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JFtpSync is for uploading web content to a server via FTP. It is designed to do FTP uploading only, and do it well, offering recursive uploading of content filtered by file type. It is primarily a command-line tool but there is a Java GUI as well.
GiraffeFTP is a Java based FTP client and server. It includes GUI and commandlinetools. Good code to see to understand the FTP Protocol and sockets. Also includes a non-standard implementation of SSL sockets.