Home directory messed up

Question

Recently, I installed Ubuntu 12.04. For some reason, i backed-up my home directory contents to another directory(say bkp dir). Precisely, I moved Documents, Pictures, Downloads, etc.. to bkp directory. Now, Deleted all my original home directory contents. I restored all the bkp directory content back to home. I find them all on my Desktop. I believe some kinda chain is broken. I don't find respective home directories icons on them. How do i restore it? Also, I don't find them in my places options.

The desktop looks like this:

Running ls -lh ~ ~/Desktop shows this:

nuthan@nuthan-desktop:~$ ls -lh ~ ~/Desktop
/home/nuthan:
total 2.8M
drwxr-x--- 11 nuthan nuthan 4.0K May 28 20:05 android-sdk-linux
drwxrwxr-x  4 nuthan nuthan 4.0K May 25 13:36 android-sdks
drwxrwxr-x  2 nuthan nuthan 4.0K May 18 17:30 convert
-rw-rw-r--  1 nuthan nuthan    0 May 30 09:07 dependancies~
drwxr-xr-x  2 nuthan nuthan 4.0K Jun  6 14:16 Desktop
drwxrwxrwx  6 nuthan nuthan 4.0K Jun  6 12:06 Documents
drwxr-xr-x 28 nuthan nuthan  12K Jun  6 13:52 Downloads
drwxrwxr-x  2 nuthan nuthan 4.0K Mar  6 13:23 examples
-rw-r--r--  1 nuthan nuthan 8.3K May 11 16:19 examples.desktop
drwxrwxr-x  4 nuthan nuthan 4.0K May 18 19:04 github
-rw-rw-r--  1 nuthan nuthan    0 May 28 18:40 linux~
drwxr-xr-x  2 nuthan nuthan 4.0K May 11 16:46 Music
drwxrwxr-x  2 nuthan nuthan 4.0K May 30 08:48 node-code
drwxrwxr-x  4 nuthan nuthan 4.0K May 30 08:40 node_modules
drwxr-xr-x  7 nuthan nuthan 4.0K May 25 13:55 noduino
drwxrwxr-x  2 nuthan nuthan 4.0K May 30 11:58 nuthan
drwxrwxrwx  3 nuthan nuthan 4.0K May 24 11:13 Pictures
drwxrwxr-x  6 nuthan nuthan 4.0K Mar  6 13:23 public
drwxr-xr-x  2 nuthan nuthan 4.0K May 25 11:44 Public
drwxrwxr-x  2 nuthan nuthan 4.0K May 29 18:50 python
-rw-rw-r--  1 nuthan nuthan 983K Jun  6 14:16 Screenshot from 2012-06-06 14:16:37.png
-rw-rw-r--  1 nuthan nuthan 980K Jun  6 14:20 Screenshot from 2012-06-06 14:20:24.png
-rw-rw-r--  1 nuthan nuthan 731K Jun  6 14:22 Screenshot from 2012-06-06 14:22:06.png
drwxrwxr-x  3 nuthan nuthan 4.0K May 31 18:17 sketchbook
drwxrwxr-x  2 nuthan nuthan 4.0K Jun  6 13:05 sql
-rw-rw-r--  1 nuthan nuthan  201 May 28 22:08 sql~
drwxr-xr-x  2 nuthan nuthan 4.0K May 11 16:46 Templates
-rw-rw-r--  1 nuthan nuthan 5.1K Jun  4 12:29 test~
drwxrwxr-x  3 nuthan nuthan 4.0K May 14 11:09 Titanium_Studio
drwxrwxr-x  4 nuthan nuthan 4.0K May 14 21:00 Titanium Studio Workspace
drwxrwxr-x  4 nuthan nuthan 4.0K Jun  1 18:29 TPM_Trak
drwxrwxr-x  2 nuthan nuthan 4.0K May 24 17:30 Ubuntu One
drwxr-xr-x  2 nuthan nuthan 4.0K May 11 16:46 Videos
drwxrwxr-x  6 nuthan nuthan 4.0K May 31 15:10 workspace
drwxrwxr-x  3 nuthan nuthan 4.0K May 14 11:57 Zend

/home/nuthan/Desktop:
total 20K
-rw-rw-r-- 1 nuthan nuthan  441 May 30 09:07 dependancies
-rw-rw-r-- 1 nuthan nuthan 1.6K May 28 18:40 linux
-rw-rw-r-- 1 nuthan nuthan  470 May 28 22:16 sql
-rw-rw-r-- 1 nuthan nuthan 5.1K Jun  4 19:34 test
nuthan@nuthan-desktop:~$ 

Answer 1

I had to change the XDG references in xdg-user-dirs-update file

Answered at: https://answers.launchpad.net/ubuntu/+question/199558

file location: /home/username/.config/user-dirs.dirs

From

# This file is written by xdg-user-dirs-update
# If you want to change or add directories, just edit the line you're
# interested in. All local changes will be retained on the next run
# Format is XDG_xxx_DIR="$HOME/yyy", where yyy is a shell-escaped
# homedir-relative path, or XDG_xxx_DIR="/yyy", where /yyy is an
# absolute path. No other format is supported.
#
XDG_DESKTOP_DIR="$HOME/"
XDG_DOWNLOAD_DIR="$HOME/"
XDG_TEMPLATES_DIR="$HOME/"
XDG_PUBLICSHARE_DIR="$HOME/"
XDG_DOCUMENTS_DIR="$HOME/"
XDG_MUSIC_DIR="$HOME/"
XDG_PICTURES_DIR="$HOME/"
XDG_VIDEOS_DIR="$HOME/"

To

# This file is written by xdg-user-dirs-update
# If you want to change or add directories, just edit the line you're
# interested in. All local changes will be retained on the next run
# Format is XDG_xxx_DIR="$HOME/yyy", where yyy is a shell-escaped
# homedir-relative path, or XDG_xxx_DIR="/yyy", where /yyy is an
# absolute path. No other format is supported.
#
XDG_DESKTOP_DIR="$HOME/Desktop"
XDG_DOWNLOAD_DIR="$HOME/Downloads"
XDG_TEMPLATES_DIR="$HOME/Templates"
XDG_PUBLICSHARE_DIR="$HOME/Public"
XDG_DOCUMENTS_DIR="$HOME/Documents"
XDG_MUSIC_DIR="$HOME/Music"
XDG_PICTURES_DIR="$HOME/Pictures"
XDG_VIDEOS_DIR="$HOME/Videos"