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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.
A command line tool that analyzes your music collection and reports its findings in a variety of formats (e.g. HTML, XML, PDF) to various targets such as the console, FTP-upload, files or eMail.
Synclair is a tool for diff'ing and synchronizing directories. It also includes a utility to find duplicate files (by name, or md5 hash). It is a command line tool, written in Java.