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I'm on a linux machine and occasionally files dropped in the automatic import directory are ignored. This especially happens if the file already existed and I moved it into the directory.
My guess is that the file has an old timestamp and calibre ignores it. If I touch those files (giving them a timestamp of now), calibre will pick them up.
Of course, I also have the reverse problem -- sometimes I save files from the web browser into the autoimport directory, and calibre picks them up before the download is done. I've found a semi-reliable work around for that.
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