feat: Update bash wrapper for unified package activation

Enhances the bash wrapper system to support the new package directive:

- BashWrapperBuilder: Adds getPackageActivateSnippet() method that
  creates package environments using the PackageManager
- command-run.txt: Adds {{package_activate}} template variable
  for package environment activation

The new system works alongside existing conda/pixi activation,
enabling gradual migration while maintaining backward compatibility.

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <[email protected]>
Signed-off-by: Edmund Miller <[email protected]>

Author: edmundmiller

modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy

@@ -342,6 +342,7 @@ class BashWrapperBuilder {
         binding.conda_activate = getCondaActivateSnippet()
         binding.spack_activate = getSpackActivateSnippet()
         binding.pixi_activate = getPixiActivateSnippet()
+        binding.package_activate = getPackageActivateSnippet()
 
         /*
          * add the task environment
@@ -584,6 +585,29 @@ class BashWrapperBuilder {
         return result
     }
 
+    private String getPackageActivateSnippet() {
+        import nextflow.packages.PackageManager
+        import nextflow.Global
+        
+        if (!packageSpec || !PackageManager.isEnabled(Global.session))
+            return null
+        
+        try {
+            def packageManager = new PackageManager(Global.session)
+            def envPath = packageManager.createEnvironment(packageSpec)
+            def activationScript = packageManager.getActivationScript(packageSpec, envPath)
+            
+            return """\
+                # ${packageSpec.provider} environment
+                ${activationScript}
+                """.stripIndent()
+        }
+        catch (Exception e) {
+            log.warn "Failed to create package environment: ${e.message}"
+            return null
+        }
+    }
+
     protected String getTraceCommand(String interpreter) {
         String result = "${interpreter} ${fileStr(scriptFile)}"
         if( input != null )

modules/nextflow/src/main/resources/nextflow/executor/command-run.txt

@@ -163,6 +163,7 @@ nxf_main() {
     {{conda_activate}}
     {{spack_activate}}
     {{pixi_activate}}
+    {{package_activate}}
     set -u
     {{task_env}}
     {{secrets_env}}