My iTunes library has some files, like purchased music from Amazon, in their own folders which is annoying but at least understandable. Most of my music is from CDs I've ripped in iTunes and I recently noticed that some files are in
user > music > iTunes> iTunes music
... and others are in:
user > music > iTunes> iTunes music > Music
It's quite common for files to be split between both locations, even in the same album that I ripped all at the same time. I've tried to put the files all in one location, but iTunes complains that the file cannot be found, would I like to locate it? Not a big deal for a few files but pretty untenable for hundreds of songs.
I'm using iTunes 12 under El Capitan on a 2011 Macbook Pro.
Is there a way to clean all this up short of doing it manually and reimporting the files to iTunes? How can I stop it from doing this in the future?