The paired path had the same defect as the unpaired one: it subtracted two
step counts and handed the differences to the signed-rank test, so a pair
holding a run the wall clock stopped at step 12 entered as a difference
neither run supports. Twenty seeds where the first arm was still clean at
step 12 and the second violated at step 5 in six of them read sign -1 and
p 0.0011, pointing at the arm that never violated.
A pair is now scored the way the unpaired comparison scores one and tested by
the exact sign test over the pairs whose order censoring determines, which is
what the log-rank stratified by seed reduces to here. The signed-rank goes
with the differences it needed: a magnitude-based paired test wants a
difference from every pair, and the arms censor on different clocks. The
median difference stays, over the pairs where both runs violated, and says so.
A run stops at whichever comes first, the step budget or --duration, so
a clean run that reached the wall clock exited with fewer steps than the
budget and was still credited with the whole of it. The model arm pays a
network call and a screenshot per step, so it reaches the wall sooner and
was handed exposure it never had.
Nothing checked that two arms shared a budget either. Thirty identical
clean runs under budgets of 400 and 100 read a12 0.000 and p 1.685e-14
from the rank-sum while the log-rank in the same report read p 1.0000.
groupArms already refused this within one arm.
The claims the old convention left in comments and report lines are
corrected rather than left standing beside the new behaviour.
--paired contrasts two arms running the same seeds seed by seed with the wilcoxon signed-rank test rather than treating them as two independent samples, reporting the per-seed differences, the sign, a12 within pairs and the seeds usable in one arm only. --question names the family holm corrected within, and the family size is recorded next to the p-values rather than left to the reader to reconstruct.
pj