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I have built a web application in Windows which uploads and then deletes a file. When I deployed my war file in Debian Linux to Tomcat server, it allows me to upload the file and save it in the file system, but when I am trying to delete that file, it doesn't work because of the file's permissions.

I want to login as a root user in Debian UI. Is there any way to do so?

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You can launch Nautilus using gksudo and manage the filesystem if you are only interested in files or folders.

As a normal user, just press alt+f2 and enter gksudo nautilus.

It is advised not to login as as root into a Linux box. Use sudo and if you want to act as root, use su.

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Depending on the UI-manager (e.g. GDM/KDM/XDM) you need to tell them (for KDM it's /etc/kdm/kdmrc) that root-logins are allowed.

An alternative (and recommanded way) is to create a normal user to login and then use sudo to run root-commands.

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