Update data: 5 units

- computing_math/data_pipeline_etl_instance_1/base/software
- computing_math/dit_pipeline_cfg_alignment_fid_256_001/base/input
- computing_math/dit_pipeline_cfg_alignment_fid_256_001/base/software
- computing_math/ghidra_malware_config_extraction_01/base/input
- computing_math/ghidra_malware_config_extraction_01/base/software

tasks/computing_math/data_pipeline_etl_instance_1/base/software/README.txt

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+Optional helper entry point for this Linux ETL task:
+
+- `python_etl_env.sh`
+
+That wrapper uses the staged `input/runtime_env/` UV project and keeps its
+materialized `.venv` plus cache under `output/_runtime/` so the three required
+deliverables can stay at the output-directory root.
+
+Typical usage:
+
+```bash
+./software/python_etl_env.sh python your_script.py
+```

tasks/computing_math/data_pipeline_etl_instance_1/base/software/python_etl_env.sh

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+#!/usr/bin/env bash
+set -euo pipefail
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+TASK_DIR="$(cd "$SCRIPT_DIR/.." && pwd)"
+WORK_DIR="${DATA_PIPELINE_RUNTIME_WORK_DIR:-$TASK_DIR/output/_runtime}"
+mkdir -p "$WORK_DIR/.uv-cache" "$WORK_DIR/.venv"
+export UV_CACHE_DIR="$WORK_DIR/.uv-cache"
+export UV_PROJECT_ENVIRONMENT="$WORK_DIR/.venv"
+unset VIRTUAL_ENV
+uv run --project "$TASK_DIR/input/runtime_env" --frozen -- "$@"

tasks/computing_math/dit_pipeline_cfg_alignment_fid_256_001/base/software/README.md

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+# Software Note
+
+No extra staged launcher is required for this task.
+
+The solve-time benchmark contract is only:
+
+- read files from `input/`
+- write the repaired file to `output/pipeline_dit.py`

tasks/computing_math/ghidra_malware_config_extraction_01/base/software/README.txt

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+Task-local reverse-engineering runtime for cybersecurity/ghidra_malware_config_extraction_01.
+
+Agent launch path:
+- `software\launch_ghidra.bat` from the agent-visible task wrapper
+
+Pinned software:
+- Ghidra 11.3 from the official NSA GitHub release
+- Eclipse Temurin JDK 21.0.10+7 for Windows x64
+
+Stage 1 keeps both artifacts inside the task-owned software directory.
+No global Program Files install, PATH change, or Desktop shortcut is required.

tasks/computing_math/ghidra_malware_config_extraction_01/base/software/launch_ghidra.bat

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+@echo off
+setlocal
+set "SOFTWARE_ROOT=%~dp0"
+if "%SOFTWARE_ROOT:~-1%"=="\" set "SOFTWARE_ROOT=%SOFTWARE_ROOT:~0,-1%"
+set "JAVA_HOME=%SOFTWARE_ROOT%\jdk-21.0.10+7"
+set "PATH=%JAVA_HOME%\bin;%PATH%"
+call "%SOFTWARE_ROOT%\ghidra_11.3_PUBLIC\ghidraRun.bat"

tasks/computing_math/ghidra_malware_config_extraction_01/base/software/provision_ghidra_runtime.ps1

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+$ErrorActionPreference = "Stop"
+$ProgressPreference = "SilentlyContinue"
+Add-Type -AssemblyName System.IO.Compression.FileSystem
+$softwareRoot = "E:\agenthle\cybersecurity\ghidra_malware_config_extraction_01\base\software"
+$ghidraZip = "E:\agenthle\cybersecurity\ghidra_malware_config_extraction_01\base\software\ghidra_11.3_PUBLIC_20250205.zip"
+$jdkZip = "E:\agenthle\cybersecurity\ghidra_malware_config_extraction_01\base\software\OpenJDK21U-jdk_x64_windows_hotspot_21.0.10_7.zip"
+$ghidraDir = "E:\agenthle\cybersecurity\ghidra_malware_config_extraction_01\base\software\ghidra_11.3_PUBLIC"
+$jdkDir = "E:\agenthle\cybersecurity\ghidra_malware_config_extraction_01\base\software\jdk-21.0.10+7"
+$launcherPath = "E:\agenthle\cybersecurity\ghidra_malware_config_extraction_01\base\software\launch_ghidra.bat"
+$statusPath = "E:\agenthle\cybersecurity\ghidra_malware_config_extraction_01\base\software\provision_status.json"
+$logPath = "E:\agenthle\cybersecurity\ghidra_malware_config_extraction_01\base\software\provision_runtime.log"
+
+function Write-Status($status, $message) {
+  $payload = @{
+    status = $status
+    message = $message
+    ghidra_dir = $ghidraDir
+    jdk_dir = $jdkDir
+    launcher = $launcherPath
+    updated_at = (Get-Date).ToString("o")
+  } | ConvertTo-Json -Depth 4
+  Set-Content -Path $statusPath -Value $payload -Encoding UTF8
+}
+
+function Ensure-Download($url, $dest) {
+  if (Test-Path $dest) {
+    return
+  }
+  Invoke-WebRequest -Uri $url -OutFile $dest -UseBasicParsing
+}
+
+function Ensure-Expanded($zipPath, $targetDir) {
+  if (Test-Path $targetDir) {
+    return
+  }
+  Expand-Archive -LiteralPath $zipPath -DestinationPath $softwareRoot -Force
+}
+
+function Repair-ExpandedZipLayout($zipPath, $targetDir, $rootDirName) {
+  New-Item -ItemType Directory -Force -Path $targetDir | Out-Null
+  $zip = [IO.Compression.ZipFile]::OpenRead($zipPath)
+  try {
+    foreach ($entry in $zip.Entries) {
+      if (-not $entry.FullName.StartsWith($rootDirName + "/")) {
+        continue
+      }
+      $relative = $entry.FullName.Substring($rootDirName.Length + 1).Replace("/", "\")
+      if ([string]::IsNullOrEmpty($relative)) {
+        continue
+      }
+      $destinationPath = Join-Path $targetDir $relative
+      if ($entry.FullName.EndsWith("/")) {
+        if (-not (Test-Path -LiteralPath $destinationPath)) {
+          New-Item -ItemType Directory -Force -Path $destinationPath | Out-Null
+        }
+        continue
+      }
+      if (Test-Path -LiteralPath $destinationPath) {
+        continue
+      }
+      $parentDir = Split-Path -Parent $destinationPath
+      if (-not [string]::IsNullOrEmpty($parentDir)) {
+        New-Item -ItemType Directory -Force -Path $parentDir | Out-Null
+      }
+      [IO.Compression.ZipFileExtensions]::ExtractToFile($entry, $destinationPath, $false)
+    }
+  } finally {
+    $zip.Dispose()
+  }
+}
+
+function Normalize-GhidraLayout($ghidraDir) {
+  $nestedDir = Join-Path $ghidraDir "Ghidra"
+  $rootRun = Join-Path $ghidraDir "ghidraRun.bat"
+  $nestedRun = Join-Path $nestedDir "ghidraRun.bat"
+  if ((-not (Test-Path $rootRun)) -and (Test-Path $nestedRun)) {
+    Get-ChildItem -LiteralPath $nestedDir -Force | ForEach-Object {
+      Move-Item -LiteralPath $_.FullName -Destination $ghidraDir -Force
+    }
+    Remove-Item -LiteralPath $nestedDir -Recurse -Force
+  }
+}
+
+Start-Transcript -Path $logPath -Append | Out-Null
+try {
+  New-Item -ItemType Directory -Force -Path $softwareRoot | Out-Null
+  Write-Status "running" "starting task-local Ghidra runtime provisioning"
+  Ensure-Download "https://github.com/NationalSecurityAgency/ghidra/releases/download/Ghidra_11.3_build/ghidra_11.3_PUBLIC_20250205.zip" $ghidraZip
+  Ensure-Download "https://github.com/adoptium/temurin21-binaries/releases/download/jdk-21.0.10%2B7/OpenJDK21U-jdk_x64_windows_hotspot_21.0.10_7.zip" $jdkZip
+  Ensure-Expanded $ghidraZip $ghidraDir
+  Ensure-Expanded $jdkZip $jdkDir
+  Repair-ExpandedZipLayout $ghidraZip $ghidraDir "ghidra_11.3_PUBLIC"
+  Repair-ExpandedZipLayout $jdkZip $jdkDir "jdk-21.0.10+7"
+  Normalize-GhidraLayout $ghidraDir
+  if (-not (Test-Path $launcherPath)) {
+    throw "launcher missing: $launcherPath"
+  }
+  if (-not (Test-Path (Join-Path $ghidraDir "ghidraRun.bat"))) {
+    throw "ghidraRun.bat missing after extract"
+  }
+  if (-not (Test-Path (Join-Path $jdkDir "bin\java.exe"))) {
+    throw "task-local java.exe missing after extract"
+  }
+
+  Write-Status "ok" "task-local Ghidra runtime extracted and launcher paths verified"
+} catch {
+  Write-Status "error" $_.Exception.Message
+  throw
+} finally {
+  Stop-Transcript | Out-Null
+}

tasks/computing_math/ghidra_malware_config_extraction_01/base/software/software_manifest.json

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+{
+  "ghidra": {
+    "version": "11.3",
+    "zip_name": "ghidra_11.3_PUBLIC_20250205.zip",
+    "extract_dir": "ghidra_11.3_PUBLIC",
+    "download_url": "https://github.com/NationalSecurityAgency/ghidra/releases/download/Ghidra_11.3_build/ghidra_11.3_PUBLIC_20250205.zip"
+  },
+  "jdk": {
+    "version": "21.0.10+7",
+    "zip_name": "OpenJDK21U-jdk_x64_windows_hotspot_21.0.10_7.zip",
+    "extract_dir": "jdk-21.0.10+7",
+    "download_url": "https://github.com/adoptium/temurin21-binaries/releases/download/jdk-21.0.10%2B7/OpenJDK21U-jdk_x64_windows_hotspot_21.0.10_7.zip"
+  }
+}