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In order to prevent file storage problems like when two people upload a file that might have the same file name…
Is it better to get each user a separate folder to prevent issues or is better to have all files in one folder for all users but change the file-name to keep them unique?
It depends on what you are trying to achieve.
What kind of service do you want to provide? A general file storage service? Then use different folders, since the number of files in a directory may be limited (depending on the file system) and can have major influence on the performance.
Do you provide an upload area for a simple blog? Use a single directory and change the file names.
Sorry, an absolute answer can only be given if you provide more information.