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If you were loged in as a user, log in as that user and open a terminal and try
ls -a
see anything there like maybe .amule , I don't know just a guess.
You can also change the path where aMule saves your finished downloaded and temp files. In aMule, go to "Options > Directories". And as suggested above, Nautilus can display hidden folders. Click on your "home" icon, then press "Ctrl + H" to see hidden folders. If you want it to _always_ display hidden folders, go to "Edit Menu > Preferences > Views Tab > Default View" and make sure that the checkbox "Show hidden and backup files" is checked.
I might also recommend you this Ubuntu Starter Guide. It's pretty neat and will help you with almost everything you will ever need
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