At the moment I am using:
SetOutPath "$INSTDIR\folder\subfolder"
File /r ..\Output\*.*
The problem is when re-installing all files will be overwritten.
Questions:
How do I copy the files from the installer only if they do not already exist in the target directory?
and
How do I overwrite those files in the target directory that are older then the ones in the installer?
Edit:
I found this macro: http://nsis.sourceforge.net/MoveFileFolder