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Synclair is a tool for diff'ing and synchronizing directories. It also includes a utility to findduplicate files (by name, or md5 hash). It is a command line tool, written in Java.
PHP::Duploc helps you findduplicate code (a \"bad smell\", prompting a refactoring) in your PHP scripts. By looking for certain patterns in a \"dotplot\" graph, you can visually get a quick overview over a large body of code.
same is a tool to findduplicate lines in multiple text files. Very useful to find and fix copy-and-paste programming. It has been designed to be simple, portable, and fast.