Thanks so much for your kind words!
So glad to hear you like the tool and find it useful. I've told this story a few times, but when I was first making the tool, I was kicking myself the whole time, thinking 'why are you reinventing the wheel, there has got to be something out there that does this already.' But I searched and searched and couldn't find anything, so I'm glad to hear you find the tool useful (perhaps showing that I was not crazy for writing it) and glad to hear it turned up when you searched for something (because I was in that spot myself not long ago ;)
BTW Since I wrote this tool, two other intrepid programmers over on OpenGameArt have come up with their own takes on the idea. You can find the results here:
and here
https://williamthompsonj.github.io/Color-Palette-Swapper/
and a big thread discussing the whole topic here:
https://opengameart.org/forumtopic/tool-for-palette-swappingchanging
Finally, thanks for the feature suggestion! And for the example picture, it really helps me understand what you're after. I'll look into implementing this. Internally, the program doesn't use Index mode at all, everything is full fat 24-bit RGB pixels, so there might be some challenges, but it does load indexed images and knows how to inspect the palette entries for an index image, so I'm sure I can figure out a way to get it working for you.
It is funny to say, because it's definitely not digging ditches, but I know what you mean about 32 clicks feeling like a lot of work! :)