I came back to the forums to suggest #1 above - guess I don't need to now
I thought that it might be easier to have a configuration under the "folders" tab so you can choose to compare files within that folder or not, a checkbox. That way you can choose two folders and ONLY compare files BETWEEN the two folders, not inside it. I have pretty much every album from Black Sabbath (and Enya, and Bauhaus and more, and yes, my tastes vary), so I obviously have duplicates in my master music library.
I'll use what I was doing as an example - I had a corrupt media library spanning back almost 15 years. Some of the files were fine, others were trashed (bits of song files got mixed together, don't ask how, suffice to say it had to do with firewire, external drives, and mac/pc issues 6 years ago). I've fixed my media library, but have a folder of over 1000 individual tracks which I suspect are in my master library already.
For folders, I chose
1) master library top-level folder
2) folder with 1000+ individual tracks
What I wanted to do was compare folder #2 to folder #1 and eliminate the duplicates in folder #2.
What I got was every duplicate from every folder. Every pink floyd duplicate across multiple albums. Every Black Sabbath duplicate across... you get the idea.
So yes, this is a feature that would be EXTREMELY helpful
And like r0lZ said, such a great piece of software so far! 5/5 stars as-is, can't wait to see what comes next!