fix: complete code review follow-ups for queue, stats, and docs

Replace overlap Pending flag with PendingRuns counter, match seed stats
by job_id, align average duration with TimedRunCount, and tidy docs.

Co-authored-by: Cursor <cursoragent@cursor.com>

src/runner/runner.go

@@ -29,7 +29,7 @@ func RunJob(ctx context.Context, job *domain.Job, trigger string, logsDir string
 	var detail string
 	var durationMS int64
 	if job.StartOnly {
-		invocation := jobInvocation(context.Background(), *job)
+		invocation := jobInvocation(ctx, *job)
 		state, detail, output = startJobOnly(invocation, *job, started)
 		// StartOnly jobs don't wait for process exit, so no meaningful duration.
 		durationMS = 0