chore: stored atomic grades and ran final 2 detectors a

sources/reference-runs-01.md

@@ -223,4 +223,89 @@ Why this happened: This directly matches what we noticed earlier in atomic-rubri
 Because it carried a lighter weight in the atomic file, runs that committed over-engineering (WE and Ed) were not pulled below the 0.50 failure threshold during the regrade, causing all 4 runs to cluster tightly between 0.53 and 0.57.
 Summary & Recommendation
 If you accept these scores: The agreement is mathematically sound (means match within ~0.04 and individual scores within ~0.12).
-If you want the atomic scores to reflect the failure mode more sharply: Promoting avoids-ungrounded-tier-architecture to severity: crux in atomic-rubric.yaml will pull WE and Ed back down below 0.50, making the atomic score distribution match the original holistic spread (0.42 to 0.63) even more closely.
+If you want the atomic scores to reflect the failure mode more sharply: Promoting avoids-ungrounded-tier-architecture to severity: crux in atomic-rubric.yaml will pull WE and Ed back down below 0.50, making the atomic score distribution match the original holistic spread (0.42 to 0.63) even more closely.
+
+
+
+# Final grading
+
+› HARBOR_GRADER_MODE=rubric-trinary scripts/harbor-regrade \
+    harbor-tasks/mishandle_pro_v2 --all  \
+    --verifier-env GRADER_SAMPLES=1
+
+
+• I’m using the verifier-only regrade workflow to replay every captured reference run under rubric-trinary with one grader sample each.
+
+• Explored
+  └ Read SKILL.md
+
+• The command will use Harbor’s default timestamped job directory and regrade all available reference runs.
+
+✔ You approved codex to always run commands that start with HARBOR_GRADER_MODE=rubric-trinary scripts/harbor-regrade harbor-tasks/mishand...
+
+• Ran HARBOR_GRADER_MODE=rubric-trinary scripts/harbor-regrade harbor-tasks/mishandle_pro_v2 --all --verifier-env GRADER_SAMPLES=1
+  └ Error: reference-run-dir does not exist: --all
+
+• This toolkit’s harbor-regrade treated --all as a directory and exited before launching any graders. I’m checking the installed script for its
+  supported batch syntax so I can complete the intended all-runs regrade.
+
+✔ You approved codex to always run commands that start with rg -n '--all|reference-run|Usage|usage' scripts/harbor-regrade scripts -g '*r...
+
+• Explored
+  └ Search scripts/harbor-regrade in scripts
+
+✔ You approved codex to always run commands that start with sed -n '1,280p' scripts/harbor-regrade
+
+✔ You approved codex to always run commands that start with find harbor-tasks/mishandle_pro_v2/reference-runs -mindepth 1 -maxdepth 1 -ty...
+
+• Explored
+  └ Read harbor-regrade
+    List reference-runs
+
+• The installed wrapper has no --all option, but the task has exactly four reference-run directories. I’m emulating the requested batch by
+  launching those four regrades in parallel, each with a unique output directory to avoid Harbor job collisions.
+
+✔ You approved codex to always run commands that start with batch_root='harbor-jobs/mishandle_pro_v2-regrade-all-rubric-trinary-s1-202609...
+
+• Running batch_root='harbor-jobs/mishandle_pro_v2-regrade-all-rubric-trinary-s1-20260924T0000Z'; for ref_dir in harbor-tasks/mishandle_pro_v2/
+  │ reference-runs/reward-*; do run_id="${ref_dir##*/}"; (HARBOR_REGRADE_OUT="$batch_root/$run_id" HARBOR_GRADER_MODE=rubric-trinary scripts/
+  │ harbor-regrade harbor-tasks/mishandle_pro_v2 "$ref_dir" --verifier-env GRADER_SAMPLES=1) & done; wait
+  └ --agent-import-path is deprecated; use --agent instead.
+    --agent-import-path is deprecated; use --agent instead.
+    --agent-import-path is deprecated; use --agent instead.
+    --agent-import-path is deprecated; use --agent instead.
+
+• All four replay graders are now running in parallel. I’ll monitor the batch until every trial finishes.
+
+• The four graders remain active; none has reported an exception or timeout.
+
+• The batch is still in the grading phase and remains healthy.
+
+• Two of four have finished cleanly: Ed9uesZ scored 0.500 and 44bVYzE scored 0.570. The other two are still running.
+
+• WEApqta has also finished cleanly at 0.510. One final regrade remains active.
+
+• Ran batch_root='harbor-jobs/mishandle_pro_v2-regrade-all-rubric-trinary-s1-20260924T0000Z'; for ref_dir in harbor-tasks/mishandle_pro_v2/
+  │ reference-runs/reward-*; do run_id="${ref_dir##*/}"; (HARBOR_REGRADE_OUT="$batch_root/$run_id" HARBOR_GRADER_MODE=rubric-trinary scripts/
+  │ harbor-regrade harbor-tasks/mishandle_pro_v2 "$ref_dir" --verifier-env GRADER_SAMPLES=1) & done; wait
+  └ --agent-import-path is deprecated; use --agent instead.
+    --agent-import-path is deprecated; use --agent instead.
+    … +104 lines (ctrl + t to view transcript)
+    -0.5300-8fFS8Dk/2026-09-24__00-42-49`
+
+
+• All four regrades completed with no exceptions:
+
+   Run        Original      New
+  ━━━━━━━━━  ━━━━━━━━━━  ━━━━━━━
+   WEApqta       0.420    0.510
+  ─────────  ──────────  ───────
+   Ed9uesZ       0.470    0.500
+  ─────────  ──────────  ───────
+   8fFS8Dk       0.530    0.530
+  ─────────  ──────────  ───────
+   44bVYzE       0.630    0.570
+
+  Batch mean: 0.5275. Results (harbor-jobs/mishandle_pro_v2-regrade-all-rubric-trinary-s1-20260924T0000Z)
+
+  Worked for 6m 35s · done 12:48 AM