Yes, you've taken the files out of their folders and placed them in the root. So, now when the document loads and the <head> section looks for "js/lightbox.js" it's not going to find it because you've taken it out of the folder 'js'.
You need to make sure your paths are correct. Either recreate the 3 folders you removed (i.e. "css", "images" & "js") and place the respective files back in, or change the paths in the <head> section to point to where the files are now (i.e. the root).
Personally, I would recreate the folders as it's always better practice to have a clean directory structure, rather than hundreds of files in the root.
That should get you going.
EDIT: You edited your post at the same time as my reply so this may seem strange to anyone reading it later on. Just a quick tip... In future I wouldn't make wholesale changes to your posts as people will be reading these later on and will lose track of the thread halfway through.