
-   - **IF EXISTS**: Read quickstart.md for integration scenarios
-
-4. **Project Setup Verification**:
-   - **REQUIRED**: Create/verify ignore files based on actual project setup:
-
-   **Detection & Creation Logic**:
-   - Check if the following command succeeds to determine if the repository is a git repo (create/verify .gitignore if so):
-
-     ```sh
-     git rev-parse --git-dir 2>/dev/null
-     ```
-
-   - Check if Dockerfile* exists or Docker in plan.md → create/verify .dockerignore
-   - Check if .eslintrc* exists → create/verify .eslintignore
-   - Check if eslint.config.* exists → ensure the config's `ignores` entries cover required patterns
-   - Check if .prettierrc* exists → create/verify .prettierignore
-   - Check if .npmrc or package.json exists → create/verify .npmignore (if publishing)
-   - Check if terraform files (*.tf) exist → create/verify .terraformignore
-   - Check if .helmignore needed (helm charts present) → create/verify .helmignore
-
-   **If ignore file already exists**: Verify it contains essential patterns, append missing critical patterns only
-   **If ignore file missing**: Create with full pattern set for detected technology
-
-   **Common Patterns by Technology** (from plan.md tech stack):
-   - **Node.js/JavaScript/TypeScript**: `node_modules/`, `dist/`, `build/`, `*.log`, `.env*`
-   - **Python**: `__pycache__/`, `*.pyc`, `.venv/`, `venv/`, `dist/`, `*.egg-info/`
-   - **Java**: `target/`, `*.class`, `*.jar`, `.gradle/`, `build/`
-   - **C#/.NET**: `bin/`, `obj/`, `*.user`, `*.suo`, `packages/`
-   - **Go**: `*.exe`, `*.test`, `vendor/`, `*.out`
-   - **Ruby**: `.bundle/`, `log/`, `tmp/`, `*.gem`, `vendor/bundle/`
-   - **PHP**: `vendor/`, `*.log`, `*.cache`, `*.env`
-   - **Rust**: `target/`, `debug/`, `release/`, `*.rs.bk`, `*.rlib`, `*.prof*`, `.idea/`, `*.log`, `.env*`
-   - **Kotlin**: `build/`, `out/`, `.gradle/`, `.idea/`, `*.class`, `*.jar`, `*.iml`, `*.log`, `.env*`
-   - **C++**: `build/`, `bin/`, `obj/`, `out/`, `*.o`, `*.so`, `*.a`, `*.exe`, `*.dll`, `.idea/`, `*.log`, `.env*`
-   - **C**: `build/`, `bin/`, `obj/`, `out/`, `*.o`, `*.a`, `*.so`, `*.exe`, `Makefile`, `config.log`, `.idea/`, `*.log`, `.env*`
-   - **Swift**: `.build/`, `DerivedData/`, `*.swiftpm/`, `Packages/`
-   - **R**: `.Rproj.user/`, `.Rhistory`, `.RData`, `.Ruserdata`, `*.Rproj`, `packrat/`, `renv/`
-   - **Universal**: `.DS_Store`, `Thumbs.db`, `*.tmp`, `*.swp`, `.vscode/`, `.idea/`
-
-   **Tool-Specific Patterns**:
-   - **Docker**: `node_modules/`, `.git/`, `Dockerfile*`, `.dockerignore`, `*.log*`, `.env*`, `coverage/`
-   - **ESLint**: `node_modules/`, `dist/`, `build/`, `coverage/`, `*.min.js`
-   - **Prettier**: `node_modules/`, `dist/`, `build/`, `coverage/`, `package-lock.json`, `yarn.lock`, `pnpm-lock.yaml`
-   - **Terraform**: `.terraform/`, `*.tfstate*`, `*.tfvars`, `.terraform.lock.hcl`
-   - **Kubernetes/k8s**: `*.secret.yaml`, `secrets/`, `.kube/`, `kubeconfig*`, `*.key`, `*.crt`
-
-5. Parse tasks.md structure and extract:
-   - **Task phases**: Setup, Tests, Core, Integration, Polish
-   - **Task dependencies**: Sequential vs parallel execution rules
-   - **Task details**: ID, description, file paths, parallel markers [P]
-   - **Execution flow**: Order and dependency requirements
-
-6. Execute implementation following the task plan:
-   - **Phase-by-phase execution**: Complete each phase before moving to the next
-   - **Respect dependencies**: Run sequential tasks in order, parallel tasks [P] can run together  
-   - **Follow TDD approach**: Execute test tasks before their corresponding implementation tasks
-   - **File-based coordination**: Tasks affecting the same files must run sequentially
-   - **Validation checkpoints**: Verify each phase completion before proceeding
-
-7. Implementation execution rules:
-   - **Setup first**: Initialize project structure, dependencies, configuration
-   - **Tests before code**: If you need to write tests for contracts, entities, and integration scenarios
-   - **Core development**: Implement models, services, CLI commands, endpoints
-   - **Integration work**: Database connections, middleware, logging, external services
-   - **Polish and validation**: Unit tests, performance optimization, documentation
-
-8. Progress tracking and error handling:
-   - Report progress after each completed task
-   - Halt execution if any non-parallel task fails
-   - For parallel tasks [P], continue with successful tasks, report failed ones
-   - Provide clear error messages with context for debugging
-   - Suggest next steps if implementation cannot proceed
-   - **IMPORTANT** For completed tasks, make sure to mark the task off as [X] in the tasks file.
-
-9. Completion validation:
-   - Verify all required tasks are completed
-   - Check that implemented features match the original specification
-   - Validate that tests pass and coverage meets requirements
-   - Confirm the implementation follows the technical plan
-   - Report final status with summary of completed work
-
-Note: This command assumes a complete task breakdown exists in tasks.md. If tasks are incomplete or missing, suggest running `/speckit.tasks` first to regenerate the task list.

nextflow/.claude/commands/speckit.plan.md

@@ -1,89 +0,0 @@
----
-description: Execute the implementation planning workflow using the plan template to generate design artifacts.
-handoffs: 
-  - label: Create Tasks
-    agent: speckit.tasks
-    prompt: Break the plan into tasks
-    send: true
-  - label: Create Checklist
-    agent: speckit.checklist
-    prompt: Create a checklist for the following domain...
----
-
-## User Input
-
-```text
-$ARGUMENTS
-```
-
-You **MUST** consider the user input before proceeding (if not empty).
-
-## Outline
-
-1. **Setup**: Run `.specify/scripts/bash/setup-plan.sh --json` from repo root and parse JSON for FEATURE_SPEC, IMPL_PLAN, SPECS_DIR, BRANCH. For single quotes in args like "I'm Groot", use escape syntax: e.g 'I'\''m Groot' (or double-quote if possible: "I'm Groot").
-
-2. **Load context**: Read FEATURE_SPEC and `.specify/memory/constitution.md`. Load IMPL_PLAN template (already copied).
-
-3. **Execute plan workflow**: Follow the structure in IMPL_PLAN template to:
-   - Fill Technical Context (mark unknowns as "NEEDS CLARIFICATION")
-   - Fill Constitution Check section from constitution
-   - Evaluate gates (ERROR if violations unjustified)
-   - Phase 0: Generate research.md (resolve all NEEDS CLARIFICATION)
-   - Phase 1: Generate data-model.md, contracts/, quickstart.md
-   - Phase 1: Update agent context by running the agent script
-   - Re-evaluate Constitution Check post-design
-
-4. **Stop and report**: Command ends after Phase 2 planning. Report branch, IMPL_PLAN path, and generated artifacts.
-
-## Phases
-
-### Phase 0: Outline & Research
-
-1. **Extract unknowns from Technical Context** above:
-   - For each NEEDS CLARIFICATION → research task
-   - For each dependency → best practices task
-   - For each integration → patterns task
-
-2. **Generate and dispatch research agents**:
-
-   ```text
-   For each unknown in Technical Context:
-     Task: "Research {unknown} for {feature context}"
-   For each technology choice:
-     Task: "Find best practices for {tech} in {domain}"
-   ```
-
-3. **Consolidate findings** in `research.md` using format:
-   - Decision: [what was chosen]
-   - Rationale: [why chosen]
-   - Alternatives considered: [what else evaluated]
-
-**Output**: research.md with all NEEDS CLARIFICATION resolved
-
-### Phase 1: Design & Contracts
-
-**Prerequisites:** `research.md` complete
-
-1. **Extract entities from feature spec** → `data-model.md`:
-   - Entity name, fields, relationships
-   - Validation rules from requirements
-   - State transitions if applicable
-
-2. **Generate API contracts** from functional requirements:
-   - For each user action → endpoint
-   - Use standard REST/GraphQL patterns
-   - Output OpenAPI/GraphQL schema to `/contracts/`
-
-3. **Agent context update**:
-   - Run `.specify/scripts/bash/update-agent-context.sh claude`
-   - These scripts detect which AI agent is in use
-   - Update the appropriate agent-specific context file
-   - Add only new technology from current plan
-   - Preserve manual additions between markers
-
-**Output**: data-model.md, /contracts/*, quickstart.md, agent-specific file
-
-## Key rules
-
-- Use absolute paths
-- ERROR on gate failures or unresolved clarifications

nextflow/.claude/commands/speckit.specify.md

@@ -1,257 +0,0 @@
----
-description: Create or update the feature specification from a natural language feature description.
-handoffs: 
-  - label: Build Technical Plan
-    agent: speckit.plan
-    prompt: Create a plan for the spec. I am building with...
-  - label: Clarify Spec Requirements
-    agent: speckit.clarify
-    prompt: Clarify specification requirements
-    send: true
----
-
-## User Input
-
-```text
-$ARGUMENTS
-```
-
-You **MUST** consider the user input before proceeding (if not empty).
-
-## Outline
-
-The text the user typed after `/speckit.specify` in the triggering message **is** the feature description. Assume you always have it available in this conversation even if `$ARGUMENTS` appears literally below. Do not ask the user to repeat it unless they provided an empty command.
-
-Given that feature description, do this:
-
-1. **Generate a concise short name** (2-4 words) for the branch:
-   - Analyze the feature description and extract the most meaningful keywords
-   - Create a 2-4 word short name that captures the essence of the feature
-   - Use action-noun format when possible (e.g., "add-user-auth", "fix-payment-bug")
-   - Preserve technical terms and acronyms (OAuth2, API, JWT, etc.)
-   - Keep it concise but descriptive enough to understand the feature at a glance
-   - Examples:
-     - "I want to add user authentication" → "user-auth"
-     - "Implement OAuth2 integration for the API" → "oauth2-api-integration"
-     - "Create a dashboard for analytics" → "analytics-dashboard"
-     - "Fix payment processing timeout bug" → "fix-payment-timeout"
-
-2. **Check for existing branches before creating new one**:
-   
-   a. First, fetch all remote branches to ensure we have the latest information:
-      ```bash
-      git fetch --all --prune
-      ```
-   
-   b. Find the highest feature number across all sources for the short-name:
-      - Remote branches: `git ls-remote --heads origin | grep -E 'refs/heads/[0-9]+-<short-name>$'`
-      - Local branches: `git branch | grep -E '^[* ]*[0-9]+-<short-name>$'`
-      - Specs directories: Check for directories matching `specs/[0-9]+-<short-name>`
-   
-   c. Determine the next available number:
-      - Extract all numbers from all three sources
-      - Find the highest number N
-      - Use N+1 for the new branch number
-   
-   d. Run the script `.specify/scripts/bash/create-new-feature.sh --json "$ARGUMENTS"` with the calculated number and short-name:
-      - Pass `--number N+1` and `--short-name "your-short-name"` along with the feature description
-      - Bash example: `.specify/scripts/bash/create-new-feature.sh --json "$ARGUMENTS" --json --number 5 --short-name "user-auth" "Add user authentication"`
-      - PowerShell example: `.specify/scripts/bash/create-new-feature.sh --json "$ARGUMENTS" -Json -Number 5 -ShortName "user-auth" "Add user authentication"`
-   
-   **IMPORTANT**:
-   - Check all three sources (remote branches, local branches, specs directories) to find the highest number
-   - Only match branches/directories with the exact short-name pattern
-   - If no existing branches/directories found with this short-name, start with number 1
-   - You must only ever run this script once per feature
-   - The JSON is provided in the terminal as output - always refer to it to get the actual content you're looking for
-   - The JSON output will contain BRANCH_NAME and SPEC_FILE paths
-   - For single quotes in args like "I'm Groot", use escape syntax: e.g 'I'\''m Groot' (or double-quote if possible: "I'm Groot")
-
-3. Load `.specify/templates/spec-template.md` to understand required sections.
-
-4. Follow this execution flow:
-
-    1. Parse user description from Input
-       If empty: ERROR "No feature description provided"
-    2. Extract key concepts from description
-       Identify: actors, actions, data, constraints
-    3. For unclear aspects:
-       - Make informed guesses based on context and industry standards
-       - Only mark with [NEEDS CLARIFICATION: specific question] if:
-         - The choice significantly impacts feature scope or user experience
-         - Multiple reasonable interpretations exist with different implications
-         - No reasonable default exists
-       - **LIMIT: Maximum 3 [NEEDS CLARIFICATION] markers total**
-       - Prioritize clarifications by impact: scope > security/privacy > user experience > technical details
-    4. Fill User Scenarios & Testing section
-       If no clear user flow: ERROR "Cannot determine user scenarios"
-    5. Generate Functional Requirements
-       Each requirement must be testable
-       Use reasonable defaults for unspecified details (document assumptions in Assumptions section)
-    6. Define Success Criteria
-       Create measurable, technology-agnostic outcomes
-       Include both quantitative metrics (time, performance, volume) and qualitative measures (user satisfaction, task completion)
-       Each criterion must be verifiable without implementation details
-    7. Identify Key Entities (if data involved)
-    8. Return: SUCCESS (spec ready for planning)
-
-5. Write the specification to SPEC_FILE using the template structure, replacing placeholders with concrete details derived from the feature description (arguments) while preserving section order and headings.
-
-6. **Specification Quality Validation**: After writing the initial spec, validate it against quality criteria:
-
-   a. **Create Spec Quality Checklist**: Generate a checklist file at `FEATURE_DIR/checklists/requirements.md` using the checklist template structure with these validation items:
-
-      ```markdown
-      # Specification Quality Checklist: [FEATURE NAME]
-      
-      **Purpose**: Validate specification completeness and quality before proceeding to planning
-      **Created**: [DATE]
-      **Feature**: [Link to spec.md]
-      
-      ## Content Quality
-      
-      - [ ] No implementation details (languages, frameworks, APIs)
-      - [ ] Focused on user value and business needs
-      - [ ] Written for non-technical stakeholders
-      - [ ] All mandatory sections completed
-      
-      ## Requirement Completeness
-      
-      - [ ] No [NEEDS CLARIFICATION] markers remain
-      - [ ] Requirements are testable and unambiguous
-      - [ ] Success criteria are measurable
-      - [ ] Success criteria are technology-agnostic (no implementation details)
-      - [ ] All acceptance scenarios are defined
-      - [ ] Edge cases are identified
-      - [ ] Scope is clearly bounded
-      - [ ] Dependencies and assumptions identified
-      
-      ## Feature Readiness
-      
-      - [ ] All functional requirements have clear acceptance criteria
-      - [ ] User scenarios cover primary flows
-      - [ ] Feature meets measurable outcomes defined in Success Criteria
-      - [ ] No implementation details leak into specification
-      
-      ## Notes
-      
-      - Items marked incomplete require spec updates before `/speckit.clarify` or `/speckit.plan`
-      ```
-
-   b. **Run Validation Check**: Review the spec against each checklist item:
-      - For each item, determine if it passes or fails
-      - Document specific issues found (quote relevant spec sections)
-
-   c. **Handle Validation Results**:
-
-      - **If all items pass**: Mark checklist complete and proceed to step 6
-
-      - **If items fail (excluding [NEEDS CLARIFICATION])**:
-        1. List the failing items and specific issues
-        2. Update the spec to address each issue
-        3. Re-run validation until all items pass (max 3 iterations)
-        4. If still failing after 3 iterations, document remaining issues in checklist notes and warn user
-
-      - **If [NEEDS CLARIFICATION] markers remain**:
-        1. Extract all [NEEDS CLARIFICATION: ...] markers from the spec
-        2. **LIMIT CHECK**: If more than 3 markers exist, keep only the 3 most critical (by scope/security/UX impact) and make informed guesses for the rest
-        3. For each clarification needed (max 3), present options to user in this format:
-
-           ```markdown
-           ## Question [N]: [Topic]
-           
-           **Context**: [Quote relevant spec section]
-           
-           **What we need to know**: [Specific question from NEEDS CLARIFICATION marker]
-           
-           **Suggested Answers**:
-           
-           | Option | Answer | Implications |
-           |--------|--------|--------------|
-           | A      | [First suggested answer] | [What this means for the feature] |
-           | B      | [Second suggested answer] | [What this means for the feature] |
-           | C      | [Third suggested answer] | [What this means for the feature] |
-           | Custom | Provide your own answer | [Explain how to provide custom input] |
-           
-           **Your choice**: _[Wait for user response]_
-           ```
-
-        4. **CRITICAL - Table Formatting**: Ensure markdown tables are properly formatted:
-           - Use consistent spacing with pipes aligned
-           - Each cell should have spaces around content: `| Content |` not `|Content|`
-           - Header separator must have at least 3 dashes: `|--------|`
-           - Test that the table renders correctly in markdown preview
-        5. Number questions sequentially (Q1, Q2, Q3 - max 3 total)
-        6. Present all questions together before waiting for responses
-        7. Wait for user to respond with their choices for all questions (e.g., "Q1: A, Q2: Custom - [details], Q3: B")
-        8. Update the spec by replacing each [NEEDS CLARIFICATION] marker with the user's selected or provided answer
-        9. Re-run validation after all clarifications are resolved
-
-   d. **Update Checklist**: After each validation iteration, update the checklist file with current pass/fail status
-
-7. Report completion with branch name, spec file path, checklist results, and readiness for the next phase (`/speckit.clarify` or `/speckit.plan`).
-
-**NOTE:** The script creates and checks out the new branch and initializes the spec file before writing.
-
-## General Guidelines
-
-## Quick Guidelines
-
-- Focus on **WHAT** users need and **WHY**.
-- Avoid HOW to implement (no tech stack, APIs, code structure).
-- Written for business stakeholders, not developers.
-- DO NOT create any checklists that are embedded in the spec. That will be a separate command.
-
-### Section Requirements
-
-- **Mandatory sections**: Must be completed for every feature
-- **Optional sections**: Include only when relevant to the feature
-- When a section doesn't apply, remove it entirely (don't leave as "N/A")
-
-### For AI Generation
-
-When creating this spec from a user prompt:
-
-1. **Make informed guesses**: Use context, industry standards, and common patterns to fill gaps
-2. **Document assumptions**: Record reasonable defaults in the Assumptions section
-3. **Limit clarifications**: Maximum 3 [NEEDS CLARIFICATION] markers - use only for critical decisions that:
-   - Significantly impact feature scope or user experience
-   - Have multiple reasonable interpretations with different implications
-   - Lack any reasonable default
-4. **Prioritize clarifications**: scope > security/privacy > user experience > technical details
-5. **Think like a tester**: Every vague requirement should fail the "testable and unambiguous" checklist item
-6. **Common areas needing clarification** (only if no reasonable default exists):
-   - Feature scope and boundaries (include/exclude specific use cases)
-   - User types and permissions (if multiple conflicting interpretations possible)
-   - Security/compliance requirements (when legally/financially significant)
-
-**Examples of reasonable defaults** (don't ask about these):
-
-- Data retention: Industry-standard practices for the domain
-- Performance targets: Standard web/mobile app expectations unless specified
-- Error handling: User-friendly messages with appropriate fallbacks
-- Authentication method: Standard session-based or OAuth2 for web apps
-- Integration patterns: RESTful APIs unless specified otherwise
-
-### Success Criteria Guidelines
-
-Success criteria must be:
-
-1. **Measurable**: Include specific metrics (time, percentage, count, rate)
-2. **Technology-agnostic**: No mention of frameworks, languages, databases, or tools
-3. **User-focused**: Describe outcomes from user/business perspective, not system internals
-4. **Verifiable**: Can be tested/validated without knowing implementation details
-
-**Good examples**:
-
-- "Users can complete checkout in under 3 minutes"
-- "System supports 10,000 concurrent users"
-- "95% of searches return results in under 1 second"
-- "Task completion rate improves by 40%"
-
-**Bad examples** (implementation-focused):
-
-- "API response time is under 200ms" (too technical, use "Users see results instantly")
-- "Database can handle 1000 TPS" (implementation detail, use user-facing metric)
-- "React components render efficiently" (framework-specific)
-- "Redis cache hit rate above 80%" (technology-specific)

nextflow/.claude/commands/speckit.tasks.md

@@ -1,137 +0,0 @@
----
-description: Generate an actionable, dependency-ordered tasks.md for the feature based on available design artifacts.
-handoffs: 
-  - label: Analyze For Consistency
-    agent: speckit.analyze
-    prompt: Run a project analysis for consistency
-    send: true
-  - label: Implement Project
-    agent: speckit.implement
-    prompt: Start the implementation in phases
-    send: true
----
-
-## User Input
-
-```text
-$ARGUMENTS
-```
-
-You **MUST** consider the user input before proceeding (if not empty).
-
-## Outline
-
-1. **Setup**: Run `.specify/scripts/bash/check-prerequisites.sh --json` from repo root and parse FEATURE_DIR and AVAILABLE_DOCS list. All paths must be absolute. For single quotes in args like "I'm Groot", use escape syntax: e.g 'I'\''m Groot' (or double-quote if possible: "I'm Groot").
-
-2. **Load design documents**: Read from FEATURE_DIR:
-   - **Required**: plan.md (tech stack, libraries, structure), spec.md (user stories with priorities)
-   - **Optional**: data-model.md (entities), contracts/ (API endpoints), research.md (decisions), quickstart.md (test scenarios)
-   - Note: Not all projects have all documents. Generate tasks based on what's available.
-
-3. **Execute task generation workflow**:
-   - Load plan.md and extract tech stack, libraries, project structure
-   - Load spec.md and extract user stories with their priorities (P1, P2, P3, etc.)
-   - If data-model.md exists: Extract entities and map to user stories
-   - If contracts/ exists: Map endpoints to user stories
-   - If research.md exists: Extract decisions for setup tasks
-   - Generate tasks organized by user story (see Task Generation Rules below)
-   - Generate dependency graph showing user story completion order
-   - Create parallel execution examples per user story
-   - Validate task completeness (each user story has all needed tasks, independently testable)
-
-4. **Generate tasks.md**: Use `.specify.specify/templates/tasks-template.md` as structure, fill with:
-   - Correct feature name from plan.md
-   - Phase 1: Setup tasks (project initialization)
-   - Phase 2: Foundational tasks (blocking prerequisites for all user stories)
-   - Phase 3+: One phase per user story (in priority order from spec.md)
-   - Each phase includes: story goal, independent test criteria, tests (if requested), implementation tasks
-   - Final Phase: Polish & cross-cutting concerns
-   - All tasks must follow the strict checklist format (see Task Generation Rules below)
-   - Clear file paths for each task
-   - Dependencies section showing story completion order
-   - Parallel execution examples per story
-   - Implementation strategy section (MVP first, incremental delivery)
-
-5. **Report**: Output path to generated tasks.md and summary:
-   - Total task count
-   - Task count per user story
-   - Parallel opportunities identified
-   - Independent test criteria for each story
-   - Suggested MVP scope (typically just User Story 1)
-   - Format validation: Confirm ALL tasks follow the checklist format (checkbox, ID, labels, file paths)
-
-Context for task generation: $ARGUMENTS
-
-The tasks.md should be immediately executable - each task must be specific enough that an LLM can complete it without additional context.
-
-## Task Generation Rules
-
-**CRITICAL**: Tasks MUST be organized by user story to enable independent implementation and testing.
-
-**Tests are OPTIONAL**: Only generate test tasks if explicitly requested in the feature specification or if user requests TDD approach.
-
-### Checklist Format (REQUIRED)
-
-Every task MUST strictly follow this format:
-
-```text
-- [ ] [TaskID] [P?] [Story?] Description with file path
-```
-
-**Format Components**:
-
-1. **Checkbox**: ALWAYS start with `- [ ]` (markdown checkbox)
-2. **Task ID**: Sequential number (T001, T002, T003...) in execution order
-3. **[P] marker**: Include ONLY if task is parallelizable (different files, no dependencies on incomplete tasks)
-4. **[Story] label**: REQUIRED for user story phase tasks only
-   - Format: [US1], [US2], [US3], etc. (maps to user stories from spec.md)
-   - Setup phase: NO story label
-   - Foundational phase: NO story label  
-   - User Story phases: MUST have story label
-   - Polish phase: NO story label
-5. **Description**: Clear action with exact file path
-
-**Examples**:
-
-- ✅ CORRECT: `- [ ] T001 Create project structure per implementation plan`
-- ✅ CORRECT: `- [ ] T005 [P] Implement authentication middleware in src/middleware/auth.py`
-- ✅ CORRECT: `- [ ] T012 [P] [US1] Create User model in src/models/user.py`
-- ✅ CORRECT: `- [ ] T014 [US1] Implement UserService in src/services/user_service.py`
-- ❌ WRONG: `- [ ] Create User model` (missing ID and Story label)
-- ❌ WRONG: `T001 [US1] Create model` (missing checkbox)
-- ❌ WRONG: `- [ ] [US1] Create User model` (missing Task ID)
-- ❌ WRONG: `- [ ] T001 [US1] Create model` (missing file path)
-
-### Task Organization
-
-1. **From User Stories (spec.md)** - PRIMARY ORGANIZATION:
-   - Each user story (P1, P2, P3...) gets its own phase
-   - Map all related components to their story:
-     - Models needed for that story
-     - Services needed for that story
-     - Endpoints/UI needed for that story
-     - If tests requested: Tests specific to that story
-   - Mark story dependencies (most stories should be independent)
-
-2. **From Contracts**:
-   - Map each contract/endpoint → to the user story it serves
-   - If tests requested: Each contract → contract test task [P] before implementation in that story's phase
-
-3. **From Data Model**:
-   - Map each entity to the user story(ies) that need it
-   - If entity serves multiple stories: Put in earliest story or Setup phase
-   - Relationships → service layer tasks in appropriate story phase
-
-4. **From Setup/Infrastructure**:
-   - Shared infrastructure → Setup phase (Phase 1)
-   - Foundational/blocking tasks → Foundational phase (Phase 2)
-   - Story-specific setup → within that story's phase
-
-### Phase Structure
-
-- **Phase 1**: Setup (project initialization)
-- **Phase 2**: Foundational (blocking prerequisites - MUST complete before user stories)
-- **Phase 3+**: User Stories in priority order (P1, P2, P3...)
-  - Within each story: Tests (if requested) → Models → Services → Endpoints → Integration
-  - Each phase should be a complete, independently testable increment
-- **Final Phase**: Polish & Cross-Cutting Concerns

nextflow/.claude/commands/speckit.taskstoissues.md

@@ -1,28 +0,0 @@
----
-description: Convert existing tasks into actionable, dependency-ordered GitHub issues for the feature based on available design artifacts.
-tools: ['github/github-mcp-server/issue_write']
----
-
-## User Input
-
-```text
-$ARGUMENTS
-```
-
-You **MUST** consider the user input before proceeding (if not empty).
-
-## Outline
-
-1. Run `.specify/scripts/bash/check-prerequisites.sh --json --require-tasks --include-tasks` from repo root and parse FEATURE_DIR and AVAILABLE_DOCS list. All paths must be absolute. For single quotes in args like "I'm Groot", use escape syntax: e.g 'I'\''m Groot' (or double-quote if possible: "I'm Groot").
-1. From the executed script, extract the path to **tasks**.
-1. Get the Git remote by running:
-
-```bash
-git config --get remote.origin.url
-```
-
-**ONLY PROCEED TO NEXT STEPS IF THE REMOTE IS A GITHUB URL**
-
-1. For each task in the list, use the GitHub MCP server to create a new issue in the repository that is representative of the Git remote.
-
-**UNDER NO CIRCUMSTANCES EVER CREATE ISSUES IN REPOSITORIES THAT DO NOT MATCH THE REMOTE URL**

nextflow/.codespellrc

@@ -1,6 +0,0 @@
-[codespell]
-skip = .git,*.pdf,*.svg,timeline-expected.html,*.fq,*.min.js,ScriptDslTest.groovy
-# some cases where we need to catch using regex
-ignore-regex = \bhel\*|fo\\
-# some variables, names, etc to ignore
-ignore-words-list = splitted,ois,tre,marge,smoot,afile,bams,bais,pre-pending,re-use

nextflow/.editorconfig

@@ -1,8 +0,0 @@
-[*]
-charset = utf-8
-indent_size = 4
-indent_style = space
-tab_width = 4
-end_of_line = lf
-insert_final_newline = true
-trim_trailing_whitespace = true

nextflow/.github/CODEOWNERS

@@ -1,7 +0,0 @@
-# DOCUMENTATION -------------------------------------------------------
-# Docs folder ownership
-/docs/ @nextflow-io/docs
-
-# COMPILER ------------------------------------------------------------
-# nf-lang module
-/modules/nf-lang/ @nextflow-io/lang 

nextflow/.github/ISSUE_TEMPLATE/bug_report.md

@@ -1,31 +0,0 @@
----
-name: Bug report
-about: Report a bug to help us improve
----
-
-## Bug report 
-
-(Please follow this template by replacing the text between parentheses with the requested information)
-
-### Expected behavior and actual behavior
-
-(Give a brief description of the expected behavior and actual behavior)
-
-### Steps to reproduce the problem
-
-(Provide a test case that reproduces the problem either with a self-contained script or GitHub repository)
-
-### Program output 
-
-(Copy and paste the output produced by the failing execution. Please highlight it as a code block. Whenever possible upload the `.nextflow.log` file.)
-
-### Environment 
-
-* Nextflow version: [?] 
-* Java version: [?]
-* Operating system: [macOS, Linux, etc]
-* Bash version: (use the command `$SHELL --version`)
-
-### Additional context
-
-(Add any other context about the problem here)

nextflow/.github/ISSUE_TEMPLATE/config.yml

@@ -1,11 +0,0 @@
-blank_issues_enabled: false
-contact_links:
-  - name: General question
-    url: https://community.seqera.io/nextflow
-    about: Ask for help with Nextflow language and usage
-  - name: Nextflow official website
-    url: https://nextflow.io/
-    about: Documentation and tutorials
-  - name: Nextflow training
-    url: https://training.nextflow.io/
-    about: Learn Nextflow with hands-on tutorials

nextflow/.github/ISSUE_TEMPLATE/new_feature.md

@@ -1,16 +0,0 @@
----
-name: New feature
-about: Propose a new feature or enhancement
----
-
-## New feature
-
-(Hi! Thanks for using Nextflow and for proposing a new feature or enhancement. Please replace this text with a brief description of your proposal.)
-
-## Use case 
-
-(What's the main use case and deployment scenario addressed by this proposal)
-
-## Suggested implementation 
-
-(Highlight the main building blocks of a possible implementation and/or related components)

nextflow/.github/PULL_REQUEST_TEMPLATE/pull_request_template.md

@@ -1,7 +0,0 @@
-Hi! Thanks for contributing to Nextflow.
-
-When submitting a Pull Request, please sign-off the DCO [1] to certify that you are the author of the contribution and you adhere to Nextflow's open source license [2] by adding a `Signed-off-by` line to the contribution commit message. See [3] for more details.
-
-1. https://developercertificate.org/
-2. https://github.com/nextflow-io/nextflow/blob/master/COPYING
-3. https://github.com/apps/dco

nextflow/.github/workflows/README.md

@@ -1,15 +0,0 @@
-# Action 
-
-## Syntax
-
-https://help.github.com/en/articles/workflow-syntax-for-github-actions
-https://help.github.com/en/articles/contexts-and-expression-syntax-for-github-actions
-https://help.github.com/en/articles/virtual-environments-for-github-actions#environment-variables
-https://help.github.com/en/articles/configuring-docker-for-use-with-github-package-registry
-https://help.github.com/en/articles/virtual-environments-for-github-actions#creating-and-using-secrets-encrypted-variables
-
-## Java 
-
-Java VMs has to match the ones at this link https://static.azul.com/zulu/bin 
-
-Check the name *-jdk(x.y.z)

nextflow/.github/workflows/build.yml

@@ -1,296 +0,0 @@
-name: Nextflow CI
-# read more here: https://help.github.com/en/articles/workflow-syntax-for-github-actions#on
-
-# Note: We don't use the `on: path` option for docs,
-# because the Build steps are *required* tests.
-# Instead, we trigger + skip the tests if the only changes
-# are in the docs folder. GitHub treats this as passing.
-
-on:
-  push:
-    branches:
-      - 'master'
-      - 'test*'
-      - 'dev*'
-      - 'STABLE-*'
-  pull_request:
-    types: [opened, reopened, synchronize]
-  workflow_dispatch:
-
-jobs:
-  build:
-    name: Build
-    runs-on: ubuntu-latest
-    timeout-minutes: 100
-    strategy:
-      fail-fast: false
-      matrix:
-        java_version: [17, 25]
-
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v4
-        with:
-          fetch-depth: 1
-          submodules: true
-
-      - name: Get the commit message
-        id: get_commit_message
-        run: |
-            if [ "${{ github.event_name }}" = "pull_request" ]; then
-                echo "GitHub event=pull_request"
-                COMMIT_SHA="${{ github.event.pull_request.head.sha }}"
-                COMMIT_MESSAGE="$(curl -s \
-                  -H "Authorization: token ${{ secrets.GITHUB_TOKEN }}" \
-                  https://api.github.com/repos/${{ github.repository }}/commits/$COMMIT_SHA | jq -r '.commit.message' | head -n 1)"
-                echo "Commit message=$(printf "%s" "$COMMIT_MESSAGE")"
-                echo "commit_message=$(printf "%s" "$COMMIT_MESSAGE")" >> $GITHUB_OUTPUT
-            else
-                echo "GitHub event=${{ github.event_name }}"
-                # Extract only the first line of the commit message
-                COMMIT_MESSAGE="$(git log -1 --pretty=format:'%s')"
-                echo "Commit message=$(printf "%s" "$COMMIT_MESSAGE")"
-                echo "commit_message=$(printf "%s" "$COMMIT_MESSAGE")" >> $GITHUB_OUTPUT
-            fi
-
-      - name: Setup env
-        run: |
-             rm -f $HOME/.gitconfig;
-             mkdir -p "$HOME/.nextflow";
-             echo "providers.github.auth='$NXF_GITHUB_ACCESS_TOKEN'" > "$HOME/.nextflow/scm"
-        env:
-          NXF_GITHUB_ACCESS_TOKEN: ${{ secrets.NXF_GITHUB_ACCESS_TOKEN }}
-
-      - name: Setup Java ${{ matrix.java_version }}
-        uses: actions/setup-java@v4
-        with:
-          java-version: ${{matrix.java_version}}
-          distribution: 'temurin'
-          architecture: x64
-          cache: gradle
-
-      - name: Compile
-        run: make assemble
-
-      - name: Test
-        run: |
-            env | sort
-            # configure test env
-            if [[ "$GOOGLE_SECRET" ]]; then
-            echo $GOOGLE_SECRET | base64 -d > $PWD/google_credentials.json
-            export GOOGLE_APPLICATION_CREDENTIALS=$PWD/google_credentials.json
-            fi
-            # run tests
-            make test
-        env:
-          AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
-          AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
-          AWS_S3FS_ACCESS_KEY: ${{ secrets.AWS_ACCESS_KEY_ID }}
-          AWS_S3FS_SECRET_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
-          NXF_BITBUCKET_ACCESS_TOKEN: ${{ secrets.NXF_BITBUCKET_ACCESS_TOKEN }}
-          NXF_GITHUB_ACCESS_TOKEN: ${{ secrets.NXF_GITHUB_ACCESS_TOKEN }}
-          NXF_GITLAB_ACCESS_TOKEN: ${{ secrets.NXF_GITLAB_ACCESS_TOKEN }}
-          NXF_AZURE_REPOS_TOKEN: ${{ secrets.NXF_AZURE_REPOS_TOKEN }}
-          GOOGLE_SECRET: ${{ secrets.GOOGLE_SECRET }}
-          AZURE_STORAGE_ACCOUNT_NAME: nfazurestore
-          AZURE_STORAGE_ACCOUNT_KEY: ${{ secrets.AZURE_STORAGE_ACCOUNT_KEY }}
-          AZURE_BATCH_ACCOUNT_NAME: nfbatchtest
-          AZURE_BATCH_ACCOUNT_KEY: ${{ secrets.AZURE_BATCH_ACCOUNT_KEY }}
-
-      - name: Publish tests report
-        if: always()
-        uses: actions/upload-artifact@v4
-        with:
-          name: report-unit-tests-jdk-${{ matrix.java_version }}
-          path: |
-            **/build/reports/tests/test
-
-    outputs:
-      commit_message: ${{ steps.get_commit_message.outputs.commit_message }}
-
-  test:
-    if: ${{ !contains(needs.build.outputs.commit_message, '[ci fast]') }}
-    needs: build
-    runs-on: ubuntu-latest
-    timeout-minutes: 90
-    strategy:
-      fail-fast: false
-      matrix:
-        java_version: [17, 25]
-        test_mode: ["test_integration", "test_parser_v2", "test_docs", "test_aws", "test_azure", "test_google", "test_wave"]
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v4
-        with:
-          fetch-depth: 1
-          submodules: true
-
-      - name: Setup env
-        run: |
-          rm -f $HOME/.gitconfig;
-          mkdir -p "$HOME/.nextflow";
-          echo "providers.github.auth='$NXF_GITHUB_ACCESS_TOKEN'" > "$HOME/.nextflow/scm"
-        env:
-          NXF_GITHUB_ACCESS_TOKEN: ${{ secrets.NXF_GITHUB_ACCESS_TOKEN }}
-
-      - name: Setup Java ${{ matrix.java_version }}
-        uses: actions/setup-java@v4
-        with:
-          java-version: ${{matrix.java_version}}
-          distribution: 'temurin'
-          architecture: x64
-          cache: gradle
-
-      - name: Run tests
-        run: |
-          env | sort
-          # configure test env
-          if [[ "$GOOGLE_SECRET" ]]; then
-          echo $GOOGLE_SECRET | base64 -d > $PWD/google_credentials.json
-          export GOOGLE_APPLICATION_CREDENTIALS=$PWD/google_credentials.json
-          fi
-          cat $HOME/.nextflow/scm
-          make clean assemble install
-          bash test-ci.sh
-        env:
-          TEST_JDK: ${{ matrix.java_version }}
-          TEST_MODE: ${{ matrix.test_mode }}
-          GRADLE_OPTS: '-Dorg.gradle.daemon=false'
-          TOWER_ACCESS_TOKEN: ${{ secrets.TOWER_ACCESS_TOKEN }}
-          AWS_DEFAULT_REGION: eu-west-1
-          AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
-          AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
-          NXF_BITBUCKET_ACCESS_TOKEN: ${{ secrets.NXF_BITBUCKET_ACCESS_TOKEN }}
-          NXF_GITHUB_ACCESS_TOKEN: ${{ secrets.NXF_GITHUB_ACCESS_TOKEN }}
-          NXF_GITLAB_ACCESS_TOKEN: ${{ secrets.NXF_GITLAB_ACCESS_TOKEN }}
-          NXF_AZURE_REPOS_TOKEN: ${{ secrets.NXF_AZURE_REPOS_TOKEN }}
-          GOOGLE_SECRET: ${{ secrets.GOOGLE_SECRET }}
-          AZURE_STORAGE_ACCOUNT_NAME: nfazurestore
-          AZURE_STORAGE_ACCOUNT_KEY: ${{ secrets.AZURE_STORAGE_ACCOUNT_KEY }}
-          AZURE_BATCH_ACCOUNT_NAME: nfbatchtest
-          AZURE_BATCH_ACCOUNT_KEY: ${{ secrets.AZURE_BATCH_ACCOUNT_KEY }}
-
-      - name: Tar integration tests
-        if: always()
-        run: | 
-            tar -cvf integration-tests.tar.gz tests/checks
-            tar -cvf validation-tests.tar.gz validation
-
-      - name: Publish tests report
-        uses: actions/upload-artifact@v4
-        if: always()
-        with:
-          name: report-${{ matrix.test_mode }}-jdk-${{ matrix.java_version }}
-          path: |
-            validation-tests.tar.gz
-            integration-tests.tar.gz
-
-  test-e2e:
-      if: ${{ contains(needs.build.outputs.commit_message,'[e2e stage]') || contains(needs.build.outputs.commit_message,'[e2e prod]') }}
-      needs: build
-      runs-on: ubuntu-latest
-      timeout-minutes: 10
-      permissions:
-          actions: write  # Allow writing to actions
-          contents: write # Allow writing to repository contents
-      steps:
-          - name: Checkout
-            uses: actions/checkout@v4
-            with:
-                fetch-depth: 1
-                submodules: true
-                
-          - name: Setup Java 17
-            uses: actions/setup-java@v4
-            with:
-                java-version: 17
-                distribution: 'temurin'
-                architecture: x64
-                cache: gradle
-
-          - name: Setup env
-            run: |
-                wget -q -O wave https://github.com/seqeralabs/wave-cli/releases/download/v1.4.1/wave-1.4.1-linux-x86_64
-                chmod +x wave
-                mv wave /usr/local/bin/
-                echo "COMMIT_MESSAGE=\"${{ needs.build.outputs.commit_message }}\"" >> $GITHUB_ENV
-
-          - name : Docker Login to Seqera public CR
-            uses : docker/login-action@v3
-            with :
-                registry : "public.cr.seqera.io"
-                username : "public-cr-admin"
-                password : ${{ secrets.SEQERA_PUBLIC_CR_PASSWORD }}
-
-          - name: Launch tests
-            run: |
-                cd test-e2e
-                bash run.sh
-            env:
-                GITHUB_TOKEN: ${{ secrets.AUTOMATION_GITHUB_TOKEN }}
-                GRADLE_OPTS: '-Dorg.gradle.daemon=false'
-
-  release:
-    if: ${{ always() && contains(needs.build.outputs.commit_message, '[release]') && needs.build.result == 'success' && (needs.test.result == 'success' || needs.test.result == 'skipped') }}
-    needs: [build, test]
-    runs-on: ubuntu-latest
-    timeout-minutes: 10
-    permissions:
-      actions: write
-      contents: write
-      packages: write
-      pull-requests: write
-      issues: write
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v4
-        with:
-          fetch-depth: 0
-          submodules: true
-
-      - name: Setup Java 17
-        uses: actions/setup-java@v4
-        with:
-          java-version: 17
-          distribution: 'temurin'
-          architecture: x64
-          cache: gradle
-
-      - name: Configure Git
-        run: |
-          git config --global user.name "${{ github.event.pusher.name || github.actor }}"
-          git config --global user.email "${{ github.event.pusher.email || format('{0}@users.noreply.github.com', github.actor) }}"
-
-      - name: Docker Login to Docker Hub
-        uses: docker/login-action@v3
-        with:
-          username: ${{ vars.DOCKERHUB_USERNAME }}
-          password: ${{ secrets.DOCKERHUB_TOKEN }}
-
-      - name: Docker Login to Seqera public CR
-        uses: docker/login-action@v3
-        with:
-          registry: "public.cr.seqera.io"
-          username: ${{ vars.SEQERA_PUBLIC_CR_USERNAME }}
-          password: ${{ secrets.SEQERA_PUBLIC_CR_PASSWORD }}
-
-      - name: Run release
-        run: |
-          echo "Starting release process..."
-          echo "npr.apiUrl=$NPR_API_URL" >> gradle.properties
-          echo "npr.apiKey=$NPR_API_KEY" >> gradle.properties
-          bash release.sh
-        env:
-          GRADLE_OPTS: '-Dorg.gradle.daemon=false'
-          AWS_JAVA_V1_DISABLE_DEPRECATION_ANNOUNCEMENT: 'true'
-          # credentials to pubslish nextflow assets
-          NXF_AWS_ACCESS: ${{ vars.NXF_AWS_ACCESS }}
-          NXF_AWS_SECRET: ${{ secrets.NXF_AWS_SECRET }}
-          # credentials to publish maven libraries
-          AWS_ACCESS_KEY_ID: ${{ vars.SEQERA_MAVEN_ACCESS_KEY }}
-          AWS_SECRET_ACCESS_KEY: ${{ secrets.SEQERA_MAVEN_SECRET_KEY }}
-          # plugin registry
-          NPR_API_URL: ${{ vars.NPR_API_URL }}
-          NPR_API_KEY: ${{ secrets.NPR_API_KEY }}
-          # GitHub secrets
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

nextflow/.github/workflows/cffconvert.yml

@@ -1,19 +0,0 @@
-name: cffconvert
-
-on:
-  push:
-    paths:
-      - CITATION.cff
-
-jobs:
-  validate:
-    name: "validate"
-    runs-on: ubuntu-latest
-    steps:
-      - name: Check out a copy of the repository
-        uses: actions/checkout@v4
-
-      - name: Check whether the citation metadata from CITATION.cff is valid
-        uses: citation-file-format/cffconvert-github-action@2.0.0
-        with:
-          args: "--validate"

nextflow/.github/workflows/claude.yml

@@ -1,36 +0,0 @@
-name: Claude PR Assistant
-
-on:
-  issue_comment:
-    types: [created]
-  pull_request_review_comment:
-    types: [created]
-  issues:
-    types: [opened, assigned]
-  pull_request_review:
-    types: [submitted]
-
-jobs:
-  claude-code-action:
-    if: |
-      (github.event_name == 'issue_comment' && contains(github.event.comment.body, '@claude')) ||
-      (github.event_name == 'pull_request_review_comment' && contains(github.event.comment.body, '@claude')) ||
-      (github.event_name == 'pull_request_review' && contains(github.event.review.body, '@claude')) ||
-      (github.event_name == 'issues' && contains(github.event.issue.body, '@claude'))
-    runs-on: ubuntu-latest
-    permissions:
-      contents: read
-      pull-requests: read
-      issues: read
-      id-token: write
-    steps:
-      - name: Checkout repository
-        uses: actions/checkout@v4
-        with:
-          fetch-depth: 1
-
-      - name: Run Claude PR Action
-        uses: anthropics/claude-code-action@beta
-        with:
-          anthropic_api_key: ${{ secrets.NEXTFLOW_ANTHROPIC_API_KEY }}
-          timeout_minutes: "60"

nextflow/.github/workflows/docs.yml

@@ -1,22 +0,0 @@
-name: Docs CI
-on:
-  pull_request:
-    types: [opened, reopened, synchronize]
-    paths:
-      - 'docs/**'
-  workflow_dispatch:
-jobs:
-  docs-build:
-    name: Build
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v4
-        with:
-          python-version: '3.9'
-
-      - name: Test docs build
-        run: |
-          cd docs/
-          pip install -r requirements.txt
-          make clean html

nextflow/.github/workflows/stale.yml

@@ -1,21 +0,0 @@
-name: 'Mark stale issues and PRs'
-on:
-  schedule:
-    - cron: '30 1 * * *'
-  workflow_dispatch:
-
-jobs:
-  stale:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/stale@v9
-        with:
-          days-before-stale: 180
-          days-before-close: -1
-          stale-issue-label: stale
-          stale-issue-message: ''
-          stale-pr-label: stale
-          stale-pr-message: ''
-          exempt-issue-labels: bug,planned,security
-          exempt-all-milestones: true
-          exempt-all-assignees: true

nextflow/.gitignore

@@ -1,48 +0,0 @@
-.idea/**
-.gradle
-.*.log*
-.cache/*
-.vagrant/*
-.cache/*
-.nextflow*
-.node-nextflow*
-.devcontainer
-.vscode/*
-.lineage/
-*/*/bin/*
-**/build/**
-build/**
-modules/**/build/
-modules/**/*.iml
-modules/nextflow/work/
-**/out/*
-tmp/*
-work/*
-nextflow.eml
-nextflow.iml
-Vagrantfile
-resources/*
-test/*
-tools/*
-tests_other
-other
-docs/_build/
-./*.txt
-errors/
-misc/
-cloud/my-*
-docker-test
-docker/dist
-docker/nextflow
-temp
-.dockerignore
-.launch.classpath
-plugins-prod
-/minio
-/sandbox
-/wave-tests
-/test-sched
-/test-module
-/results
-/x/*
-mise.toml

nextflow/.specify/memory/constitution.md

@@ -1,198 +0,0 @@
-# Nextflow Development Constitution
-
-<!--
-SYNC IMPACT REPORT
-==================
-Version Change: INITIAL → 1.0.0 (Initial constitution)
-Modified Principles: N/A (new constitution)
-Added Sections:
-  - All principles (I-VII)
-  - Development Workflow
-  - Quality Standards
-  - Governance
-
-Removed Sections: N/A (initial version)
-
-Templates Status:
-  ✅ plan-template.md - Reviewed, aligned with modular architecture and testing principles
-  ✅ spec-template.md - Reviewed, aligned with user scenario focus and requirements structure
-  ✅ tasks-template.md - Reviewed, aligned with test-driven and parallel development principles
-  ✅ agent-file-template.md - Reviewed, no agent-specific conflicts
-  ✅ checklist-template.md - Reviewed, compatible with quality standards
-
-Follow-up TODOs:
-  - None at this time
-==================
--->
-
-## Core Principles
-
-### I. Modular Architecture
-
-Nextflow MUST maintain a clear separation between core functionality and extensions through its modular architecture:
-
-- **Core modules** (`modules/`) contain essential functionality: core workflow runtime & plugin system (nextflow), shared utilities (nf-commons), language parsing (nf-lang), HTTP filesystem support (nf-httpfs), and lineage tracking (nf-lineage)
-- **Core plugins** (`plugins/`) provides cloud provider integrations (AWS, Azure, GCP), execution platforms (Kubernetes), and specialized services (Seqera Platform, Wave container management)
-- New features MUST be evaluated for placement: core features belong in `modules/`, specialized/cloud-specific features belong in `plugins/`
-- Each module and plugin MUST be independently buildable and testable
-- Plugin dependencies MUST be explicitly declared in `build.gradle` with semantic versioning
-
-**Rationale**: This architecture enables independent development of cloud provider features without core engine changes, supports third-party plugin development, and maintains a clean separation of concerns across a large multi-module codebase.
-
-### II. Test-Driven Quality Assurance (NON-NEGOTIABLE)
-
-Testing MUST be comprehensive and multi-layered before any code is merged:
-
-- **Unit tests** MUST use Spock Framework for all Groovy code, be independently executable, and achieve meaningful coverage (measured via JaCoCo)
-- **Integration tests** (`tests/` directory) MUST validate end-to-end workflows using actual `.nf` scripts with expected outputs
-- **Smoke tests** (`make smoke` or `NXF_SMOKE=1`) MUST be available to skip long-running and cloud-dependent tests during rapid development
-- **Cloud validation tests** (`validation/` directory) MUST verify cloud provider integrations end-to-end before release
-- **Documentation tests** (`docs/snippets/`) MUST ensure all documentation examples remain functional
-- All tests MUST pass before commits, and `make test` MUST be run locally before pushing
-
-**Rationale**: Scientific workflows demand reliability and reproducibility. Multi-layered testing catches issues at appropriate levels: unit tests for logic, integration tests for workflow correctness, and validation tests for cloud provider compatibility.
-
-### III. Dataflow Programming Model
-
-Nextflow's core abstraction MUST adhere to following principles and guidelines:
-
-- The dataflow programming model is the fundamental abstraction in the Nextflow programming model.
-- Workflows are defined as dataflow graphs where data flows between processes.
-- Processes MUST be stateless, side-effect-free transformations that communicate via channels.
-- Workflows should be defined in a platform agnostic manner to enable portability across clusters and clouds.
-- The DSL MUST prioritize expressiveness for concurrent and parallel pipeline definition.
-- Changes to the language parser (ANTLR grammars in `nf-lang`) MUST preserve backward compatibility with existing pipelines unless explicitly versioned (DSL1 vs DSL2).
-- Concurrency primitives (GPars actors/dataflow) MUST be used correctly to maintain the dataflow semantics.
-
-**Rationale**: The dataflow model is Nextflow's fundamental abstraction, enabling automatic parallelization and distribution. Preserving this model ensures existing scientific pipelines continue to work and users can reason about workflow behavior.
-
-### IV. Apache 2.0 License Compliance
-
-All source code MUST include Apache 2.0 license headers:
-
-- Every source file MUST begin with the Apache 2.0 license header
-- All contributions MUST comply with Apache 2.0 terms
-- Third-party dependencies MUST use compatible licenses
-- License compliance MUST be verified during code review
-
-**Rationale**: Legal clarity protects both contributors and users. Consistent licensing enables academic and commercial use, which is critical for scientific software adoption.
-
-### V. Developer Certificate of Origin (DCO) Sign-off
-
-All commits MUST be signed with DCO certification:
-
-- Contributors MUST certify they have the right to submit the code by using `git commit -s` or `git commit --signoff`
-- Every commit message MUST include a `Signed-off-by` line
-- The DCO bot MUST verify sign-off before any PR can be merged
-- Contributors MUST NOT bypass the DCO requirement
-
-**Rationale**: DCO provides legal protection and clear chain of custody for contributions, which is essential for open-source projects with diverse contributors.
-
-### VI. Semantic Versioning and Release Discipline
-
-Version management MUST follow strict semantic versioning with calendar-based releases:
-
-- **Project versions** use calendar-based scheme: `YY.MM.PATCH` where April (`.04.`) and October (`.10.`) are stable releases, all other months use `-edge` suffix (e.g., `25.09.0-edge`)
-- **Plugin versions** MUST use semantic versioning (`MAJOR.MINOR.PATCH`)
-- Version changes MUST be documented in `changelog.txt` files (both project root and per-plugin)
-- Breaking changes MUST increment MAJOR version for plugins and be clearly documented
-- Release process MUST follow the documented procedure in `CLAUDE.md` including: updating changelogs, version files, running `make releaseInfo`, using `[release]` tag in commit message
-
-**Rationale**: Predictable versioning enables users to understand compatibility and stability expectations. Calendar-based versioning for the main project makes release timing transparent, while semantic versioning for plugins enables clear communication of breaking changes.
-
-### VII. Groovy Idioms and Code Standards
-
-Code MUST follow Groovy best practices and Nextflow conventions:
-
-- Use Groovy idioms (closures, operator overloading, DSL builders) appropriately
-- Follow existing code patterns and conventions from similar modules
-- Leverage Groovy's dynamic capabilities judiciously without sacrificing type safety where beneficial
-- Use Groovy's `@CompileStatic` where performance is critical or type safety is desired
-- AST transformations (in `modules/nextflow`) MUST be well-documented due to their compile-time magic
-- Code MUST be formatted consistently (consider CodeNarc configuration in `gradle/codenarc.groovy`)
-
-**Rationale**: Groovy enables powerful DSL capabilities that make Nextflow's language expressive, but requires discipline to maintain readability and debuggability. Consistency across the large codebase improves maintainability.
-
-## Development Workflow
-
-### Build and Development Process
-
-- **Build tool**: Gradle with wrapper (`./gradlew`) is the authoritative build system
-- **Quick commands**: Makefile provides convenience targets (`make compile`, `make test`, `make assemble`, `make check`, `make clean`)
-- **Development testing**: Use `./launch.sh run script.nf` for testing changes against real workflows without full installation
-- **Local installation**: `make install` publishes to Maven local for integration testing
-- **Dependency management**: All dependencies MUST be declared in `build.gradle` with explicit versions; use `make deps` to analyze dependency trees
-
-### Git Workflow
-
-- **Branch management**: Work on feature branches, never commit directly to `master`
-- **Commit sign-off**: Always use `git commit -s` to add DCO sign-off
-- **CI control tags**: Use special commit message tags to control CI behavior:
-  - `[ci skip]` - Skip CI tests entirely
-  - `[ci fast]` - Run only unit tests, skip integration tests
-  - `[e2e stage]` - Run end-to-end tests against Seqera platform staging environment
-  - `[e2e prod]` - Run end-to-end tests against production platform
-  - `[release]` - Trigger release automation
-- **Pull requests**: Must pass all CI checks, require code review, and have DCO verification
-
-### Architecture Decision Records (ADRs)
-
-- Significant structural and technical decisions MUST be documented as ADRs in the `adr/` directory
-- ADRs MUST follow the template format: date prefix + descriptive name (e.g., `20251114-module-system.md`)
-- ADRs provide historical context for why architectural decisions were made
-- When changing fundamental architecture, review existing ADRs and create new ones documenting the rationale
-
-## Quality Standards
-
-### Code Review Requirements
-
-- All changes MUST go through pull request review
-- Reviewers MUST verify:
-  - Tests are included and passing
-  - Code follows Groovy idioms and project conventions
-  - License headers are present
-  - DCO sign-off is present
-  - Changes align with modular architecture principles
-  - Breaking changes are appropriately versioned and documented
-
-### Testing Gates
-
-- `make test` MUST pass before committing locally
-- All CI tests MUST pass before merging
-- Integration tests MUST be run for changes affecting workflow execution
-- Cloud validation tests MUST be run before releases touching cloud provider plugins
-- Smoke tests enable rapid iteration but MUST NOT replace full test execution
-
-### Performance and Compatibility
-
-- Target platform: Java 17 runtime compatibility (development uses Java 21 toolchain)
-- Performance-critical paths SHOULD be profiled and optimized
-- Memory usage SHOULD be monitored for large-scale workflows
-- Backward compatibility MUST be maintained for existing DSL features unless a new DSL version is introduced
-
-## Governance
-
-### Amendment Process
-
-This constitution supersedes all other development practices. Amendments require:
-
-1. **Proposal**: Submit amendment proposal via GitHub issue or pull request
-2. **Discussion**: Community discussion period (minimum 1 week for major changes)
-3. **Approval**: Approval from core maintainers
-4. **Documentation**: Update this constitution with version bump following semantic versioning:
-   - **MAJOR**: Backward incompatible governance changes, principle removal/redefinition
-   - **MINOR**: New principle added or materially expanded guidance
-   - **PATCH**: Clarifications, wording improvements, typo fixes
-
-### Compliance and Review
-
-- All pull requests and code reviews MUST verify compliance with these principles
-- Deviations from principles MUST be explicitly justified in PR description
-- Complexity additions MUST be justified against the "simplicity first" principle
-- Constitution compliance is enforced through code review and CI automation where possible
-
-### Ratification and Version History
-
-**Version**: 1.0.0 | **Ratified**: 2025-11-17 | **Last Amended**: 2025-11-17
-
-This constitution was derived from the Nextflow project's documented practices in `CLAUDE.md`, `CONTRIBUTING.md`, and the project's existing architectural patterns. It codifies the development principles that have made Nextflow a successful scientific workflow management system.

nextflow/.specify/scripts/bash/check-prerequisites.sh

@@ -1,166 +0,0 @@
-#!/usr/bin/env bash
-
-# Consolidated prerequisite checking script
-#
-# This script provides unified prerequisite checking for Spec-Driven Development workflow.
-# It replaces the functionality previously spread across multiple scripts.
-#
-# Usage: ./check-prerequisites.sh [OPTIONS]
-#
-# OPTIONS:
-#   --json              Output in JSON format
-#   --require-tasks     Require tasks.md to exist (for implementation phase)
-#   --include-tasks     Include tasks.md in AVAILABLE_DOCS list
-#   --paths-only        Only output path variables (no validation)
-#   --help, -h          Show help message
-#
-# OUTPUTS:
-#   JSON mode: {"FEATURE_DIR":"...", "AVAILABLE_DOCS":["..."]}
-#   Text mode: FEATURE_DIR:... \n AVAILABLE_DOCS: \n ✓/✗ file.md
-#   Paths only: REPO_ROOT: ... \n BRANCH: ... \n FEATURE_DIR: ... etc.
-
-set -e
-
-# Parse command line arguments
-JSON_MODE=false
-REQUIRE_TASKS=false
-INCLUDE_TASKS=false
-PATHS_ONLY=false
-
-for arg in "$@"; do
-    case "$arg" in
-        --json)
-            JSON_MODE=true
-            ;;
-        --require-tasks)
-            REQUIRE_TASKS=true
-            ;;
-        --include-tasks)
-            INCLUDE_TASKS=true
-            ;;
-        --paths-only)
-            PATHS_ONLY=true
-            ;;
-        --help|-h)
-            cat << 'EOF'
-Usage: check-prerequisites.sh [OPTIONS]
-
-Consolidated prerequisite checking for Spec-Driven Development workflow.
-
-OPTIONS:
-  --json              Output in JSON format
-  --require-tasks     Require tasks.md to exist (for implementation phase)
-  --include-tasks     Include tasks.md in AVAILABLE_DOCS list
-  --paths-only        Only output path variables (no prerequisite validation)
-  --help, -h          Show this help message
-
-EXAMPLES:
-  # Check task prerequisites (plan.md required)
-  ./check-prerequisites.sh --json
-  
-  # Check implementation prerequisites (plan.md + tasks.md required)
-  ./check-prerequisites.sh --json --require-tasks --include-tasks
-  
-  # Get feature paths only (no validation)
-  ./check-prerequisites.sh --paths-only
-  
-EOF
-            exit 0
-            ;;
-        *)
-            echo "ERROR: Unknown option '$arg'. Use --help for usage information." >&2
-            exit 1
-            ;;
-    esac
-done
-
-# Source common functions
-SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
-source "$SCRIPT_DIR/common.sh"
-
-# Get feature paths and validate branch
-eval $(get_feature_paths)
-check_feature_branch "$CURRENT_BRANCH" "$HAS_GIT" || exit 1
-
-# If paths-only mode, output paths and exit (support JSON + paths-only combined)
-if $PATHS_ONLY; then
-    if $JSON_MODE; then
-        # Minimal JSON paths payload (no validation performed)
-        printf '{"REPO_ROOT":"%s","BRANCH":"%s","FEATURE_DIR":"%s","FEATURE_SPEC":"%s","IMPL_PLAN":"%s","TASKS":"%s"}\n' \
-            "$REPO_ROOT" "$CURRENT_BRANCH" "$FEATURE_DIR" "$FEATURE_SPEC" "$IMPL_PLAN" "$TASKS"
-    else
-        echo "REPO_ROOT: $REPO_ROOT"
-        echo "BRANCH: $CURRENT_BRANCH"
-        echo "FEATURE_DIR: $FEATURE_DIR"
-        echo "FEATURE_SPEC: $FEATURE_SPEC"
-        echo "IMPL_PLAN: $IMPL_PLAN"
-        echo "TASKS: $TASKS"
-    fi
-    exit 0
-fi
-
-# Validate required directories and files
-if [[ ! -d "$FEATURE_DIR" ]]; then
-    echo "ERROR: Feature directory not found: $FEATURE_DIR" >&2
-    echo "Run /speckit.specify first to create the feature structure." >&2
-    exit 1
-fi
-
-if [[ ! -f "$IMPL_PLAN" ]]; then
-    echo "ERROR: plan.md not found in $FEATURE_DIR" >&2
-    echo "Run /speckit.plan first to create the implementation plan." >&2
-    exit 1
-fi
-
-# Check for tasks.md if required
-if $REQUIRE_TASKS && [[ ! -f "$TASKS" ]]; then
-    echo "ERROR: tasks.md not found in $FEATURE_DIR" >&2
-    echo "Run /speckit.tasks first to create the task list." >&2
-    exit 1
-fi
-
-# Build list of available documents
-docs=()
-
-# Always check these optional docs
-[[ -f "$RESEARCH" ]] && docs+=("research.md")
-[[ -f "$DATA_MODEL" ]] && docs+=("data-model.md")
-
-# Check contracts directory (only if it exists and has files)
-if [[ -d "$CONTRACTS_DIR" ]] && [[ -n "$(ls -A "$CONTRACTS_DIR" 2>/dev/null)" ]]; then
-    docs+=("contracts/")
-fi
-
-[[ -f "$QUICKSTART" ]] && docs+=("quickstart.md")
-
-# Include tasks.md if requested and it exists
-if $INCLUDE_TASKS && [[ -f "$TASKS" ]]; then
-    docs+=("tasks.md")
-fi
-
-# Output results
-if $JSON_MODE; then
-    # Build JSON array of documents
-    if [[ ${#docs[@]} -eq 0 ]]; then
-        json_docs="[]"
-    else
-        json_docs=$(printf '"%s",' "${docs[@]}")
-        json_docs="[${json_docs%,}]"
-    fi
-    
-    printf '{"FEATURE_DIR":"%s","AVAILABLE_DOCS":%s}\n' "$FEATURE_DIR" "$json_docs"
-else
-    # Text output
-    echo "FEATURE_DIR:$FEATURE_DIR"
-    echo "AVAILABLE_DOCS:"
-    
-    # Show status of each potential document
-    check_file "$RESEARCH" "research.md"
-    check_file "$DATA_MODEL" "data-model.md"
-    check_dir "$CONTRACTS_DIR" "contracts/"
-    check_file "$QUICKSTART" "quickstart.md"
-    
-    if $INCLUDE_TASKS; then
-        check_file "$TASKS" "tasks.md"
-    fi
-fi

nextflow/.specify/scripts/bash/common.sh

@@ -1,157 +0,0 @@
-#!/usr/bin/env bash
-# Common functions and variables for all scripts
-
-# Get repository root, with fallback for non-git repositories
-get_repo_root() {
-    if git rev-parse --show-toplevel >/dev/null 2>&1; then
-        git rev-parse --show-toplevel
-    else
-        # Fall back to script location for non-git repos
-        local script_dir="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
-        (cd "$script_dir/../../.." && pwd)
-    fi
-}
-
-# Get current branch, with fallback for non-git repositories
-get_current_branch() {
-    # First check if SPECIFY_FEATURE environment variable is set
-    if [[ -n "${SPECIFY_FEATURE:-}" ]]; then
-        echo "$SPECIFY_FEATURE"
-        return
-    fi
-
-    # Then check git if available
-    if git rev-parse --abbrev-ref HEAD >/dev/null 2>&1; then
-        git rev-parse --abbrev-ref HEAD
-        return
-    fi
-
-    # For non-git repos, try to find the latest feature directory
-    local repo_root=$(get_repo_root)
-    local specs_dir="$repo_root/specs"
-
-    if [[ -d "$specs_dir" ]]; then
-        local latest_feature=""
-        local highest=0
-
-        for dir in "$specs_dir"/*; do
-            if [[ -d "$dir" ]]; then
-                local dirname=$(basename "$dir")
-                if [[ "$dirname" =~ ^([0-9]{6})- ]]; then
-                    local number=${BASH_REMATCH[1]}
-                    number=$((10#$number))
-                    if [[ "$number" -gt "$highest" ]]; then
-                        highest=$number
-                        latest_feature=$dirname
-                    fi
-                fi
-            fi
-        done
-
-        if [[ -n "$latest_feature" ]]; then
-            echo "$latest_feature"
-            return
-        fi
-    fi
-
-    echo "main"  # Final fallback
-}
-
-# Check if we have git available
-has_git() {
-    git rev-parse --show-toplevel >/dev/null 2>&1
-}
-
-check_feature_branch() {
-    local branch="$1"
-    local has_git_repo="$2"
-
-    # For non-git repos, we can't enforce branch naming but still provide output
-    if [[ "$has_git_repo" != "true" ]]; then
-        echo "[specify] Warning: Git repository not detected; skipped branch validation" >&2
-        return 0
-    fi
-
-    # Accept date-based format (YYMMDD-feature)
-    if [[ ! "$branch" =~ ^[0-9]{6}- ]]; then
-        echo "ERROR: Not on a feature branch. Current branch: $branch" >&2
-        echo "Feature branches should be named like: YYMMDD-feature-name (e.g., 251030-nextflow-modules)" >&2
-        return 1
-    fi
-
-    return 0
-}
-
-get_feature_dir() { echo "$1/specs/$2"; }
-
-# Find feature directory by numeric prefix instead of exact branch match
-# This allows multiple branches to work on the same spec (e.g., 251030-fix-bug, 251030-add-feature)
-find_feature_dir_by_prefix() {
-    local repo_root="$1"
-    local branch_name="$2"
-    local specs_dir="$repo_root/specs"
-
-    # Extract numeric prefix from branch (e.g., "251030" from "251030-whatever")
-    if [[ ! "$branch_name" =~ ^([0-9]{6})- ]]; then
-        # If branch doesn't have numeric prefix, fall back to exact match
-        echo "$specs_dir/$branch_name"
-        return
-    fi
-
-    local prefix="${BASH_REMATCH[1]}"
-
-    # Search for directories in specs/ that start with this prefix
-    local matches=()
-    if [[ -d "$specs_dir" ]]; then
-        for dir in "$specs_dir"/"$prefix"-*; do
-            if [[ -d "$dir" ]]; then
-                matches+=("$(basename "$dir")")
-            fi
-        done
-    fi
-
-    # Handle results
-    if [[ ${#matches[@]} -eq 0 ]]; then
-        # No match found - return the branch name path (will fail later with clear error)
-        echo "$specs_dir/$branch_name"
-    elif [[ ${#matches[@]} -eq 1 ]]; then
-        # Exactly one match - perfect!
-        echo "$specs_dir/${matches[0]}"
-    else
-        # Multiple matches - this shouldn't happen with proper naming convention
-        echo "ERROR: Multiple spec directories found with prefix '$prefix': ${matches[*]}" >&2
-        echo "Please ensure only one spec directory exists per numeric prefix." >&2
-        echo "$specs_dir/$branch_name"  # Return something to avoid breaking the script
-    fi
-}
-
-get_feature_paths() {
-    local repo_root=$(get_repo_root)
-    local current_branch=$(get_current_branch)
-    local has_git_repo="false"
-
-    if has_git; then
-        has_git_repo="true"
-    fi
-
-    # Use prefix-based lookup to support multiple branches per spec
-    local feature_dir=$(find_feature_dir_by_prefix "$repo_root" "$current_branch")
-
-    cat <<EOF
-REPO_ROOT='$repo_root'
-CURRENT_BRANCH='$current_branch'
-HAS_GIT='$has_git_repo'
-FEATURE_DIR='$feature_dir'
-FEATURE_SPEC='$feature_dir/spec.md'
-IMPL_PLAN='$feature_dir/plan.md'
-TASKS='$feature_dir/tasks.md'
-RESEARCH='$feature_dir/research.md'
-DATA_MODEL='$feature_dir/data-model.md'
-QUICKSTART='$feature_dir/quickstart.md'
-CONTRACTS_DIR='$feature_dir/contracts'
-EOF
-}
-
-check_file() { [[ -f "$1" ]] && echo "  ✓ $2" || echo "  ✗ $2"; }
-check_dir() { [[ -d "$1" && -n $(ls -A "$1" 2>/dev/null) ]] && echo "  ✓ $2" || echo "  ✗ $2"; }
-

nextflow/.specify/scripts/bash/create-new-feature.sh

@@ -1,200 +0,0 @@
-#!/usr/bin/env bash
-
-set -e
-
-JSON_MODE=false
-SHORT_NAME=""
-ARGS=()
-i=1
-while [ $i -le $# ]; do
-    arg="${!i}"
-    case "$arg" in
-        --json) 
-            JSON_MODE=true 
-            ;;
-        --short-name)
-            if [ $((i + 1)) -gt $# ]; then
-                echo 'Error: --short-name requires a value' >&2
-                exit 1
-            fi
-            i=$((i + 1))
-            next_arg="${!i}"
-            # Check if the next argument is another option (starts with --)
-            if [[ "$next_arg" == --* ]]; then
-                echo 'Error: --short-name requires a value' >&2
-                exit 1
-            fi
-            SHORT_NAME="$next_arg"
-            ;;
-        --help|-h)
-            echo "Usage: $0 [--json] [--short-name <name>] <feature_description>"
-            echo ""
-            echo "Options:"
-            echo "  --json              Output in JSON format"
-            echo "  --short-name <name> Provide a custom short name (2-4 words) for the branch"
-            echo "  --help, -h          Show this help message"
-            echo ""
-            echo "Branch naming: Uses YYMMDD-<feature-name> format (e.g., 251023-user-auth)"
-            echo ""
-            echo "Examples:"
-            echo "  $0 'Add user authentication system' --short-name 'user-auth'"
-            echo "  # Creates: 251023-user-auth (if run on Oct 23, 2025)"
-            echo ""
-            echo "  $0 'Implement OAuth2 integration for API'"
-            echo "  # Creates: 251023-oauth2-integration-api"
-            exit 0
-            ;;
-        *) 
-            ARGS+=("$arg") 
-            ;;
-    esac
-    i=$((i + 1))
-done
-
-FEATURE_DESCRIPTION="${ARGS[*]}"
-if [ -z "$FEATURE_DESCRIPTION" ]; then
-    echo "Usage: $0 [--json] [--short-name <name>] <feature_description>" >&2
-    exit 1
-fi
-
-# Function to find the repository root by searching for existing project markers
-find_repo_root() {
-    local dir="$1"
-    while [ "$dir" != "/" ]; do
-        if [ -d "$dir/.git" ] || [ -d "$dir/.specify" ]; then
-            echo "$dir"
-            return 0
-        fi
-        dir="$(dirname "$dir")"
-    done
-    return 1
-}
-
-# Resolve repository root. Prefer git information when available, but fall back
-# to searching for repository markers so the workflow still functions in repositories that
-# were initialised with --no-git.
-SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
-
-if git rev-parse --show-toplevel >/dev/null 2>&1; then
-    REPO_ROOT=$(git rev-parse --show-toplevel)
-    HAS_GIT=true
-else
-    REPO_ROOT="$(find_repo_root "$SCRIPT_DIR")"
-    if [ -z "$REPO_ROOT" ]; then
-        echo "Error: Could not determine repository root. Please run this script from within the repository." >&2
-        exit 1
-    fi
-    HAS_GIT=false
-fi
-
-cd "$REPO_ROOT"
-
-SPECS_DIR="$REPO_ROOT/specs"
-mkdir -p "$SPECS_DIR"
-
-# Use YYMMDD format for feature numbering (date-based prefix)
-FEATURE_NUM=$(date +%y%m%d)
-
-# Function to generate branch name with stop word filtering and length filtering
-generate_branch_name() {
-    local description="$1"
-    
-    # Common stop words to filter out
-    local stop_words="^(i|a|an|the|to|for|of|in|on|at|by|with|from|is|are|was|were|be|been|being|have|has|had|do|does|did|will|would|should|could|can|may|might|must|shall|this|that|these|those|my|your|our|their|want|need|add|get|set)$"
-    
-    # Convert to lowercase and split into words
-    local clean_name=$(echo "$description" | tr '[:upper:]' '[:lower:]' | sed 's/[^a-z0-9]/ /g')
-    
-    # Filter words: remove stop words and words shorter than 3 chars (unless they're uppercase acronyms in original)
-    local meaningful_words=()
-    for word in $clean_name; do
-        # Skip empty words
-        [ -z "$word" ] && continue
-        
-        # Keep words that are NOT stop words AND (length >= 3 OR are potential acronyms)
-        if ! echo "$word" | grep -qiE "$stop_words"; then
-            if [ ${#word} -ge 3 ]; then
-                meaningful_words+=("$word")
-            elif echo "$description" | grep -q "\b${word^^}\b"; then
-                # Keep short words if they appear as uppercase in original (likely acronyms)
-                meaningful_words+=("$word")
-            fi
-        fi
-    done
-    
-    # If we have meaningful words, use first 3-4 of them
-    if [ ${#meaningful_words[@]} -gt 0 ]; then
-        local max_words=3
-        if [ ${#meaningful_words[@]} -eq 4 ]; then max_words=4; fi
-        
-        local result=""
-        local count=0
-        for word in "${meaningful_words[@]}"; do
-            if [ $count -ge $max_words ]; then break; fi
-            if [ -n "$result" ]; then result="$result-"; fi
-            result="$result$word"
-            count=$((count + 1))
-        done
-        echo "$result"
-    else
-        # Fallback to original logic if no meaningful words found
-        echo "$description" | tr '[:upper:]' '[:lower:]' | sed 's/[^a-z0-9]/-/g' | sed 's/-\+/-/g' | sed 's/^-//' | sed 's/-$//' | tr '-' '\n' | grep -v '^$' | head -3 | tr '\n' '-' | sed 's/-$//'
-    fi
-}
-
-# Generate branch name
-if [ -n "$SHORT_NAME" ]; then
-    # Use provided short name, just clean it up
-    BRANCH_SUFFIX=$(echo "$SHORT_NAME" | tr '[:upper:]' '[:lower:]' | sed 's/[^a-z0-9]/-/g' | sed 's/-\+/-/g' | sed 's/^-//' | sed 's/-$//')
-else
-    # Generate from description with smart filtering
-    BRANCH_SUFFIX=$(generate_branch_name "$FEATURE_DESCRIPTION")
-fi
-
-BRANCH_NAME="${FEATURE_NUM}-${BRANCH_SUFFIX}"
-
-# GitHub enforces a 244-byte limit on branch names
-# Validate and truncate if necessary
-MAX_BRANCH_LENGTH=244
-if [ ${#BRANCH_NAME} -gt $MAX_BRANCH_LENGTH ]; then
-    # Calculate how much we need to trim from suffix
-    # Account for: feature number (3) + hyphen (1) = 4 chars
-    MAX_SUFFIX_LENGTH=$((MAX_BRANCH_LENGTH - 4))
-    
-    # Truncate suffix at word boundary if possible
-    TRUNCATED_SUFFIX=$(echo "$BRANCH_SUFFIX" | cut -c1-$MAX_SUFFIX_LENGTH)
-    # Remove trailing hyphen if truncation created one
-    TRUNCATED_SUFFIX=$(echo "$TRUNCATED_SUFFIX" | sed 's/-$//')
-    
-    ORIGINAL_BRANCH_NAME="$BRANCH_NAME"
-    BRANCH_NAME="${FEATURE_NUM}-${TRUNCATED_SUFFIX}"
-    
-    >&2 echo "[specify] Warning: Branch name exceeded GitHub's 244-byte limit"
-    >&2 echo "[specify] Original: $ORIGINAL_BRANCH_NAME (${#ORIGINAL_BRANCH_NAME} bytes)"
-    >&2 echo "[specify] Truncated to: $BRANCH_NAME (${#BRANCH_NAME} bytes)"
-fi
-
-if [ "$HAS_GIT" = true ]; then
-    git checkout -b "$BRANCH_NAME"
-else
-    >&2 echo "[specify] Warning: Git repository not detected; skipped branch creation for $BRANCH_NAME"
-fi
-
-FEATURE_DIR="$SPECS_DIR/$BRANCH_NAME"
-mkdir -p "$FEATURE_DIR"
-
-TEMPLATE="$REPO_ROOT/.specify/templates/spec-template.md"
-SPEC_FILE="$FEATURE_DIR/spec.md"
-if [ -f "$TEMPLATE" ]; then cp "$TEMPLATE" "$SPEC_FILE"; else touch "$SPEC_FILE"; fi
-
-# Set the SPECIFY_FEATURE environment variable for the current session
-export SPECIFY_FEATURE="$BRANCH_NAME"
-
-if $JSON_MODE; then
-    printf '{"BRANCH_NAME":"%s","SPEC_FILE":"%s","FEATURE_NUM":"%s"}\n' "$BRANCH_NAME" "$SPEC_FILE" "$FEATURE_NUM"
-else
-    echo "BRANCH_NAME: $BRANCH_NAME"
-    echo "SPEC_FILE: $SPEC_FILE"
-    echo "FEATURE_NUM: $FEATURE_NUM"
-    echo "SPECIFY_FEATURE environment variable set to: $BRANCH_NAME"
-fi

nextflow/.specify/scripts/bash/setup-plan.sh

@@ -1,61 +0,0 @@
-#!/usr/bin/env bash
-
-set -e
-
-# Parse command line arguments
-JSON_MODE=false
-ARGS=()
-
-for arg in "$@"; do
-    case "$arg" in
-        --json) 
-            JSON_MODE=true 
-            ;;
-        --help|-h) 
-            echo "Usage: $0 [--json]"
-            echo "  --json    Output results in JSON format"
-            echo "  --help    Show this help message"
-            exit 0 
-            ;;
-        *) 
-            ARGS+=("$arg") 
-            ;;
-    esac
-done
-
-# Get script directory and load common functions
-SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
-source "$SCRIPT_DIR/common.sh"
-
-# Get all paths and variables from common functions
-eval $(get_feature_paths)
-
-# Check if we're on a proper feature branch (only for git repos)
-check_feature_branch "$CURRENT_BRANCH" "$HAS_GIT" || exit 1
-
-# Ensure the feature directory exists
-mkdir -p "$FEATURE_DIR"
-
-# Copy plan template if it exists
-TEMPLATE="$REPO_ROOT/.specify/templates/plan-template.md"
-if [[ -f "$TEMPLATE" ]]; then
-    cp "$TEMPLATE" "$IMPL_PLAN"
-    echo "Copied plan template to $IMPL_PLAN"
-else
-    echo "Warning: Plan template not found at $TEMPLATE"
-    # Create a basic plan file if template doesn't exist
-    touch "$IMPL_PLAN"
-fi
-
-# Output results
-if $JSON_MODE; then
-    printf '{"FEATURE_SPEC":"%s","IMPL_PLAN":"%s","SPECS_DIR":"%s","BRANCH":"%s","HAS_GIT":"%s"}\n' \
-        "$FEATURE_SPEC" "$IMPL_PLAN" "$FEATURE_DIR" "$CURRENT_BRANCH" "$HAS_GIT"
-else
-    echo "FEATURE_SPEC: $FEATURE_SPEC"
-    echo "IMPL_PLAN: $IMPL_PLAN" 
-    echo "SPECS_DIR: $FEATURE_DIR"
-    echo "BRANCH: $CURRENT_BRANCH"
-    echo "HAS_GIT: $HAS_GIT"
-fi
-

nextflow/.specify/scripts/bash/update-agent-context.sh

@@ -1,772 +0,0 @@
-#!/usr/bin/env bash
-
-# Update agent context files with information from plan.md
-#
-# This script maintains AI agent context files by parsing feature specifications 
-# and updating agent-specific configuration files with project information.
-#
-# MAIN FUNCTIONS:
-# 1. Environment Validation
-#    - Verifies git repository structure and branch information
-#    - Checks for required plan.md files and templates
-#    - Validates file permissions and accessibility
-#
-# 2. Plan Data Extraction
-#    - Parses plan.md files to extract project metadata
-#    - Identifies language/version, frameworks, databases, and project types
-#    - Handles missing or incomplete specification data gracefully
-#
-# 3. Agent File Management
-#    - Creates new agent context files from templates when needed
-#    - Updates existing agent files with new project information
-#    - Preserves manual additions and custom configurations
-#    - Supports multiple AI agent formats and directory structures
-#
-# 4. Content Generation
-#    - Generates language-specific build/test commands
-#    - Creates appropriate project directory structures
-#    - Updates technology stacks and recent changes sections
-#    - Maintains consistent formatting and timestamps
-#
-# 5. Multi-Agent Support
-#    - Handles agent-specific file paths and naming conventions
-#    - Supports: Claude, Gemini, Copilot, Cursor, Qwen, opencode, Codex, Windsurf, Kilo Code, Auggie CLI, Roo Code, CodeBuddy CLI, Amp, or Amazon Q Developer CLI
-#    - Can update single agents or all existing agent files
-#    - Creates default Claude file if no agent files exist
-#
-# Usage: ./update-agent-context.sh [agent_type]
-# Agent types: claude|gemini|copilot|cursor-agent|qwen|opencode|codex|windsurf|kilocode|auggie|q
-# Leave empty to update all existing agent files
-
-set -e
-
-# Enable strict error handling
-set -u
-set -o pipefail
-
-#==============================================================================
-# Configuration and Global Variables
-#==============================================================================
-
-# Get script directory and load common functions
-SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
-source "$SCRIPT_DIR/common.sh"
-
-# Get all paths and variables from common functions
-eval $(get_feature_paths)
-
-NEW_PLAN="$IMPL_PLAN"  # Alias for compatibility with existing code
-AGENT_TYPE="${1:-}"
-
-# Agent-specific file paths  
-CLAUDE_FILE="$REPO_ROOT/CLAUDE.md"
-GEMINI_FILE="$REPO_ROOT/GEMINI.md"
-COPILOT_FILE="$REPO_ROOT/.github/copilot-instructions.md"
-CURSOR_FILE="$REPO_ROOT/.cursor/rules/specify-rules.mdc"
-QWEN_FILE="$REPO_ROOT/QWEN.md"
-AGENTS_FILE="$REPO_ROOT/AGENTS.md"
-WINDSURF_FILE="$REPO_ROOT/.windsurf/rules/specify-rules.md"
-KILOCODE_FILE="$REPO_ROOT/.kilocode/rules/specify-rules.md"
-AUGGIE_FILE="$REPO_ROOT/.augment/rules/specify-rules.md"
-ROO_FILE="$REPO_ROOT/.roo/rules/specify-rules.md"
-CODEBUDDY_FILE="$REPO_ROOT/CODEBUDDY.md"
-AMP_FILE="$REPO_ROOT/AGENTS.md"
-Q_FILE="$REPO_ROOT/AGENTS.md"
-
-# Template file
-TEMPLATE_FILE="$REPO_ROOT/.specify/templates/agent-file-template.md"
-
-# Global variables for parsed plan data
-NEW_LANG=""
-NEW_FRAMEWORK=""
-NEW_DB=""
-NEW_PROJECT_TYPE=""
-
-#==============================================================================
-# Utility Functions
-#==============================================================================
-
-log_info() {
-    echo "INFO: $1"
-}
-
-log_success() {
-    echo "✓ $1"
-}
-
-log_error() {
-    echo "ERROR: $1" >&2
-}
-
-log_warning() {
-    echo "WARNING: $1" >&2
-}
-
-# Cleanup function for temporary files
-cleanup() {
-    local exit_code=$?
-    rm -f /tmp/agent_update_*_$$
-    rm -f /tmp/manual_additions_$$
-    exit $exit_code
-}
-
-# Set up cleanup trap
-trap cleanup EXIT INT TERM
-
-#==============================================================================
-# Validation Functions
-#==============================================================================
-
-validate_environment() {
-    # Check if we have a current branch/feature (git or non-git)
-    if [[ -z "$CURRENT_BRANCH" ]]; then
-        log_error "Unable to determine current feature"
-        if [[ "$HAS_GIT" == "true" ]]; then
-            log_info "Make sure you're on a feature branch"
-        else
-            log_info "Set SPECIFY_FEATURE environment variable or create a feature first"
-        fi
-        exit 1
-    fi
-    
-    # Check if plan.md exists
-    if [[ ! -f "$NEW_PLAN" ]]; then
-        log_error "No plan.md found at $NEW_PLAN"
-        log_info "Make sure you're working on a feature with a corresponding spec directory"
-        if [[ "$HAS_GIT" != "true" ]]; then
-            log_info "Use: export SPECIFY_FEATURE=your-feature-name or create a new feature first"
-        fi
-        exit 1
-    fi
-    
-    # Check if template exists (needed for new files)
-    if [[ ! -f "$TEMPLATE_FILE" ]]; then
-        log_warning "Template file not found at $TEMPLATE_FILE"
-        log_warning "Creating new agent files will fail"
-    fi
-}
-
-#==============================================================================
-# Plan Parsing Functions
-#==============================================================================
-
-extract_plan_field() {
-    local field_pattern="$1"
-    local plan_file="$2"
-    
-    grep "^\*\*${field_pattern}\*\*: " "$plan_file" 2>/dev/null | \
-        head -1 | \
-        sed "s|^\*\*${field_pattern}\*\*: ||" | \
-        sed 's/^[ \t]*//;s/[ \t]*$//' | \
-        grep -v "NEEDS CLARIFICATION" | \
-        grep -v "^N/A$" || echo ""
-}
-
-parse_plan_data() {
-    local plan_file="$1"
-    
-    if [[ ! -f "$plan_file" ]]; then
-        log_error "Plan file not found: $plan_file"
-        return 1
-    fi
-    
-    if [[ ! -r "$plan_file" ]]; then
-        log_error "Plan file is not readable: $plan_file"
-        return 1
-    fi
-    
-    log_info "Parsing plan data from $plan_file"
-    
-    NEW_LANG=$(extract_plan_field "Language/Version" "$plan_file")
-    NEW_FRAMEWORK=$(extract_plan_field "Primary Dependencies" "$plan_file")
-    NEW_DB=$(extract_plan_field "Storage" "$plan_file")
-    NEW_PROJECT_TYPE=$(extract_plan_field "Project Type" "$plan_file")
-    
-    # Log what we found
-    if [[ -n "$NEW_LANG" ]]; then
-        log_info "Found language: $NEW_LANG"
-    else
-        log_warning "No language information found in plan"
-    fi
-    
-    if [[ -n "$NEW_FRAMEWORK" ]]; then
-        log_info "Found framework: $NEW_FRAMEWORK"
-    fi
-    
-    if [[ -n "$NEW_DB" ]] && [[ "$NEW_DB" != "N/A" ]]; then
-        log_info "Found database: $NEW_DB"
-    fi
-    
-    if [[ -n "$NEW_PROJECT_TYPE" ]]; then
-        log_info "Found project type: $NEW_PROJECT_TYPE"
-    fi
-}
-
-format_technology_stack() {
-    local lang="$1"
-    local framework="$2"
-    local parts=()
-    
-    # Add non-empty parts
-    [[ -n "$lang" && "$lang" != "NEEDS CLARIFICATION" ]] && parts+=("$lang")
-    [[ -n "$framework" && "$framework" != "NEEDS CLARIFICATION" && "$framework" != "N/A" ]] && parts+=("$framework")
-    
-    # Join with proper formatting
-    if [[ ${#parts[@]} -eq 0 ]]; then
-        echo ""
-    elif [[ ${#parts[@]} -eq 1 ]]; then
-        echo "${parts[0]}"
-    else
-        # Join multiple parts with " + "
-        local result="${parts[0]}"
-        for ((i=1; i<${#parts[@]}; i++)); do
-            result="$result + ${parts[i]}"
-        done
-        echo "$result"
-    fi
-}
-
-#==============================================================================
-# Template and Content Generation Functions
-#==============================================================================
-
-get_project_structure() {
-    local project_type="$1"
-    
-    if [[ "$project_type" == *"web"* ]]; then
-        echo "backend/\\nfrontend/\\ntests/"
-    else
-        echo "src/\\ntests/"
-    fi
-}
-
-get_commands_for_language() {
-    local lang="$1"
-    
-    case "$lang" in
-        *"Python"*)
-            echo "cd src && pytest && ruff check ."
-            ;;
-        *"Rust"*)
-            echo "cargo test && cargo clippy"
-            ;;
-        *"JavaScript"*|*"TypeScript"*)
-            echo "npm test \\&\\& npm run lint"
-            ;;
-        *)
-            echo "# Add commands for $lang"
-            ;;
-    esac
-}
-
-get_language_conventions() {
-    local lang="$1"
-    echo "$lang: Follow standard conventions"
-}
-
-create_new_agent_file() {
-    local target_file="$1"
-    local temp_file="$2"
-    local project_name="$3"
-    local current_date="$4"
-    
-    if [[ ! -f "$TEMPLATE_FILE" ]]; then
-        log_error "Template not found at $TEMPLATE_FILE"
-        return 1
-    fi
-    
-    if [[ ! -r "$TEMPLATE_FILE" ]]; then
-        log_error "Template file is not readable: $TEMPLATE_FILE"
-        return 1
-    fi
-    
-    log_info "Creating new agent context file from template..."
-    
-    if ! cp "$TEMPLATE_FILE" "$temp_file"; then
-        log_error "Failed to copy template file"
-        return 1
-    fi
-    
-    # Replace template placeholders
-    local project_structure
-    project_structure=$(get_project_structure "$NEW_PROJECT_TYPE")
-    
-    local commands
-    commands=$(get_commands_for_language "$NEW_LANG")
-    
-    local language_conventions
-    language_conventions=$(get_language_conventions "$NEW_LANG")
-    
-    # Perform substitutions with error checking using safer approach
-    # Escape special characters for sed by using a different delimiter or escaping
-    local escaped_lang=$(printf '%s\n' "$NEW_LANG" | sed 's/[\[\.*^$()+{}|]/\\&/g')
-    local escaped_framework=$(printf '%s\n' "$NEW_FRAMEWORK" | sed 's/[\[\.*^$()+{}|]/\\&/g')
-    local escaped_branch=$(printf '%s\n' "$CURRENT_BRANCH" | sed 's/[\[\.*^$()+{}|]/\\&/g')
-    
-    # Build technology stack and recent change strings conditionally
-    local tech_stack
-    if [[ -n "$escaped_lang" && -n "$escaped_framework" ]]; then
-        tech_stack="- $escaped_lang + $escaped_framework ($escaped_branch)"
-    elif [[ -n "$escaped_lang" ]]; then
-        tech_stack="- $escaped_lang ($escaped_branch)"
-    elif [[ -n "$escaped_framework" ]]; then
-        tech_stack="- $escaped_framework ($escaped_branch)"
-    else
-        tech_stack="- ($escaped_branch)"
-    fi
-
-    local recent_change
-    if [[ -n "$escaped_lang" && -n "$escaped_framework" ]]; then
-        recent_change="- $escaped_branch: Added $escaped_lang + $escaped_framework"
-    elif [[ -n "$escaped_lang" ]]; then
-        recent_change="- $escaped_branch: Added $escaped_lang"
-    elif [[ -n "$escaped_framework" ]]; then
-        recent_change="- $escaped_branch: Added $escaped_framework"
-    else
-        recent_change="- $escaped_branch: Added"
-    fi
-
-    local substitutions=(
-        "s|\[PROJECT NAME\]|$project_name|"
-        "s|\[DATE\]|$current_date|"
-        "s|\[EXTRACTED FROM ALL PLAN.MD FILES\]|$tech_stack|"
-        "s|\[ACTUAL STRUCTURE FROM PLANS\]|$project_structure|g"
-        "s|\[ONLY COMMANDS FOR ACTIVE TECHNOLOGIES\]|$commands|"
-        "s|\[LANGUAGE-SPECIFIC, ONLY FOR LANGUAGES IN USE\]|$language_conventions|"
-        "s|\[LAST 3 FEATURES AND WHAT THEY ADDED\]|$recent_change|"
-    )
-    
-    for substitution in "${substitutions[@]}"; do
-        if ! sed -i.bak -e "$substitution" "$temp_file"; then
-            log_error "Failed to perform substitution: $substitution"
-            rm -f "$temp_file" "$temp_file.bak"
-            return 1
-        fi
-    done
-    
-    # Convert \n sequences to actual newlines
-    newline=$(printf '\n')
-    sed -i.bak2 "s/\\\\n/${newline}/g" "$temp_file"
-    
-    # Clean up backup files
-    rm -f "$temp_file.bak" "$temp_file.bak2"
-    
-    return 0
-}
-
-
-
-
-update_existing_agent_file() {
-    local target_file="$1"
-    local current_date="$2"
-    
-    log_info "Updating existing agent context file..."
-    
-    # Use a single temporary file for atomic update
-    local temp_file
-    temp_file=$(mktemp) || {
-        log_error "Failed to create temporary file"
-        return 1
-    }
-    
-    # Process the file in one pass
-    local tech_stack=$(format_technology_stack "$NEW_LANG" "$NEW_FRAMEWORK")
-    local new_tech_entries=()
-    local new_change_entry=""
-    
-    # Prepare new technology entries
-    if [[ -n "$tech_stack" ]] && ! grep -q "$tech_stack" "$target_file"; then
-        new_tech_entries+=("- $tech_stack ($CURRENT_BRANCH)")
-    fi
-    
-    if [[ -n "$NEW_DB" ]] && [[ "$NEW_DB" != "N/A" ]] && [[ "$NEW_DB" != "NEEDS CLARIFICATION" ]] && ! grep -q "$NEW_DB" "$target_file"; then
-        new_tech_entries+=("- $NEW_DB ($CURRENT_BRANCH)")
-    fi
-    
-    # Prepare new change entry
-    if [[ -n "$tech_stack" ]]; then
-        new_change_entry="- $CURRENT_BRANCH: Added $tech_stack"
-    elif [[ -n "$NEW_DB" ]] && [[ "$NEW_DB" != "N/A" ]] && [[ "$NEW_DB" != "NEEDS CLARIFICATION" ]]; then
-        new_change_entry="- $CURRENT_BRANCH: Added $NEW_DB"
-    fi
-    
-    # Check if sections exist in the file
-    local has_active_technologies=0
-    local has_recent_changes=0
-    
-    if grep -q "^## Active Technologies" "$target_file" 2>/dev/null; then
-        has_active_technologies=1
-    fi
-    
-    if grep -q "^## Recent Changes" "$target_file" 2>/dev/null; then
-        has_recent_changes=1
-    fi
-    
-    # Process file line by line
-    local in_tech_section=false
-    local in_changes_section=false
-    local tech_entries_added=false
-    local changes_entries_added=false
-    local existing_changes_count=0
-    local file_ended=false
-    
-    while IFS= read -r line || [[ -n "$line" ]]; do
-        # Handle Active Technologies section
-        if [[ "$line" == "## Active Technologies" ]]; then
-            echo "$line" >> "$temp_file"
-            in_tech_section=true
-            continue
-        elif [[ $in_tech_section == true ]] && [[ "$line" =~ ^##[[:space:]] ]]; then
-            # Add new tech entries before closing the section
-            if [[ $tech_entries_added == false ]] && [[ ${#new_tech_entries[@]} -gt 0 ]]; then
-                printf '%s\n' "${new_tech_entries[@]}" >> "$temp_file"
-                tech_entries_added=true
-            fi
-            echo "$line" >> "$temp_file"
-            in_tech_section=false
-            continue
-        elif [[ $in_tech_section == true ]] && [[ -z "$line" ]]; then
-            # Add new tech entries before empty line in tech section
-            if [[ $tech_entries_added == false ]] && [[ ${#new_tech_entries[@]} -gt 0 ]]; then
-                printf '%s\n' "${new_tech_entries[@]}" >> "$temp_file"
-                tech_entries_added=true
-            fi
-            echo "$line" >> "$temp_file"
-            continue
-        fi
-        
-        # Handle Recent Changes section
-        if [[ "$line" == "## Recent Changes" ]]; then
-            echo "$line" >> "$temp_file"
-            # Add new change entry right after the heading
-            if [[ -n "$new_change_entry" ]]; then
-                echo "$new_change_entry" >> "$temp_file"
-            fi
-            in_changes_section=true
-            changes_entries_added=true
-            continue
-        elif [[ $in_changes_section == true ]] && [[ "$line" =~ ^##[[:space:]] ]]; then
-            echo "$line" >> "$temp_file"
-            in_changes_section=false
-            continue
-        elif [[ $in_changes_section == true ]] && [[ "$line" == "- "* ]]; then
-            # Keep only first 2 existing changes
-            if [[ $existing_changes_count -lt 2 ]]; then
-                echo "$line" >> "$temp_file"
-                ((existing_changes_count++))
-            fi
-            continue
-        fi
-        
-        # Update timestamp
-        if [[ "$line" =~ \*\*Last\ updated\*\*:.*[0-9][0-9][0-9][0-9]-[0-9][0-9]-[0-9][0-9] ]]; then
-            echo "$line" | sed "s/[0-9][0-9][0-9][0-9]-[0-9][0-9]-[0-9][0-9]/$current_date/" >> "$temp_file"
-        else
-            echo "$line" >> "$temp_file"
-        fi
-    done < "$target_file"
-    
-    # Post-loop check: if we're still in the Active Technologies section and haven't added new entries
-    if [[ $in_tech_section == true ]] && [[ $tech_entries_added == false ]] && [[ ${#new_tech_entries[@]} -gt 0 ]]; then
-        printf '%s\n' "${new_tech_entries[@]}" >> "$temp_file"
-        tech_entries_added=true
-    fi
-    
-    # If sections don't exist, add them at the end of the file
-    if [[ $has_active_technologies -eq 0 ]] && [[ ${#new_tech_entries[@]} -gt 0 ]]; then
-        echo "" >> "$temp_file"
-        echo "## Active Technologies" >> "$temp_file"
-        printf '%s\n' "${new_tech_entries[@]}" >> "$temp_file"
-        tech_entries_added=true
-    fi
-    
-    if [[ $has_recent_changes -eq 0 ]] && [[ -n "$new_change_entry" ]]; then
-        echo "" >> "$temp_file"
-        echo "## Recent Changes" >> "$temp_file"
-        echo "$new_change_entry" >> "$temp_file"
-        changes_entries_added=true
-    fi
-    
-    # Move temp file to target atomically
-    if ! mv "$temp_file" "$target_file"; then
-        log_error "Failed to update target file"
-        rm -f "$temp_file"
-        return 1
-    fi
-    
-    return 0
-}
-#==============================================================================
-# Main Agent File Update Function
-#==============================================================================
-
-update_agent_file() {
-    local target_file="$1"
-    local agent_name="$2"
-    
-    if [[ -z "$target_file" ]] || [[ -z "$agent_name" ]]; then
-        log_error "update_agent_file requires target_file and agent_name parameters"
-        return 1
-    fi
-    
-    log_info "Updating $agent_name context file: $target_file"
-    
-    local project_name
-    project_name=$(basename "$REPO_ROOT")
-    local current_date
-    current_date=$(date +%Y-%m-%d)
-    
-    # Create directory if it doesn't exist
-    local target_dir
-    target_dir=$(dirname "$target_file")
-    if [[ ! -d "$target_dir" ]]; then
-        if ! mkdir -p "$target_dir"; then
-            log_error "Failed to create directory: $target_dir"
-            return 1
-        fi
-    fi
-    
-    if [[ ! -f "$target_file" ]]; then
-        # Create new file from template
-        local temp_file
-        temp_file=$(mktemp) || {
-            log_error "Failed to create temporary file"
-            return 1
-        }
-        
-        if create_new_agent_file "$target_file" "$temp_file" "$project_name" "$current_date"; then
-            if mv "$temp_file" "$target_file"; then
-                log_success "Created new $agent_name context file"
-            else
-                log_error "Failed to move temporary file to $target_file"
-                rm -f "$temp_file"
-                return 1
-            fi
-        else
-            log_error "Failed to create new agent file"
-            rm -f "$temp_file"
-            return 1
-        fi
-    else
-        # Update existing file
-        if [[ ! -r "$target_file" ]]; then
-            log_error "Cannot read existing file: $target_file"
-            return 1
-        fi
-        
-        if [[ ! -w "$target_file" ]]; then
-            log_error "Cannot write to existing file: $target_file"
-            return 1
-        fi
-        
-        if update_existing_agent_file "$target_file" "$current_date"; then
-            log_success "Updated existing $agent_name context file"
-        else
-            log_error "Failed to update existing agent file"
-            return 1
-        fi
-    fi
-    
-    return 0
-}
-
-#==============================================================================
-# Agent Selection and Processing
-#==============================================================================
-
-update_specific_agent() {
-    local agent_type="$1"
-    
-    case "$agent_type" in
-        claude)
-            update_agent_file "$CLAUDE_FILE" "Claude Code"
-            ;;
-        gemini)
-            update_agent_file "$GEMINI_FILE" "Gemini CLI"
-            ;;
-        copilot)
-            update_agent_file "$COPILOT_FILE" "GitHub Copilot"
-            ;;
-        cursor-agent)
-            update_agent_file "$CURSOR_FILE" "Cursor IDE"
-            ;;
-        qwen)
-            update_agent_file "$QWEN_FILE" "Qwen Code"
-            ;;
-        opencode)
-            update_agent_file "$AGENTS_FILE" "opencode"
-            ;;
-        codex)
-            update_agent_file "$AGENTS_FILE" "Codex CLI"
-            ;;
-        windsurf)
-            update_agent_file "$WINDSURF_FILE" "Windsurf"
-            ;;
-        kilocode)
-            update_agent_file "$KILOCODE_FILE" "Kilo Code"
-            ;;
-        auggie)
-            update_agent_file "$AUGGIE_FILE" "Auggie CLI"
-            ;;
-        roo)
-            update_agent_file "$ROO_FILE" "Roo Code"
-            ;;
-        codebuddy)
-            update_agent_file "$CODEBUDDY_FILE" "CodeBuddy CLI"
-            ;;
-        amp)
-            update_agent_file "$AMP_FILE" "Amp"
-            ;;
-        q)
-            update_agent_file "$Q_FILE" "Amazon Q Developer CLI"
-            ;;
-        *)
-            log_error "Unknown agent type '$agent_type'"
-            log_error "Expected: claude|gemini|copilot|cursor-agent|qwen|opencode|codex|windsurf|kilocode|auggie|roo|amp|q"
-            exit 1
-            ;;
-    esac
-}
-
-update_all_existing_agents() {
-    local found_agent=false
-    
-    # Check each possible agent file and update if it exists
-    if [[ -f "$CLAUDE_FILE" ]]; then
-        update_agent_file "$CLAUDE_FILE" "Claude Code"
-        found_agent=true
-    fi
-    
-    if [[ -f "$GEMINI_FILE" ]]; then
-        update_agent_file "$GEMINI_FILE" "Gemini CLI"
-        found_agent=true
-    fi
-    
-    if [[ -f "$COPILOT_FILE" ]]; then
-        update_agent_file "$COPILOT_FILE" "GitHub Copilot"
-        found_agent=true
-    fi
-    
-    if [[ -f "$CURSOR_FILE" ]]; then
-        update_agent_file "$CURSOR_FILE" "Cursor IDE"
-        found_agent=true
-    fi
-    
-    if [[ -f "$QWEN_FILE" ]]; then
-        update_agent_file "$QWEN_FILE" "Qwen Code"
-        found_agent=true
-    fi
-    
-    if [[ -f "$AGENTS_FILE" ]]; then
-        update_agent_file "$AGENTS_FILE" "Codex/opencode"
-        found_agent=true
-    fi
-    
-    if [[ -f "$WINDSURF_FILE" ]]; then
-        update_agent_file "$WINDSURF_FILE" "Windsurf"
-        found_agent=true
-    fi
-    
-    if [[ -f "$KILOCODE_FILE" ]]; then
-        update_agent_file "$KILOCODE_FILE" "Kilo Code"
-        found_agent=true
-    fi
-
-    if [[ -f "$AUGGIE_FILE" ]]; then
-        update_agent_file "$AUGGIE_FILE" "Auggie CLI"
-        found_agent=true
-    fi
-    
-    if [[ -f "$ROO_FILE" ]]; then
-        update_agent_file "$ROO_FILE" "Roo Code"
-        found_agent=true
-    fi
-
-    if [[ -f "$CODEBUDDY_FILE" ]]; then
-        update_agent_file "$CODEBUDDY_FILE" "CodeBuddy CLI"
-        found_agent=true
-    fi
-
-    if [[ -f "$Q_FILE" ]]; then
-        update_agent_file "$Q_FILE" "Amazon Q Developer CLI"
-        found_agent=true
-    fi
-    
-    # If no agent files exist, create a default Claude file
-    if [[ "$found_agent" == false ]]; then
-        log_info "No existing agent files found, creating default Claude file..."
-        update_agent_file "$CLAUDE_FILE" "Claude Code"
-    fi
-}
-print_summary() {
-    echo
-    log_info "Summary of changes:"
-    
-    if [[ -n "$NEW_LANG" ]]; then
-        echo "  - Added language: $NEW_LANG"
-    fi
-    
-    if [[ -n "$NEW_FRAMEWORK" ]]; then
-        echo "  - Added framework: $NEW_FRAMEWORK"
-    fi
-    
-    if [[ -n "$NEW_DB" ]] && [[ "$NEW_DB" != "N/A" ]]; then
-        echo "  - Added database: $NEW_DB"
-    fi
-    
-    echo
-
-    log_info "Usage: $0 [claude|gemini|copilot|cursor-agent|qwen|opencode|codex|windsurf|kilocode|auggie|codebuddy|q]"
-}
-
-#==============================================================================
-# Main Execution
-#==============================================================================
-
-main() {
-    # Validate environment before proceeding
-    validate_environment
-    
-    log_info "=== Updating agent context files for feature $CURRENT_BRANCH ==="
-    
-    # Parse the plan file to extract project information
-    if ! parse_plan_data "$NEW_PLAN"; then
-        log_error "Failed to parse plan data"
-        exit 1
-    fi
-    
-    # Process based on agent type argument
-    local success=true
-    
-    if [[ -z "$AGENT_TYPE" ]]; then
-        # No specific agent provided - update all existing agent files
-        log_info "No agent specified, updating all existing agent files..."
-        if ! update_all_existing_agents; then
-            success=false
-        fi
-    else
-        # Specific agent provided - update only that agent
-        log_info "Updating specific agent: $AGENT_TYPE"
-        if ! update_specific_agent "$AGENT_TYPE"; then
-            success=false
-        fi
-    fi
-    
-    # Print summary
-    print_summary
-    
-    if [[ "$success" == true ]]; then
-        log_success "Agent context update completed successfully"
-        exit 0
-    else
-        log_error "Agent context update completed with errors"
-        exit 1
-    fi
-}
-
-# Execute main function if script is run directly
-if [[ "${BASH_SOURCE[0]}" == "${0}" ]]; then
-    main "$@"
-fi
-