When you create scripts or tasks that reference files that are included an Application Pack, it's important to know where the files will be extracted on the target machine. The contents of Application Packs are extracted to C:\Windows\Temp\SD\%Application Pack Title%\Files\.
For example, the absolute path in a script that targets a file named "Configuration.xml" under the "Files" folder of an Application Pack named "MyAppPack" would be C:\Windows\Temp\SD\MyAppPack\Files\Configuration.xml.