Missing files, user folder, application folder and system folder

I am using a MacBook Pro 2011 model with OS X 10.9.4.
Since I bought the machine several years ago, I have had only a few small problems with it. Yesterday I wanted to reduce the size of a video, so I downloaded a video compressor/converter software, and left the computer on and the program compressing my video whilst I went off to work. When I returned home, the compressing program had a pop-up saying ''Could not complete compression, system full'' or something along those lines.... After trying to play the movie without success, I decided that I would restart my computer, as it had been on all day.
When the computer restarted, it came up with the grey loading bar, which usually comes up when I have done a software update. It disappeared quite soon and several minutes later, my user profile appeared. I logged in as normal, and then tried to open my browser. An error message popped up stating"Can't open user profile directory, because you lack sufficient privileges. You might want to contact the administrator of this machine". I then tried to open other programs and they all came up with similar messages and did not open. Skype stated "Can't create a lock file at Users/Lauren/Library...etc".
I then went to Finder to look at my applications and they were ALL GONE! Then I went to a folder I have with all my files called "My files", and although the primary folders were visible, "SCHOOL,WORK, HOLIDAYS PICS, etc", these folders were empty. I then checked my User folder, and my systems folder and these were empty too. However, the Desktop and Documents folders still contain the documents that were previously there, and my background images remained the same.
I tried to open Word, and although it is also missing from the applications folder, and it opened, also allowing me to open a document which I know is located within the 'empty' folders. I have a feeling that my documents and files are still on my computer, but I don't know how to access them!
Please if someone could shed light on the situation! All my work files and personal files are on this computer and I would be devastated to loose them!
Let me know if you need any more ino or screen shots!
Kind regards,
Lauren

OS X- Gray progress bar appears under Apple logo during startup
You need to start by doing the following:
Reinstall Lion, Mountain Lion, or Mavericks without erasing drive
Boot to the Recovery HD:
Restart the computer and after the chime press and hold down the COMMAND and R keys until the menu screen appears. Alternatively, restart the computer and after the chime press and hold down the OPTION key until the boot manager screen appears. Select the Recovery HD and click on the downward pointing arrow button.
Repair
When the recovery menu appears select Disk Utility. After DU loads select your hard drive entry (mfgr.'s ID and drive size) from the the left side list.  In the DU status area you will see an entry for the S.M.A.R.T. status of the hard drive.  If it does not say "Verified" then the hard drive is failing or failed. (SMART status is not reported on external Firewire or USB drives.) If the drive is "Verified" then select your OS X volume from the list on the left (sub-entry below the drive entry,) click on the First Aid tab, then click on the Repair Disk button. If DU reports any errors that have been fixed, then re-run Repair Disk until no errors are reported. If no errors are reported then click on the Repair Permissions button. When the process is completed, then quit DU and return to the main menu.
Reinstall Lion, Mountain Lion, or Mavericks
OS X Mavericks- Reinstall OS X
OS X Mountain Lion- Reinstall OS X
OS X Lion- Reinstall Mac OS X
     Note: You will need an active Internet connection. I suggest using Ethernet
                 if possible because it is three times faster than wireless.

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