I haven't read the whole thread so I apologise if this has already been mentioned. The way I merge two folders in OSX is to use rsync in Terminal.
Code:
rsync -av folder/ /path/to/other/folder/
This will recursively scan the 2 folders and create a list of differences then fill in all of the gaps for all of the subdirectories.
You got to be careful with the slashes though since
Code:
rsync -av folder /path/to/other/folder/
does something slightly different.
You can read the man pages for rsync for more options, by typing `man rsync` in terminal. It's an amazingly handy and powerful copy command and it's the way most backup apps work I believe.