5 added, 2 removed. Audit A to A.
---
name: retro
description: "Post-run retrospective: reads .experiments/ JSONL, computes Wilcoxon significance, detects dead iterations, flags suspicious jumps, generates next-hypothesis queue for --hypothesis flag."
argument-hint: "[<run-id>] [--compare <run-id-2>] [--threshold <delta>] [--alpha <significance>]"
effort: medium
allowed-tools: Read, Write, Bash, Grep, Glob, Agent, TaskCreate, TaskUpdate, AskUserQuestion
disable-model-invocation: true
---
<objective>
Post-run retrospective analysis. After `/research:run` completes, reads `.experiments/state/<run-id>/experiments.jsonl`, computes statistical significance, detects dead iterations, flags suspicious metric jumps, generates learning summary with next-hypothesis queue.
NOT for: running experiments (use `/research:run`); designing experiments (use `/research:plan`); validating methodology (use `/research:judge`); verifying paper implementation (use `/research:verify`); comparing runs from different programs/goals — `--compare` valid only for same-program, same-metric runs. Read-only — never modifies code, commits, or experiment state.
</objective>
<workflow>
## Agent Resolution
**Agent resolution**: load and follow the protocol below. Contains: foundry check + fallback table. `research:scientist` in same plugin — no fallback needed if research plugin installed.
```bash
+ export CSID="${CLAUDE_CODE_SESSION_ID:-$PPID}"
_RESEARCH_SHARED=$(python "${CLAUDE_PLUGIN_ROOT:-plugins/cc_research}/bin/resolve_shared.py" 2>/dev/null) # timeout: 5000
[ -z "$_RESEARCH_SHARED" ] && { echo "! Plugin path resolution failed — ensure research plugin installed and CLAUDE_PLUGIN_ROOT set, or invoke /research:retro from project root."; exit 1; }
+ echo "$_RESEARCH_SHARED" > "${TMPDIR:-/tmp}/research-shared-${CSID}" # cold resolve — every later site reads this sentinel instead of re-running python
cat "$_RESEARCH_SHARED/agent-resolution.md"
```
## Retro Mode (Steps T1–T7)
Triggered by `retro`, `retro <run-id>`, or `retro <run-id> --compare <run-id-2>`.
**Defaults**: `--threshold 0.001`, `--alpha 0.05`.
**Unsupported flag check**: load and follow the protocol below. Supported flags for this skill: `--compare`, `--threshold`, `--alpha`.
```bash
# loads: unsupported-flag-protocol.md
- _RESEARCH_SHARED=$(python "${CLAUDE_PLUGIN_ROOT:-plugins/cc_research}/bin/resolve_shared.py" 2>/dev/null) # timeout: 5000
+ export CSID="${CLAUDE_CODE_SESSION_ID:-$PPID}"
+ IFS= read -r _RESEARCH_SHARED < "${TMPDIR:-/tmp}/research-shared-${CSID}" 2>/dev/null || _RESEARCH_SHARED="" # warm read (Check 41)
cat "$_RESEARCH_SHARED/unsupported-flag-protocol.md"
```
**Task tracking**: create tasks for T1–T7 at start — before any tool calls.
### Step T1: Locate and load run data
**Input resolution** (priority order):
1. Explicit `<run-id>` arg → read `.experiments/state/<run-id>/`
2. No arg → scan `.experiments/state/`, pick latest dir where `state.json` has `status: completed` or `status: goal-achieved`
3. None found → stop with error:
```text
No completed run found. Run /research:run first, or provide: /research:retro <run-id>
```
**Newer-in-progress check** (only when path 2 used — no explicit run-id given): after selecting completed run, scan `.experiments/state/` for any dir with `status: running` and mtime newer than selected dir. If found, surface warning but don't stop — user may intentionally retro prior completed run:
```text
⚠ Newer in-progress run found: <newer-run-id> (status: running, started <ISO timestamp>). Retro will analyse <selected-run-id> instead. Use /research:retro <run-id> to override.
```
**Load files** from `.experiments/state/<run-id>/`:
- `state.json`: extract `goal`, `best_metric`, `config` (incl. `metric.direction`), `iteration` count, `best_commit`. Compute `baseline_metric` from iteration 0 in `experiments.jsonl`.
- `experiments.jsonl`: full iteration history — validate each line parses as JSON. If last line truncated, warn and **rewrite sanitized copy to `$RUN_DIR/experiments-clean.jsonl`** (skip truncated last line). All downstream steps (T2 retro_analyze.py, T3 dead-iter scan, T5 scientist) must read sanitized copy — never raw file — so every step sees same iteration set. Persist sanitized path: `echo "$RUN_DIR/experiments-clean.jsonl" > "${TMPDIR:-/tmp}/retro-jsonl-path-${CSID}"` (consumers re-hydrate from this file). If JSONL untruncated, sanitized copy byte-identical to raw file.
- `diary.md`: if present, read for qualitative context in T5.
If `--compare <run-id-2>` present: load second run identically from `.experiments/state/<run-id-2>/`. If not found, stop: `"Compare target not found: .experiments/state/<run-id-2>/. Check run ID and retry."`
**Assign `RUN_ID_ARG`** from `$ARGUMENTS` — first positional non-flag token, empty if absent (ADV-H17):
```bash
export CSID="${CLAUDE_CODE_SESSION_ID:-$PPID}"
_REMAINDER=$(echo "$ARGUMENTS" | sed -E 's/--compare[= ]+[^ ]+//g; s/--threshold[= ]+[^ ]+//g; s/--alpha[= ]+[^ ]+//g')
RUN_ID_ARG=$(echo "$_REMAINDER" | awk '{for (i=1; i<=NF; i++) if ($i !~ /^--/) { print $i; exit }}')
RUN_ID_ARG="${RUN_ID_ARG:-}"
echo "$RUN_ID_ARG" > "${TMPDIR:-/tmp}/retro-run-id-${CSID}" # persist for T3 (vars lost between Bash calls)
```
**Pre-compute run directory** — also fix `$RUN_ID` (resolved from input resolution above), persist `$RUN_DIR` for T3 (ADV-H18 + ADV-L16):
```bash
export CSID="${CLAUDE_CODE_SESSION_ID:-$PPID}"
RUN_ID="${RUN_ID_ARG:-$(python "${CLAUDE_PLUGIN_ROOT:-plugins/cc_research}/bin/find_run_id.py" .experiments/state 2>/dev/null)}" # loads: find_run_id.py
- # T-G2: find_run_id.py errors suppressed by 2>/dev/null; surface empty case to avoid double-slash path
+ # T-G2: find_run_id.py errors suppressed 2>/dev/null; empty case surfaced to avoid double-slash path
[ -z "$RUN_ID" ] && { echo "! Failed to resolve run ID — no completed run found or bin/find_run_id.py unavailable; check research plugin install."; exit 1; }
BRANCH=$(git branch --show-current 2>/dev/null | tr '/' '-' || echo 'main') # timeout: 3000
echo "$RUN_ID" > "${TMPDIR:-/tmp}/retro-run-id-resolved-${CSID}"
```
```bash
export CSID="${CLAUDE_CODE_SESSION_ID:-$PPID}"
RUN_DIR=$(python "${CLAUDE_PLUGIN_ROOT:-plugins/cc_research}/bin/make_run_dir.py" "retro" ".experiments" 2>/dev/null) # timeout: 5000
mkdir -p "$RUN_DIR/scripts" # timeout: 3000
echo "$RUN_DIR" > "${TMPDIR:-/tmp}/retro-run-dir-${CSID}" # T3 + fallback path reload from temp file
```
### Step T2: Statistical significance analysis
Run the Wilcoxon signed-rank test via the bundled bin/ script — pure Python with scipy.stats:
```bash
export CSID="${CLAUDE_CODE_SESSION_ID:-$PPID}"
IFS= read -r RUN_ID < "${TMPDIR:-/tmp}/retro-run-id-resolved-${CSID}" 2>/dev/null || RUN_ID="" # re-hydrate RUN_ID from T1 (Check 41: fresh shell)
ALPHA="${ALPHA:-0.05}"
METRIC_DIRECTION=$(python "${CLAUDE_PLUGIN_ROOT:-plugins/cc_research}/bin/read_state_field.py" ".experiments/state/$RUN_ID/state.json" "config.metric.direction" --default "higher" 2>/dev/null || echo "higher") # loads: read_state_field.py
IFS= read -r RETRO_JSONL < "${TMPDIR:-/tmp}/retro-jsonl-path-${CSID}" 2>/dev/null || RETRO_JSONL=".experiments/state/$RUN_ID/experiments-clean.jsonl" # re-hydrate sanitized path from T1 (Check 41: fresh shell)
RETRO_RESULT=$(python "${CLAUDE_PLUGIN_ROOT:-plugins/cc_research}/bin/retro_analyze.py" --jsonl "$RETRO_JSONL" --baseline "baseline" --alpha "$ALPHA" --direction "$METRIC_DIRECTION") # timeout: 30000
RETRO_EXIT=$?
echo "$RETRO_RESULT" > "${TMPDIR:-/tmp}/retro-result-${CSID}" # persist for effect-size block (Check 41: fresh shell)
[ "$RETRO_EXIT" -eq 2 ] && { echo "retro: Input error (exit 2) — run-id '$RUN_ID' missing, malformed, or has no baseline record; re-run /research:run to create baseline"; exit 1; }
```
**Contract** — script reads JSONL, extracts metric values for ALL iterations with `status == "kept"`, runs one-sided **one-sample** Wilcoxon signed-rank test of "kept iterations vs single baseline metric" (`status == "baseline"`). Not a paired test — run records one baseline metric, no per-iteration matched baseline; baseline scalar compared against each kept value. Prints single line of JSON to stdout:
- `{"significant": bool, "p_value": float, "statistic": float, "n": int}` on success
- `{"significant": false, "p_value": null, "statistic": null, "n": <N>, "reason": "<msg>"}` when `N < 6` or scipy missing
- `{"error": "<msg>"}` on input error (exit 2 — missing file, malformed JSON, no baseline record)
Exit codes: `0` = significant · `1` = not significant (or insufficient data) · `2` = input error.
**Direction handling** — script branches on `--direction`:
- `higher` → `alternative = "greater"` (improvement = candidate > baseline)
- `lower` → `alternative = "less"` (improvement = candidate < baseline — for loss, latency, error)
Read `direction` from `state.json` config (or infer from goal text), pass via `$METRIC_DIRECTION`.
**Effect size** — script does not return rank-biserial `r` directly. Compute via the bundled bin/ script:
```bash
export CSID="${CLAUDE_CODE_SESSION_ID:-$PPID}"
IFS= read -r RETRO_RESULT < "${TMPDIR:-/tmp}/retro-result-${CSID}" 2>/dev/null || RETRO_RESULT="" # re-hydrate from T2 (Check 41: fresh shell)
EFFECT_R=$(echo "$RETRO_RESULT" | python "${CLAUDE_PLUGIN_ROOT:-plugins/cc_research}/bin/compute_effect_size.py") # timeout: 5000
```
**If `--compare`**: invoke script second time on second run's `experiments.jsonl`; downstream report renders second row.
Write the combined results (parsed JSON plus computed `r`) to `$RUN_DIR/stats-results.json` via Write tool.
### Step T3: Dead iteration detection
**Definition**: dead iteration window = 3+ consecutive iterations (any status) where `abs(metric_delta) < threshold` (default `--threshold 0.001`).
**Scale check** (after loading baseline_metric in T1): if `baseline_metric > 100 * threshold`, print:
```text
! Threshold advisory: baseline_metric=[value] is >100x the default threshold (0.001).
For this metric scale, consider: --threshold [baseline_metric * 0.0001:.4f]
Proceeding with --threshold [threshold] — override with: /research:retro <run-id> --threshold <value>
```
Apply advisory threshold automatically only when `--threshold` not explicitly provided by user.
**Timeout detection**: when scanning reverted iterations, check `status` field. If `status == "timeout"`: classify as `timeout-as-revert` (see Notes). Else: flag any reverted iteration where `delta` is in correct improvement direction (metric moved toward goal) as "possible timeout — verify commit [sha]"; don't count delta as valid.
Scan `experiments.jsonl` sequentially, skipping iteration 0 (baseline). For each window of 3+ consecutive iterations where `abs(delta) < threshold`:
- Record: `start_iter`, `end_iter`, `count`
- Classify type: `dead-plateau` if all iterations in window have `status: kept`; `dead-churn` if mixed `kept`/`reverted`/other
- Compute `wasted_iters` = total iterations in all dead windows
Re-hydrate cross-Bash state at the start of every separate Bash invocation in T3 (each Bash call is a fresh shell — `$RUN_DIR` / `$RUN_ID_ARG` lost across calls; ADV-H18 / ADV-L16):
```bash
export CSID="${CLAUDE_CODE_SESSION_ID:-$PPID}"
IFS= read -r RUN_DIR < "${TMPDIR:-/tmp}/retro-run-dir-${CSID}" 2>/dev/null || RUN_DIR=""
IFS= read -r RUN_ID_ARG < "${TMPDIR:-/tmp}/retro-run-id-${CSID}" 2>/dev/null || RUN_ID_ARG=""
IFS= read -r RUN_ID < "${TMPDIR:-/tmp}/retro-run-id-resolved-${CSID}" 2>/dev/null || RUN_ID=""
IFS= read -r RETRO_JSONL < "${TMPDIR:-/tmp}/retro-jsonl-path-${CSID}" 2>/dev/null || RETRO_JSONL=".experiments/state/$RUN_ID/experiments-clean.jsonl"
# T-C1: separate guards — `|| ... &&` has subtle precedence. `exit 1` terminates the Bash
# subprocess only — orchestrator must treat non-zero exit as hard stop, not proceed to T4.
# One call reports both missing values; a trailing `[ -z ] && { …; }` guard would also
# leave the block's exit status at 1 whenever the value IS present (T-C1).
python "${CLAUDE_PLUGIN_ROOT:-plugins/cc_research}/bin/require-vars.py" "$RUN_DIR" "retro T3: RUN_DIR missing — T1 must run first" "$RUN_ID" "retro T3: RUN_ID missing — T1 must run first" || exit 1
```
Write summary to `$RUN_DIR/dead-iters.json` via Write tool. Format:
```json
{
"windows": [{"start": 5, "end": 8, "count": 4, "type": "dead-churn"}],
"total_dead": 4,
"total_iterations": 20,
"dead_pct": 20.0
}
```
Write dead-iteration scan script to `$RUN_DIR/scripts/dead-iter-scan.py` via Write tool, then execute in a separate Bash call. Never inline Python in the Bash command. (Different from T2: T3 writes a fresh dynamic script per invocation; T2 invokes a static bin/ script.)
### Step T4: Suspicious jump detection
Compute per-iteration absolute metric deltas for kept iterations only. Build sliding window of 5 kept iterations to compute running mean and std of deltas.
Flag any single-step improvement where `abs(delta) > running_mean + 2 * running_std`:
| Severity | Condition |
| --- | --- |
| HIGH | `abs(delta) > running_mean + 3 * running_std` |
| MEDIUM | `abs(delta) > running_mean + 2 * running_std` (and not HIGH) |
For each flagged jump, record:
- `iteration`, `delta`, `sigma` (how many std above mean), `commit` SHA, `files` changed (from experiments.jsonl `files` field)
- Label: `"suspicious — investigate"` — NEVER auto-label `"data leakage"` or imply causation
- Include corresponding `diary.md` entry for that iteration if present
**Minimum data**: require ≥6 kept iterations before flagging (need 5 for window + 1 to test). Fewer → skip suspicious-jump detection entirely, write `"⚠ Insufficient data for trend analysis (need ≥6 data points, have <N>)"` in Suspicious Metric Jumps section of report.
Write to `$RUN_DIR/suspicious-jumps.json` via Write tool.
### Step T5: Scientist learning summary
Pre-compute all file paths before spawning. Verify `$RUN_DIR/stats-results.json`, `$RUN_DIR/dead-iters.json`, `$RUN_DIR/suspicious-jumps.json` exist (T2–T4 must complete first).
> **Agent budget** — each spawn costs ~120,851 tok of fixed overhead (~73 tool-calls' worth) plus ~12.0 s/call, so work under ~73 calls is cheaper done inline: spawn nothing. Keep each agent near ~55 tool-calls; past ~60 they stall without returning an envelope, forcing reconstruction from disk. Every spawn prompt must require an envelope even on exhaustion — `partial: true` plus what was finished.
Spawn `research:scientist` via `Agent(subagent_type="research:scientist", prompt="...")`:
```markdown
Act as a research retrospective analyst.
Read:
- experiments-clean.jsonl at <RETRO_JSONL path — the sanitized copy written by T1; fall back to experiments.jsonl if clean copy absent> (full iteration history)
- diary.md at <path> (if exists — for qualitative context)
- stats results at <RUN_DIR>/stats-results.json
- dead iteration summary at <RUN_DIR>/dead-iters.json
- suspicious jumps at <RUN_DIR>/suspicious-jumps.json
Produce a retrospective analysis covering:
1. **Strategy effectiveness**: which agent types (perf/code/ml/arch) had highest kept-rate and average delta? Rank them. Include per-agent iteration count, kept count, and mean delta.
2. **Failure pattern analysis**: what approaches were repeatedly tried and reverted? Common failure modes? Group by pattern, not individual iteration.
3. **Diminishing returns**: at which iteration did improvement rate drop below 0.5% per iteration? Was the stopping point appropriate?
4. **Next hypotheses**: based on what worked and failed, generate 3–5 concrete next hypotheses. Write them as a hypotheses.jsonl-compatible file to <RUN_DIR>/hypotheses.jsonl — one JSON object per line with fields: hypothesis (str), rationale (str), confidence (float 0–1), expected_delta (str like "+2%"), priority (int 1=highest), source: "retro". Do NOT include feasible/blocker/codebase_mapping — feasibility annotation is optional in this context; /research:run treats absent feasibility fields as feasible:true. Note: full feasibility-annotation workflow is defined in research:scientist — see that agent for complete annotation spec.
5. **Cross-run insights** (only if compare data present in stats-results.json): which run's strategy was more effective and why?
Write full retrospective to <RUN_DIR>/retrospective.md using Write tool.
Include ## Confidence block per quality-gates rules.
Return ONLY: {"status":"done","hypotheses":N,"file":"<RUN_DIR>/retrospective.md","confidence":0.N}
```
**Health monitoring note** (CLAUDE.md §6 deviation): research:scientist agent here spawned synchronously (not `run_in_background=true`), so CLAUDE.md §6 sentinel polling unreachable mid-call. Health monitoring approximated post-hoc: if Agent() call returns after >15 min with no output file, treat as timed out. CLAUDE.md §6 full protocol applies only to background agents.
**Post-call timeout check**: after Agent() returns, verify:
- File `$RUN_DIR/retrospective.md` exists and has content → success
- File missing or empty → set `scientist_status = "timed_out"`, continue to T6; surface with ⏱ in report
Parse returned JSON envelope. Record `hypotheses` count and `confidence` for T6.
### Step T6: Write retro report
```bash
mkdir -p .reports/research # timeout: 3000
BRANCH=$(git branch --show-current 2>/dev/null | tr '/' '-' || echo 'main') # timeout: 3000
```
Write full report to `.reports/research/retro-$BRANCH-$(date +%Y-%m-%d).md` via Write tool. Anti-overwrite: `BASE=".reports/research/retro-$BRANCH-$(date +%Y-%m-%d).md"; OUT="$BASE"; COUNT=2; while [ -f "$OUT" ]; do OUT="${BASE%.md}-${COUNT}.md"; COUNT=$((COUNT+1)); done`
```markdown
---
Title: Retro — [goal]
Date: [YYYY-MM-DD]
Scope: [run-id] / [total] iterations
Focus: retrospective analysis of ML optimization run
Agents: research:scientist (T5)
Outcome: IMPROVED | STALLED | PLATEAU | DIVERGED
Significance: p=[value] ([significant|not significant] at alpha=[alpha])
Hypotheses: [N] next steps generated
Confidence: [score] — [key gaps]
Next steps: /research:run … --hypothesis | /research:fortify
Path: → .reports/research/retro-<branch>-<date>.md
---
## Retrospective: <goal>
**Run**: <run-id>
**Date**: <date>
**Iterations**: <total> (<kept> kept, <reverted> reverted, <other> other)
**Baseline**: <metric_key> = <baseline>
**Best**: <metric_key> = <best> (<delta>% improvement)
### Statistical Significance
| Test | N | Statistic | p-value | Significant? | Effect size |
| --- | --- | --- | --- | --- | --- |
| Wilcoxon vs baseline | N | ... | ... | YES/NO (alpha=<alpha>) | r=... (<small/medium/large>) |
| Wilcoxon run-1 vs run-2 | N | ... | ... | YES/NO | r=... |
(Second row only if `--compare` used. If N < 6: replace table with descriptive stats table — mean, median, min, max, std — and note "Insufficient data for significance testing (N=<N>)".)
**Effect size interpretation**: |r| < 0.3 = small, 0.3–0.5 = medium, > 0.5 = large.
> **Independence caveat** — Wilcoxon assumes independent samples. Sequential optimization iterations are typically autocorrelated; p-value is indicative only, not formally valid. If `dead_pct > 30%` from the Dead Iterations section, escalate caveat to HIGH: "p-value unreliable — high autocorrelation from dead-plateau windows."
### Dead Iterations
| Start | End | Count | Type | Notes |
| --- | --- | --- | --- | --- |
| ... | ... | ... | dead-plateau / dead-churn | ... |
Total dead: <N> of <total> (<pct>% of compute)
(If no dead windows: "No dead iteration windows detected (threshold=<threshold>)")
### Suspicious Metric Jumps
| Iteration | Delta | Sigma | Severity | Commit | Files Changed |
| --- | --- | --- | --- | --- | --- |
| ... | ... | ... | HIGH/MEDIUM | <sha> | <files> |
(If none: "No suspicious jumps detected")
(If insufficient data: "Insufficient data for jump detection (N=<N>)")
### Strategy Effectiveness
| Strategy | Kept | Tried | Keep-rate | Avg Delta | Best Delta |
| --- | --- | --- | --- | --- | --- |
| ... | ... | ... | ...% | ... | ... |
(From scientist retrospective. If scientist timed out: "Scientist agent timed out — strategy analysis unavailable")
### Failure Patterns
<From scientist retrospective — grouped failure modes>
### Diminishing Returns
<Iteration where improvement rate dropped below 0.5% per iteration, or "not applicable">
### Suggested Next Hypotheses
| # | Hypothesis | Rationale | Expected Delta | Confidence |
| --- | --- | --- | --- | --- |
| 1 | ... | ... | ... | 0.N |
Full retrospective: <RUN_DIR>/retrospective.md
Next hypotheses queue: <RUN_DIR>/hypotheses.jsonl
## Confidence
**Score**: 0.N — [high|moderate|low]
**Gaps**:
- Finding confidence (dead windows, suspicious jumps, classification errors, pattern detection): [high|moderate|low] — independent of statistical test availability
- Statistical confidence (Wilcoxon p-value): [available: p=X | unavailable: scipy not installed — descriptive stats only]
- [other specific limitations]
```
### Step T7: Terminal summary and follow-up gate
Print compact summary to terminal only — do NOT repeat full report:
```text
---
Retro — <goal>
Run: <run-id> (<total> iterations, <kept> kept)
Significance: p=<value> (<significant|not significant> at alpha=<alpha>) [or: N=<N> insufficient]
Effect size: r=<value> (<small|medium|large>) [or: n/a]
Dead iters: <N>/<total> (<pct>%) [or: none]
Suspicious: <N> jumps (<severity> — investigate: <sha1>, <sha2>) [or: none]
Hypotheses: <N> next steps generated
-> saved to .reports/research/retro-<branch>-<date>.md
---
Next: /research:run <program.md> --hypothesis <RUN_DIR>/hypotheses.jsonl [only if scientist_status != "timed_out" AND <RUN_DIR>/hypotheses.jsonl exists]
/research:fortify <run-id> ← stress-test top hypothesis before full re-run
```
If `scientist_status == "timed_out"` or `<RUN_DIR>/hypotheses.jsonl` does not exist on disk, omit the `--hypothesis` Next line entirely and replace with: `Next: /research:fortify <run-id> ← scientist analysis unavailable; no hypotheses queue generated`.
</workflow>
<notes>
- Retro read-only — never modifies code, commits, or writes to `.experiments/state/<run-id>/`
- `.experiments/retro-<timestamp>/` stores analysis scripts, intermediate JSON, scientist output, hypotheses.jsonl
- Retro run dirs don't write `result.jsonl` — exempt from automated 30-day TTL cleanup (exempt per `.claude/rules/foundry-artifact-lifecycle.md` — no `result.jsonl` = cleanup skipped); remove manually when done (`rm -rf .experiments/retro-*/`)
- `hypotheses.jsonl` uses `source: "retro"` — compatible with `--hypothesis` flag of `/research:run`; `"retro"` extends oracle schema (see `protocol.md`); feasibility fields omitted, treated as feasible:true by run
- `--compare` requires both runs use same metric; if metric names differ, stop: `"Cannot compare runs with different metrics: <metric-1> vs <metric-2>"`
- Dead iteration threshold (`--threshold`) should match metric's noise floor — default 0.001 for normalized metrics; adjust for raw values (e.g. `--threshold 0.1` for loss in hundreds)
- Statistical tests assume metric values are independent samples — if iterations highly correlated (e.g. cumulative optimization), note limitation in report
- **Requires `scipy` in active Python environment** (`pip install scipy`) — `retro_analyze.py` runs Wilcoxon signed-rank test via `scipy.stats`. Without scipy, test skipped and `retro_analyze.py` returns `{"significant": false, "p_value": null, "reason": "scipy not installed"}`; report includes descriptive stats only (mean/median/min/max/std). Install: `pip install scipy` or `uv add scipy`.
- **Named anomaly patterns** (use consistently across reports):
- `kept-regression`: kept iteration where metric moved in wrong direction (positive delta for higher-is-better, negative delta for lower-is-better)
- `reverted-improvement`: reverted iteration where metric moved in correct direction — reverted for non-metric reasons (performance, OOM, instability); flag as "improvement-when-reverted — consider revisiting with adjusted constraints"
- `timeout-as-revert`: reverted iteration with `status: "timeout"` — metric value unreliable; never count delta as valid improvement
- `config-repetition`: same agent + same file(s) attempted 3+ times without crossing threshold — flag as "repeated-failure pattern"
</notes>