The generated patcher can receive also commandline switches.
Patcher Command Line Usage
/silent
No Dialog and MessageBoxes will be shown.
/backup
Make backup of every file which is patched (only for "/silent" mode).
/overwrite
Overwrite existing files when exporting an file attachment (only for "/silent"mode).
/startupworkdir
Set the startup working directory for the patcher (example: "/startupworkdir c:\windows\system"). Its also possible to use environment variables (example "/workdir %windir%\system".