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but each photo which is taken vertically, automatically rotates when imported and is put to that "modified" folder.

Rotating the picture makes a modification to it, so it goes in the "modified" folder.

When I used iPhoto, I would use the Image Capture program to make sure my photos were correctly rotated, and then have it import the photos into iPhoto.

I have two digital cameras. My old Sony didn't auto rotate my photos. My new Canon does.

So on the Sony, I manually rotate all photos taken in the portrait orientation.

I also use the camera for downloading (as opposed to a card reader). iPhoto imports all pictures in the correct orientation and I don't have to rotate, therefore, I don't have a boatload of photos in the modified folder.
 
My Canon's not 100% about correctly rotating them, which is why I use the Image Capture program to verify (and rotate, if needed) before importing. Piece of cake. :)
 
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