FTP client that keeps track of the files and only uploads the files that have changed from last session
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Incremental FTP Client

This is a FTP client that keeps track of the files, and only uploads those that have changed. It works better in those projects that have thousands of small files.

It's a improved version of a similar program I found two years ago, but I don't remember where.

It has a configurable list of hosts, and it can resync with the server if the files were changed for whatever reason (using a remote PHP script)