I stared at that headline thinking… 46 grey boxes… what am I not understanding.
Linux
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Linux is a family of open source Unix-like operating systems based on the Linux kernel, an operating system kernel first released on September 17, 1991 by Linus Torvalds. Linux is typically packaged in a Linux distribution (or distro for short).
Distributions include the Linux kernel and supporting system software and libraries, many of which are provided by the GNU Project. Many Linux distributions use the word "Linux" in their name, but the Free Software Foundation uses the name GNU/Linux to emphasize the importance of GNU software, causing some controversy.
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I'm not a Gnome expert and are using the 'dash2dock' extension, but if I right click on rightmost 'show apps' icon, and select 'dash2dock settings, I can change opacity, bg color and such.
Not sure where else to change those settings, so apol's if this is not applicable in your case.
I don't use that extension, it was the theme that had to be updated because gnome 46 changed some stuff.
Anyway thanks for helping troubleshooting!
For me it looks like this, the same as in gnome 46. What distro are you using?