Your comments

There is no way (yet) to get it displayed in the Changes tab. But you can invoke the script as a external tool upon request which is configured to show the command's output.

I like this idea because it could provide the linear history of the Journal in the Log window.

So you only would need the directory tree to filter out the displayed files - or do you also would like to perform commands on this directory level?

No, I mean to create a script that pipes the output to files and then invokes your preferred compare tool. If the compare tool shows the result to the command line, SmartGit can show the output.

Unfortunately, we need to sort the requests by priority. Regarding this topic, a work-around would be: create an external tool that does what you want and invoke that, or another: configure an external compare tool that does the compare.

I like the idea of using a different color, maybe a green checkmark for staged changes?