The first part of this is taken from this page. In a directory of FLAC (Free Lossless Audio Codec) files and a file of album cover art named cover.jpg which looks like this in the terminal
total 321052
-rw-r--r-- 1 stuart stuart 29812 Oct 30 11:56 cover.jpg
-rw-r--r-- 1 stuart stuart 29338989 Oct 30 12:50 'Disc 1 - 01 - Drive.flac'
-rw-r--r-- 1 stuart stuart 28464150 Oct 30 12:50 'Disc 1 - 02 - Try Not to Breathe.flac'
-rw-r--r-- 1 stuart stuart 30688630 Oct 30 12:51 'Disc 1 - 03 - The Sidewinder Sleeps Tonite.flac'
-rw-r--r-- 1 stuart stuart 31871345 Oct 30 12:51 'Disc 1 - 04 - Everybody Hurts.flac'
-rw-r--r-- 1 stuart stuart 10201899 Oct 30 12:52 'Disc 1 - 05 - New Orleans Instrumental No. 1.flac'
-rw-r--r-- 1 stuart stuart 27389504 Oct 30 12:52 'Disc 1 - 06 - Sweetness Follows.flac'
-rw-r--r-- 1 stuart stuart 23791188 Oct 30 12:52 'Disc 1 - 07 - Monty Got a Raw Deal.flac'
-rw-r--r-- 1 stuart stuart 34406615 Oct 30 12:53 'Disc 1 - 08 - Ignoreland.flac'
-rw-r--r-- 1 stuart stuart 22177867 Oct 30 12:53 'Disc 1 - 09 - Star Me Kitten.flac'
-rw-r--r-- 1 stuart stuart 38196844 Oct 30 12:53 'Disc 1 - 10 - Man on the Moon.flac'
-rw-r--r-- 1 stuart stuart 26055456 Oct 30 12:54 'Disc 1 - 11 - Nightswimming.flac'
-rw-r--r-- 1 stuart stuart 26113191 Oct 30 12:54 'Disc 1 - 12 - Find the River.flac'
and like this in the file manager:

Type the following
metaflac --import-picture-from="3|image/jpeg|||cover.jpg" *.flac
--import-picture-from= uses the following options and cover art"3|image/jpeg|||" 3 means this is front cover art, image/jpeg is the mime type likely optional, cover.jpg is the name of the image file, | is the option separator and all of them are needed*.flac update all .flac files in the current directoryAfter which file sizes will increase by slightly less than the size of the image file, strangely.
total 321396
-rw-r--r-- 1 stuart stuart 29812 Oct 30 11:56 cover.jpg
-rw-r--r-- 1 stuart stuart 29368847 Oct 30 13:00 'Disc 1 - 01 - Drive.flac'
-rw-r--r-- 1 stuart stuart 28494008 Oct 30 13:00 'Disc 1 - 02 - Try Not to Breathe.flac'
-rw-r--r-- 1 stuart stuart 30718488 Oct 30 13:00 'Disc 1 - 03 - The Sidewinder Sleeps Tonite.flac'
-rw-r--r-- 1 stuart stuart 31901203 Oct 30 13:00 'Disc 1 - 04 - Everybody Hurts.flac'
-rw-r--r-- 1 stuart stuart 10231757 Oct 30 13:00 'Disc 1 - 05 - New Orleans Instrumental No. 1.flac'
-rw-r--r-- 1 stuart stuart 27419362 Oct 30 13:00 'Disc 1 - 06 - Sweetness Follows.flac'
-rw-r--r-- 1 stuart stuart 23821046 Oct 30 13:00 'Disc 1 - 07 - Monty Got a Raw Deal.flac'
-rw-r--r-- 1 stuart stuart 34436473 Oct 30 13:00 'Disc 1 - 08 - Ignoreland.flac'
-rw-r--r-- 1 stuart stuart 22207725 Oct 30 13:00 'Disc 1 - 09 - Star Me Kitten.flac'
-rw-r--r-- 1 stuart stuart 38226702 Oct 30 13:00 'Disc 1 - 10 - Man on the Moon.flac'
-rw-r--r-- 1 stuart stuart 26085314 Oct 30 13:00 'Disc 1 - 11 - Nightswimming.flac'
-rw-r--r-- 1 stuart stuart 26143049 Oct 30 13:00 'Disc 1 - 12 - Find the River.flac'
However the thumbnails will remain as in the picture until you clear the thumbnail cache. This is only needed if you have visited this directory in file manager and default thumbnails have been created. If you run the above command before viewing the files in file manager everything will be as wanted.
rm -rf ~/.cache/thumbnails/*
and then the file manager will look like this.
