Circular purple icon with white arrow inside

Where the icon is defined

The representation of an application in Dash and the the Unity launcher is defined in a .desktop file. Such a .desktop files includes a line to set the command to run the application, a line to set the icon of the application and a varying number of possible lines to set additional properties.

To see the current Unity launcher's content by command:

gsettings get com.canonical.Unity.Launcher favorites 

If you run this command, you will (a.o.) get a list of references to .desktop files, in the order like they appear in the launcher. An application's mention in the list looks like: application://thunderbird.desktop. It refers (in this example) to the file, thunderbird.desktop.

When Unity gathers its information on login, it first looks into the local directory for .desktop files, (~/.local/share/applications), and secondly in /usr/share/applications. If a .desktop file exists in both directory, the local one has preference. Normally, during your session, the launcher's icon stays linked to the .desktop file in either one of these directories.

When the content of the linked desktop file is edited during your session, the result is applied immediately. However, the icon as it appears in the Unity launcher does not change until you either:

• log out / login
• remove the icon from the launcher and lock it again

Since you cannot remove the icon of a running application from the launcher, changing the icon of a running application is not possible.
To change the icon of an application in the launcher which is not running however, you can use the two scripts below.
The first one copies the .desktop file to the local directory and edits the Icon= line in the local copy. The second one refreshes the icon in the launcher (and relinks it if necessary).

Script 1; change the icon

how to use

Copy the script below into an empty file, save it as change_icon.py, run it by the command:

python3 change_icon.py <applicationnamme.desktop> </path/to/new/icon>

for example:

python3 change_icon.py thunderbird.desktop </path/to/new/icon>

for smoother use:

create a directory ~/bin, copy the script into the directory, remove the language extension from the script, make it executable and (after logout / login), you can simly use the script by the command:

change_icon <applicationnamme.desktop> </path/to/new/icon>

More info on where to store and how to define icons, you can find here

The script

#!/usr/bin/env python3

import os
import shutil
import sys

file = sys.argv[1]
new_icon = sys.argv[2]

user_home = os.environ["HOME"]
dir_1 = user_home+"/.local/share/applications/"
dir_2 = "/usr/share/applications/"
dtfile_list1 = os.listdir(dir_1)
dtfile_list2 = os.listdir(dir_2)

subject = dir_1+file

if not os.path.exists(subject):
    try:
        shutil.copyfile(dir_2+file, dir_1+file)
    except FileNotFoundError:
        print("the file "+file+" does not exist")
        
def read_file(file):
    with open(file) as edit:
        return edit.readlines()

def write_file(file, linelist):
    with open(file, "wt") as edit:
        for line in linelist:
            edit.write(line)

subject_lines = read_file(subject)
index = [i for i in range(len(subject_lines)) \
         if subject_lines[i].startswith("Icon=")][0]
subject_lines[index] = "Icon="+new_icon+"\n"
write_file(subject, subject_lines)

Script 2; refresh the icon in the launcher

how to use

Copy the script below into an empty file, save it as refresh.py, run it by the command:

python3 refresh.py <applicationnamme.desktop>

for smoother use:

Like in the script above, copy the script into ~/bin, remove the language extension, make it executable and (after logout / login), you can simly use the script by the command:

refresh <applicationnamme.desktop>

for example:

refresh thunderbird.desktop

The script

#!/usr/bin/env python3

import subprocess
import time
import sys

desktopfile = sys.argv[-1]

def read_currentlauncher():
    # reads the current launcher contents
    return subprocess.check_output([
        "gsettings", "get", "com.canonical.Unity.Launcher", "favorites"
        ]).decode("utf-8")

def set_launcher(llist):
    # sets a defined unity launcher list
    current_launcher = str(llist).replace(", ", ",")
    subprocess.Popen([
        "gsettings", "set", "com.canonical.Unity.Launcher", "favorites",
        current_launcher,
        ])

def refresh_icon(desktopfile):
    current_launcher = read_currentlauncher()
    current_launcher_temp = eval(current_launcher)
    item = [item for item in current_launcher_temp if desktopfile in item][0]
    index = current_launcher_temp.index(item)
    current_launcher_temp.pop(index)
    set_launcher(current_launcher_temp)
    time.sleep(2)
    set_launcher(current_launcher)

refresh_icon(desktopfile)

Your ~/.config/user-dirs.dirs file has some incorrect settings, in particular you have lost the correct setting for 'DESKTOP'. Possibly others have been changed as well and may need some editing, (the contents of your ~/.config/user-dirs.dirs file will reveal this).

My own ~/.config/user-dirs.dirs file is as follows:

andrew@ithaca:~$ cat ~/.config/user-dirs.dirs
# 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="$HOME/Videos"
andrew@ithaca:~$ 

You can certainly edit the file directly as is suggested above but another way to correct the missing entries in your own file is to run the following commands one after the other from a Terminal window:

xdg-user-dirs-update --set DESKTOP "$HOME/Desktop"
xdg-user-dirs-update --set DOWNLOAD "$HOME/Downloads"
xdg-user-dirs-update --set TEMPLATES "$HOME/Templates"
xdg-user-dirs-update --set DOCUMENTS "$HOME/Documents"
xdg-user-dirs-update --set PICTURES "$HOME/Pictures"
xdg-user-dirs-update --set VIDEOS "$HOME/Videos"

Then logout and subsequently login or simply reboot, and all should be well. For reference here are all of the values that can be manipulated in this way:

DESKTOP
DOWNLOAD
TEMPLATES
PUBLICSHARE
DOCUMENTS
MUSIC
PICTURES
VIDEOS

The commands I have given you should return you to the defaults, and to remove the $HOME icon from the Desktop:

gsettings set org.gnome.nautilus.desktop home-icon-visible false

References:

• Arch Linux: Xdg user directories
• Ubuntu Linux: user.dirs.dirs man pages
• Ubuntu Linux: xdg-user-dirs-update man pages