this is not the same issue... the issues described here relates to linux only - your issue is not certificate related.
I think the issue you have is you upgrade from an old 'test' version that was past 'end of life', so the auto upgrade 'fails'
(I did post here that all test users had to upgrade, but I guess you missed this post)
anyway, all you need to do is go to file/preferences and do 'reset all'
ALSO... I see that you have added a couple of files in the axoloti-factory sub directory (see the 'untracked' messages in your console log) , if you wish to keep these, you should move them somewhere else
axoloti/patches is the 'normal' place.