Join many MP3, OGG, and FLAC files into one WAV or FLAC

You can do this with ffmpeg and sox:

for i in *.mp3 *.ogg *.flac
do
  ffmpeg -i "$i" "$i.wav"
done

sox *.wav combined.wav

Assuming you want to merge them alphabetically, by filename:

for f in ./*.{ogg,flac,mp3}; do echo "file '$f'" >> inputs.txt; done
ffmpeg -f concat -i inputs.txt output.wav

The for loop puts all the filenames in a file called inputs.txt, one-per-line, and the second one uses ffmpeg's concat demuxer to merge the files. It is possible to use printf instead of the loop like so:

printf "file '%s'\n" ./*.{ogg,flac,mp3} > inputs.txt

Assuming a modern shell, you can also use command substitution to do the whole thing in a single line.

ffmpeg -f concat -i <(printf "file '%s'\n" ./*.{ogg,flac,mp3}) output.wav

If you start with only lossless files, you can use use shntool:

shntool join *.flac

It seems that the Sound Juicer that comes with Ubuntu writes broken FLAC files, which result in no MD5 signature in the file. MAKE A COPY of the directory containing the files you want to concatenate, then run the script below.
echo fixing broken FLAC files
find . -type f|grep .flac$ |while read file
do
flac -f --decode "$file" -o temp.wav
flac -f -8 temp.wav -o "$file"
done
rm temp.wav

Then run
shntool join *.flac
as above.

However, be aware that the shntool join will insist on joining them in collating sequence (alphabetical) order EVEN IF you specify them otherwise.

shntool join fileB.flac fileA.flac

will put A before B.

You can either rename the files first or use the -r parameter ("-r ask" will prompt for the order).

Frankly I find this irritating...

Also you can force the output mode, so if you're joining FLACs:

shntool join *.flac -o flac

will result in joined.flac rather than joined.wav