Thanks for pointing out to omissions in the manual. We'll correct them shortly.
Regarding spaces in the commandline, it's a common thing in all operating systems. When you need to pass a filename that contains one space or multiple spaces, you have to make it surrounded with double qoutes.
nucoder.exe -r -c 5.2 --copyall "c:\Program Files\Apache Group\Apache2\htdocs\Bronnen_Framework" C:\Temp\Bronnen_Framework
^^^ will work
BTW with -r, you may want to add -n, just to make all files encoded even if there are errors on some of them.