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are you using the GUI as "root"?
The path in e-uae says "/root/my-applications/...." and you are showing the content of the folders "~/my-applications/..."
if you are using the system as "root" (I doubt that) the symbol "~" means "/root/" but if you are using the system as user "zeke1312" (just to say a username) the symbol "~" means "/home/zeke1312/" so it is normal that e-uae doesn't find the files it needs on "/root/my-applications/...."
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