&G. Schirmer has a new series of books out called The Flute Collection. There are three books in the series, a Easy-Intermediate, Intermediate, and Intermediate-Advanced. These are excellent books. They come with a Flute and a Piano part, the CD (or CDs) come with full performance and accompaniment tracks. Caen Thomason-Redus on Flute and Elena Abend on Piano.
Plus, if you use the CDs on a computer (Mac or PC), you can run the included Amazing Slowdowner program on the tracks.