Don't set deprecated option during setup

ignore-kde-structure is deprecated in favour of directory-layout, which
is a more flexible alternative.
2 jobs for work/jzarl/default-dirstructure in 2 minutes and 32 seconds (queued for 88 minutes and 58 seconds)
latest
Status Job ID Name Coverage
  Test
passed #104973
smoke-test

00:01:54

passed #104972
unit-test

00:00:37