bin/ci: Ensure that all jobs have nodes in DAG

bin/ci: Ensure that all jobs have nodes in DAG

Some automatic jobs, such as 'rustfmt' and 'clang-format', are skipped
during the graph sweep because their parents are already included in the
node set.

This commit ensures all visited jobs are in DAG and fixes iteration
modification using deepcopy.

Closes: https://gitlab.freedesktop.org/mesa/mesa/-/issues/9376

Signed-off-by: Guilherme Gallo <guilherme.gallo@collabora.com>
Acked-by: David Heidelberg <david.heidelberg@collabora.com>
Reviewed-by: Eric Engestrom <eric@engestrom.ch>
Part-of: <https://gitlab.freedesktop.org/mesa/mesa/-/merge_requests/24176>