If you're doing anything even the least bit complicated on your computer, chances are you're generating anywhere from several- to a whole bunch of files. Source code files, word processing documents, images, and everything else may be scattered across your hard drive. If you're really disciplined and tidy, then you know where all that stuff is and can keep track of it all. But if your organizational skills leave something to be desired, or if you're trying to keep track of multiple versions of a project—today's work, last Tuesday's work, the version from last month—your life can get exponentially more complicated. What you need is a tool that can help you keep track of all these files to make sure you've got what you want but aren't keeping unnecessary copies of old work.
FreeFileSync may be able to give you a hand with this. To use it, all you need to do is drag and drop the two directories you want to compare and then press the magic button. Then if you want to continue and synchronize the contents of those two folders, click the Synchronize button and FreeFileSnc takes care of the rest. There are oodles of settings you can tweak to give you the behavior you're looking for, including an option to stick files into the Recycle Bin instead of just deleting or overwriting them. You can also build filters to exempt certain files (maybe configuration info?) from being synchronized.
FreeFileSync is a free download. It runs under both Linux and Windows.