I created this simple AutoIT script to clear the "File System" and "Registry" folders for portable apps packaged with JauntPE. This one was created for TeamViewer but you can use it as a template for other applications.
Save the following code as Launch_Teamviewer.Au3 then compile it to Launch_TeamViewer.exe (Substitute your app name in place of TeamViewer).
Code:
#cs ----------------------------------------------------------------------------
Launch_Teamviewer:
Portable TeamViewer Launcher: Allows you to remotely control PCs even through firewalls.
AutoIt Version: 3.2.2.0
Author: Mickey72
Script Function:
Clear portable session settings from previous session then launch TeamViewer.
#ce ----------------------------------------------------------------------------
; Delete previous temp profile then temp registry.
DirRemove ("TeamViewer\File System\User", 1)
FileDelete("TeamViewer\Registry\TeamViewer_registry.reg")
; Launch JauntPE portable executable.
Run("TeamViewer\TeamViewer_portable.exe")