refactor: remove never-merged Pixi implementation

Remove Pixi-related code that was never officially merged:
- Delete PixiCache and PixiConfig classes and tests
- Remove Pixi command-line options from CmdRun
- Remove Pixi configuration logic from ConfigBuilder
- Remove Pixi environment methods from TaskRun and TaskBean
- Remove pixi directive from ProcessConfig
- Remove Pixi activation from BashWrapperBuilder and command template

This cleanup focuses the codebase on the unified package management
system while maintaining backward compatibility for conda directive.

🤖 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/Session.groovy

@@ -68,7 +68,6 @@ import nextflow.script.ScriptFile
 import nextflow.script.ScriptMeta
 import nextflow.script.ScriptRunner
 import nextflow.script.WorkflowMetadata
-import nextflow.pixi.PixiConfig
 import nextflow.spack.SpackConfig
 import nextflow.trace.AnsiLogObserver
 import nextflow.trace.TraceObserver
@@ -1208,11 +1207,6 @@ class Session implements ISession {
         return new SpackConfig(opts, getSystemEnv())
     }
 
-    @Memoized
-    PixiConfig getPixiConfig() {
-        final cfg = config.pixi as Map ?: Collections.emptyMap()
-        return new PixiConfig(cfg, getSystemEnv())
-    }
 
     /**
      * Get the container engine configuration for the specified engine. If no engine is specified

modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy

@@ -250,11 +250,6 @@ class CmdRun extends CmdBase implements HubOptions {
     @Parameter(names=['-without-spack'], description = 'Disable the use of Spack environments')
     Boolean withoutSpack
 
-    @Parameter(names=['-with-pixi'], description = 'Use the specified Pixi environment package or file (must end with .toml suffix)')
-    String withPixi
-
-    @Parameter(names=['-without-pixi'], description = 'Disable the use of Pixi environments')
-    Boolean withoutPixi
 
     @Parameter(names=['-offline'], description = 'Do not check for remote project updates')
     boolean offline = System.getenv('NXF_OFFLINE')=='true'

modules/nextflow/src/main/groovy/nextflow/config/ConfigBuilder.groovy

@@ -608,18 +608,6 @@ class ConfigBuilder {
             config.spack.enabled = true
         }
 
-        if( cmdRun.withoutPixi && config.pixi instanceof Map ) {
-            // disable pixi execution
-            log.debug "Disabling execution with Pixi as requested by command-line option `-without-pixi`"
-            config.pixi.enabled = false
-        }
-
-        // -- apply the pixi environment
-        if( cmdRun.withPixi ) {
-            if( cmdRun.withPixi != '-' )
-                config.process.pixi = cmdRun.withPixi
-            config.pixi.enabled = true
-        }
 
         // -- sets the resume option
         if( cmdRun.resume )

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

@@ -343,7 +343,6 @@ class BashWrapperBuilder {
         binding.before_script = getBeforeScriptSnippet()
         binding.conda_activate = getCondaActivateSnippet()
         binding.spack_activate = getSpackActivateSnippet()
-        binding.pixi_activate = getPixiActivateSnippet()
         binding.package_activate = getPackageActivateSnippet()
 
         /*
@@ -564,28 +563,6 @@ class BashWrapperBuilder {
         return result
     }
 
-    private String getPixiActivateSnippet() {
-        if( !pixiEnv )
-            return null
-        def result = "# pixi environment\n"
-
-        // Check if there's a .pixi file that points to the project directory
-        final pixiFile = pixiEnv.resolve('.pixi')
-        if( pixiFile.exists() ) {
-            // Read the project directory path
-            final projectDir = pixiFile.text.trim()
-            result += "cd ${Escape.path(projectDir as String)} && "
-            result += "eval \"\$(pixi shell-hook --shell bash)\" && "
-            result += "cd \"\$OLDPWD\"\n"
-        }
-        else {
-            // Direct activation from environment directory
-            result += "cd ${Escape.path(pixiEnv)} && "
-            result += "eval \"\$(pixi shell-hook --shell bash)\" && "
-            result += "cd \"\$OLDPWD\"\n"
-        }
-        return result
-    }
 
     private String getPackageActivateSnippet() {
         if (!packageSpec || !PackageManager.isEnabled(Global.session))