Fix all P0/P1/P2 review findings in autoresearch plugin

SKILL.md:
- P0: Add init subcommand call in setup, include JSONL in initial commit
- P0: Reorder keep flow: log to JSONL before git commit (prevents entry loss)
- P0: Replace git clean -fd with backup/restore pattern for state files
- P1: Add concrete baseline commands in Step 4
- P1: Add --asi flag to all log invocation examples
- P1: Handle existing branch on resume (checkout || checkout -b)
- P2: Fix evaluate text (compare against best-kept, not baseline)
- P2: Skip user confirmation in mission worker finalization
- P2: Reference status subcommand in resume section
- P2: Show --metrics flag in log examples

autoresearch_helper.py:
- P0: Replace > 0 metric filter with status-based filter (supports zero/negative metrics)
- P1: Use find_baseline() consistently in compute_confidence
- P1: Add init-before-log guard (exit 1 if no config)

Co-authored-by: factory-droid[bot] <138933559+factory-droid[bot]@users.noreply.github.com>

Author: enoreyes

plugins/autoresearch/skills/autoresearch/SKILL.md

@@ -41,7 +41,7 @@ Ask the user (or infer from context) for:
 ### Step 2: Create Branch and State Files
 
 ```bash
-git checkout -b autoresearch/<goal>-<date>
+git checkout autoresearch/<goal>-<date> 2>/dev/null || git checkout -b autoresearch/<goal>-<date>
 ```
 
 Read the source files thoroughly. Understand the workload deeply before writing anything.
@@ -115,16 +115,41 @@ pnpm test --run --reporter=dot 2>&1 | tail -50
 pnpm typecheck 2>&1 | grep -i error || true
 ```
 
-### Step 3: Commit State Files
+### Step 3: Initialize JSONL and Commit State Files
+
+Initialize the experiment log:
+
+```bash
+python3 autoresearch_helper.py init --jsonl autoresearch.jsonl --name '<goal>' --metric-name '<metric_name>' --direction <lower|higher>
+```
+
+Commit all state files:
 
 ```bash
-git add autoresearch.md autoresearch.sh
+git add autoresearch.md autoresearch.sh autoresearch.jsonl
 git commit -m "autoresearch: initialize experiment session"
 ```
 
 ### Step 4: Run Baseline
 
-Run the experiment command and record the baseline result. This is experiment #1 — it establishes the starting point.
+Run the benchmark and record the baseline result:
+
+```bash
+bash autoresearch.sh
+```
+
+Parse the METRIC lines from the output, then log the baseline as a keep:
+
+```bash
+python3 autoresearch_helper.py log --jsonl autoresearch.jsonl \
+  --commit $(git rev-parse --short=7 HEAD) \
+  --metric <baseline_value> \
+  --status keep \
+  --description "baseline" \
+  --asi '{"hypothesis": "baseline measurement"}'
+```
+
+This is experiment #1 — it establishes the starting point for all future comparisons.
 
 ## The Experiment Loop
 
@@ -163,7 +188,7 @@ If checks fail, log as `checks_failed` and revert.
 
 #### 4. Evaluate Results
 
-Compare the primary metric against the baseline using the helper script:
+Compare the primary metric against the current best (or baseline if no keeps yet) using the helper script:
 
 ```bash
 python3 autoresearch_helper.py evaluate --jsonl autoresearch.jsonl --metric <value> --direction <lower|higher>
@@ -182,44 +207,58 @@ Decision rules:
 
 **On keep:**
 
-```bash
-# Commit the changes
-git add -A
-git commit -m "<description>
-
-Result: {\"status\": \"keep\", \"<metric_name>\": <value>}"
-```
-
-Append to `autoresearch.jsonl`:
+Log to JSONL first (so the entry is included in the commit):
 ```bash
 python3 autoresearch_helper.py log --jsonl autoresearch.jsonl \
   --commit $(git rev-parse --short=7 HEAD) \
   --metric <value> \
   --status keep \
   --description "<what was tried>" \
+  --asi '{"hypothesis": "<what you tried>"}' \
+  # --metrics '{"compile_us": <value>, "render_us": <value>}'  # optional secondary metrics
   --direction <lower|higher>
 ```
 
-**On discard/crash/checks_failed:**
-
+Then commit all changes (including the JSONL entry):
 ```bash
-# Revert changes (preserve autoresearch state files)
-git checkout -- .
-git clean -fd 2>/dev/null
-# Re-stage state files in case they were unstaged
-git add autoresearch.jsonl autoresearch.md autoresearch.ideas.md autoresearch.sh autoresearch.checks.sh 2>/dev/null || true
+git add -A
+git commit -m "<description>
+
+Result: {\"status\": \"keep\", \"<metric_name>\": <value>}"
 ```
 
-Append to `autoresearch.jsonl`:
+**On discard/crash/checks_failed:**
+
+Log to JSONL first (before reverting, so the entry is preserved):
 ```bash
 python3 autoresearch_helper.py log --jsonl autoresearch.jsonl \
   --commit "0000000" \
   --metric <value_or_0> \
   --status <discard|crash|checks_failed> \
   --description "<what was tried>" \
+  --asi '{"hypothesis": "<what you tried>", "rollback_reason": "<why it failed>"}' \
+  # --metrics '{"compile_us": <value>, "render_us": <value>}'  # optional secondary metrics
   --direction <lower|higher>
 ```
 
+Then revert changes, backing up state files so `git clean -fd` doesn't destroy them:
+```bash
+# Backup state files
+cp autoresearch.jsonl autoresearch.jsonl.bak 2>/dev/null || true
+cp autoresearch.md autoresearch.md.bak 2>/dev/null || true
+cp autoresearch.ideas.md autoresearch.ideas.md.bak 2>/dev/null || true
+
+# Revert all changes
+git checkout -- .
+git clean -fd 2>/dev/null
+
+# Restore state files
+cp autoresearch.jsonl.bak autoresearch.jsonl 2>/dev/null || true
+cp autoresearch.md.bak autoresearch.md 2>/dev/null || true
+cp autoresearch.ideas.md.bak autoresearch.ideas.md 2>/dev/null || true
+rm -f autoresearch.jsonl.bak autoresearch.md.bak autoresearch.ideas.md.bak
+```
+
 #### 6. Update Research Journal
 
 After every few experiments (or after significant findings), update the "What's Been Tried" section in `autoresearch.md`. Include:
@@ -296,7 +335,10 @@ Droid sessions have finite context. To handle this gracefully:
 1. **Track experiment count** in the current session. After ~15 experiments, context is getting heavy.
 2. **Save state proactively** — all state lives in files (jsonl, md), so a new session can resume immediately.
 3. **When context is getting exhausted**: update `autoresearch.md` with current findings, commit state files, and stop. The next session reads the files and continues.
-4. **On resume**: read `autoresearch.md`, `autoresearch.jsonl`, and `git log --oneline -20` to understand where things stand.
+4. **On resume**: read `autoresearch.md`, `autoresearch.jsonl`, and `git log --oneline -20` to understand where things stand. Check current status:
+```bash
+python3 autoresearch_helper.py status --jsonl autoresearch.jsonl
+```
 
 ## Loop Rules Summary
 
@@ -347,7 +389,7 @@ Group 2: "Switch to cosine LR schedule"
   Experiments: #15, #18
 ```
 
-Wait for user confirmation before proceeding.
+Wait for user confirmation before proceeding. In mission worker mode, proceed with the best grouping without waiting for confirmation.
 
 ### Step 3: Resolve File Conflicts
 

plugins/autoresearch/skills/autoresearch/autoresearch_helper.py

@@ -76,7 +76,7 @@ def compute_confidence(results, segment, direction):
 
     Returns None if fewer than 3 data points or MAD is 0.
     """
-    cur = [r for r in current_segment_results(results, segment) if r.get("metric", 0) > 0]
+    cur = [r for r in current_segment_results(results, segment) if r.get("status") not in ("crash", "checks_failed")]
     if len(cur) < 3:
         return None
 
@@ -85,11 +85,13 @@ def compute_confidence(results, segment, direction):
     if mad == 0:
         return None
 
-    baseline = cur[0]["metric"]
+    baseline = find_baseline(results, segment)
+    if baseline is None:
+        return None
 
     best_kept = None
     for r in cur:
-        if r.get("status") == "keep" and r.get("metric", 0) > 0:
+        if r.get("status") == "keep":
             val = r["metric"]
             if best_kept is None:
                 best_kept = val
@@ -116,7 +118,7 @@ def find_best_kept(results, segment, direction):
     cur = current_segment_results(results, segment)
     best = None
     for r in cur:
-        if r.get("status") == "keep" and r.get("metric", 0) > 0:
+        if r.get("status") == "keep":
             val = r["metric"]
             if best is None:
                 best = val
@@ -150,6 +152,10 @@ def cmd_log(args):
     """Append an experiment result to the JSONL file."""
     config, results = read_jsonl(args.jsonl)
 
+    if config is None:
+        print("Error: No config found. Run 'init' first.", file=sys.stderr)
+        sys.exit(1)
+
     segment = config.get("_segment", 0) if config else 0
     direction = args.direction or (config.get("bestDirection", "lower") if config else "lower")