Files lost?

Hello, I was installing a mod for Minecraft and entered this in the terminal:

This was so that I could place some files into the Minecraft Jar file. However, it would not install properly (this was not the first time I've installed it and the other times it worked fine) so I decided to delete the Minecraft Jar file and start again, in case there was any other conflicting mods that were causing it not to work. So I then used the command to put the folder back. Then it started coming up with something like "permission denied to documents" or something a long those lines and it started doing it to other folders, such as downloads, desktop and library. When I checked the folders they had nothing in them. I think they might still be somewhere on my computer though because my hard drive space doesn't seem to have changed. I googled for a while trying to find a solution, but I could not find anything. It has also come up with 'Keychain Not Found' for both my gmail and airport. I'm really not sure what to do, I stupidly didn't back up my system because I don't have a lot of things of importance, however I will have to re-download some large files which will be rather annoying, also have to find all of my bookmarked websites, fonts, start save games on my games again and all of my photoshop work will need to be re-done.

Since I wrote this (I posted it on MacRumours because I couldn't get on here) I have tried 'TinkerTool' to show hidden files, but with no luck.

So does anybody have a possible solution for this?