Create lifecycle directories with non-shared modes #489

Source review comment:
#477 (comment)

Exact reviewed SHA: 5ef7c1ffe5200ffb68f5d1b5b425c63961790c37

Trigger

Run prepare_run or shard merge under a collaborative process umask such as
002 or 000.

Expected

Fresh lifecycle directories satisfy the atomic publication principal boundary.

Actual

Plain Path.mkdir can create group/other-writable directories, after which the
first lifecycle JSON write rejects the directory and aborts the run.

Impact

Valid benchmark and shard workflows fail on shared hosts with collaborative
umasks.

Required regression

Request a non-shared mode when creating run, input, artifact, observation, and
shard output directories. Prove successful preparation and shard output under
umask 000.