Split .ape files with cue and convert to flac format is not so difficult.
We do it on an Ubuntu box for example:
First, install the dependency of shntool, flac, mac, cuetools
sudo aptitdue install flac shntool cuetools
and download mac package in form of deb or tarball.
Run the following command in a terminal:
shntool split -f FileName.cue -t '%n. %t' -o flac FileName.ape
and the output .flac files’ name follows this sequence:
1. Track1name.flac
2.Track2name.flac
Update:
2011-02-20:
FFmpeg supports decoding APE format since 0.5 release, and it’s very easy to convert APE to FLAC now:
ffmpeg -i Filename.ape -acodec flac Filename.flac
And Clementine supports CUE+APE/FLAC natively.