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3. File Exist rules rely on size only, FlashFXP does not allow the user to do things based on file dates. I think allowing dates would be a good idea, however I have found it very difficult to create a user friendly way to allow for this. A site manager setting for allowing the user to define the time zone of the server would probably be needed, along with an option to set the file time on upload.
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How about, for a basic solution to download the first X bytes (say 10k - should be enough to get past most file formats id's + stuff ), run a CRC on it and compare? Much cleaner than a date based comparison (although documents with one corrected spelling mistake might trick it)