Log in cPanel. Choose the icon 'File manager' from the files label. You will see the File manager interface. You can use file manager to upload files to your account, delete files, and change the file permissions and various other functions.
On the left side is the collapsible list of folders in your account. The right side will show the files and folders present in the folder selected on left hand side. Public_html folder will contain your website files.
For example, let us upload a sample CGI script to cgi-bin folder in the account. Click cgi-bin folder on left side, click upload on the options given above. Now select the files (browse them) and select the required file. Click the option to return to file manager screen to see that the file has been added to cgi folder. You can click on the new file to change its permissions. You can change the location by move file option, on the upper side. Enter the new location and save it. The new change will take place at that very moment.
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