I noticed that some Linux apps installed on my Chromebook would be given a generic penguin icon in the launcher, while others have their own icons. It turns out that many of these apps install custom icons but the file that defines the launcher icon doesn't connect to them properly. Here's the process for fixing that.

1. Find a PNG icon to use. It may already be installed in one of the following locations: /usr/share/icons/hicolor/(resolution)/apps/(appname).png or /home/(linuxuser)/.local/share/icons/hicolor/(resolution)/apps/(appname).png Where (linuxuser) is the linux username, (resolution) is a folder, e.g. "48x48", and where (appname) is a short name of the app, e.g. /usr/share/icons/hicolor/48x48/apps/gftp.png or /home/penguin/.local/share/icons/hicolor/512x512/apps/joplin.png
2. Find the .desktop file for the app. It may be found at /usr/share/applications/(appname).desktop or /home/(linxusername)/.local/share/applications/(appname).desktop e.g. /usr/share/applications/gftp.desktop or /home/penguin/.local/share/applications/appimagekit-joplin.desktop
3. Edit the .desktop file with your favorite text editor and change the Icon= line to point to the png icon file identified above.

The launcher seems to cache the icon information in such a way that you may need to completely shut down the chromebook and restart it more than once for the icon to show up, and it may show up hours later than you expect. In some cases you may see the new icon on the toolbar when you run the app, but not yet see it in the launcher. In my experience it took anywhere from 2 immediate reboots to waiting three hours before restarting for the launcher icon to update. I wasn't able to find help for how to hasten this process.

Thanks to:

• This helpful video: https://www.youtube.com/watch?v=Jotu-6Qd2fg