Allow Client commands from transfer queue

Relating ticket 478 (Client commands like remote commands) and ticket 479 (Recursive compare to transfer queue), allow executing client commands from the transfer queue. This will make it a lot easier to execute client commands on differing files and then continue the upload.
For example, when using a diff/merge tool.

what's a specific use-case for this?
how exactly would you use diff/merge tool in this case?

The diff/mergetool could be ran from a context-menu or toolbutton hosting available commands for selected items in the transfer-queue. As source and destination locations would be known at this point it would be a case of sequentially running the tool over each of the selected files. With the choice of storing the result remotely or locally.

e.g. kdiff3 %1 %2

It sounds like all 3 of your recent suggestions are looking to solve a problem that should be handled by source code version control systems such as cvs, svn, github or a million other projects.
If you use one of those systems, you will not have problems of overwriting unknown changes.
Trying to solve this problem using an FTP client is a wrong approach.