Folders Suddenly Empty?!

I was playing with m.necraft mods using the terminal commands below that I saved as a text file:
FIRST PART:
cd ~
mkdir mctmp
cd mctmp
jar xf ~/Library/Application Support/minecraft/bin/minecraft.jar
SECOND PART:
rm META-INF/MOJANG_C.*
jar uf ~/Library/Application Support/minecraft/bin/minecraft.jar ./
cd ..
rm -rf mctmp
While doing that, I had my Documents folder, my Files folder (/Users/--/Files) and Desktop opened in finder. For some apparent reason, these folders' content disappeared. Although, I, myself am not sure whether it was deleted because my Trash was empty, my FREE hd space was not higher (as there was plenty of files 20-40GB lost in total) and there was no "deleting ..." window.
My guess is that when I was playing with the commands, I forgot a line or two OR I only did the second part. Point is, after playing with the terminal, I can still see the "mctmp" folder that was in the Users/--/ folder. And I made that folder gone by now.
Thank you for your help.

Additional notes: I have used this command plenty of times. I can proudly say over 100 times, and only this time has it gone wrong.
Have read-->tried the following:
<https://discussions.apple.com/thread/3732006>
<https://discussions.apple.com/message/15855371>
<https://discussions.apple.com/message/18662032#18662032>
<https://discussions.apple.com/message/12438197>

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