Try make symlinc, folder /var/www/html. No, it make in /home/user. Same happen, upload file. File go /home/user. Make new file, same problem. Always /home/user, why?
More explain problem: I in different directory in FileManager. But file not go in this directory. Always go /home/user. Why always /home/user? Not understand. Need help.
Okay, here how I do, you try see problem:
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Open FileManager.
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Go directory /var/www/html.
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Try make symlink here. But no, it make in /home/user, why?
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Same with upload file. I in /var/www/html, but file go /home/user, not here.
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Try make new file too. Still, it go /home/user. Not right place.
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This also happen other directory. Not only /var/www/html.
FileManager always put file in /home/user. Not directory where I am. This the problem. You try, you see. Why like this? Need fix.