How do I split a flac with a cue?

Shnsplit can read a cue file directly, which also means it can access the other data from the cue file (not just the breakpoints) and generate nicer filenames than split-*.flac:

shnsplit -f file.cue -t %n-%t -o flac file.flac

Granted, this makes it more difficult to use cuetag.sh if the original flac file is in the same directory.

I only know a CLI way. You will need cuetools and shntool.

cuebreakpoints file.cue | shnsplit -o flac file.flac
cuetag.sh file.cue "split-*".flac

Flacon is an intuitive open-source GUI that does exactly that: split a FLAC with a CUE.

Flacon extracts individual tracks from one big audio file containing the entire album of music and saves them as separate audio files. To do this, it uses information from the appropriate CUE file.

It supports among other things:

Supported input formats: WAV, FLAC, APE, WavPack, True Audio (TTA).

Supported out formats: FLAC, WAV, WavPack, AAC, OGG or MP3.

Automatic character set detection for CUE files.

To use it you only need to open the *.cue file with Flacon. It should then automatically detect the big *.flac file (if not, you can specify this manually), and then you should select Flac output format (and optionally configure the encoder), and start the conversion process.