If you use Dropbox, you can place symbolic links in your Dropbox folder. This is a great way to backup directories while maintaining the local file structure you desire. As a bonus, the green checkmarks won't display on items backed up in this manner, though they will show up on other computers.
To create a symbolic link, open Terminal, and cd into your Dropbox folder. Then run a command like this. This command would add a symbolic link for a folder called Test that is in your Documents folder:
ln -s ~/Documents/TestUsing symbolic links allows you to add items to your Dropbox folder yet leave them in their "correct" location. So you could, for example, put your entire Documents folder in your Dropbox folder - if you have enough space - yet leave it in its standard location in your home folder.
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