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Definitely you want uploads, and you should call file_exists() before you write to any directory. If a file already exists in the directory, append a random number to the end of the file name, check that it exists again, and when it doesn't, insert it into the directory.
hmm, i could use a system like hot scripts.com which only keeps the info on scripts (e.g. what they are and where they are), this way i will not only save on the space but also it will sto the renameing problem