This demonstrates the problem:
\relative c' {
c4 d e f
d e
\repeat volta 2 {
f g
a, b c d
}
\alternative {
{
e2
}
{
e2~ e2
}
}
}
I need the first ending to be half a measure, and the second ending to be a whole measure to work out musically. For a published example, see Idumea from the Sacred Harp. Though this is in 3/2, the idea is the same:
Apparently, LilyPond is treating the second ending as the second half the measure beginning in the first ending. I guess I don't expect LilyPond to have more sense than that; it would be a very subtle thing to get right, but how can I convince Lilypond to do the right thing here?