/usr/bin/env bash << 'PREFLIGHT_EOF'
set -euo pipefail

undefined

/usr/bin/env bash << 'FIND_SESSIONS_EOF'
set -euo pipefail

undefined

/usr/bin/env bash << 'TOOLS_EOF'
set -euo pipefail

---

AskUserQuestion:
  question: "What do you want to trace provenance for?"
  header: "Target"
  multiSelect: false
  options:
    - label: "Research finding/session"
      description: "Document a research session with full session context for reproducibility"
    - label: "Specific code/feature"
      description: "Trace who created a specific function, feature, or code block"
    - label: "Configuration/decision"
      description: "Trace when and why a configuration or architectural decision was made"
    - label: "Custom search"
      description: "Search session logs for specific keywords or patterns"

AskUserQuestion:
  question: "Who should be attributed as the creator?"
  header: "Attribution"
  multiSelect: false
  options:
    - label: "Use git config user (Recommended)"
      description: "Attribute to $(git config user.name) / $(git config user.email)"
    - label: "Specify GitHub username"
      description: "I'll provide the GitHub username manually"
    - label: "Team attribution"
      description: "Multiple contributors - list all GitHub usernames"

AskUserQuestion:
  question: "Which sessions should be recorded in the registry?"
  header: "Sessions"
  multiSelect: false
  options:
    - label: "ALL sessions (main + subagent) (Recommended)"
      description: "Record every session file - complete provenance for future maintainers"
    - label: "Main sessions only"
      description: "Exclude agent-* subagent sessions (loses context)"
    - label: "Manual selection"
      description: "I'll specify which sessions to include"

AskUserQuestion:
  question: "Review the session_contexts array that will be recorded:"
  header: "Review"
  multiSelect: false
  options:
    - label: "Looks correct - proceed"
      description: "Write this to the registry"
    - label: "Add descriptions"
      description: "Let me add descriptions to some sessions"
    - label: "Filter some sessions"
      description: "Remove sessions that aren't relevant"
    - label: "Cancel"
      description: "Don't write to registry yet"

{
  "session_contexts": [
    {
      "session_uuid": "abc123",
      "type": "main",
      "entries": 980,
      "description": "..."
    },
    {
      "session_uuid": "agent-xyz",
      "type": "subagent",
      "entries": 113,
      "description": "..."
    }
  ]
}

AskUserQuestion:
  question: "What outputs should be generated?"
  header: "Outputs"
  multiSelect: true
  options:
    - label: "registry.jsonl entry (Recommended)"
      description: "Master index entry with ALL session UUIDs and GitHub attribution"
    - label: "iterations.jsonl entries"
      description: "Detailed iteration records in sessions/<id>/"
    - label: "Full session chain archive (.jsonl.br)"
      description: "Compress sessions with Brotli for archival"
    - label: "Markdown finding document"
      description: "findings/<name>.md with embedded provenance table"
    - label: "Git commit with provenance"
      description: "Structured commit message with session references"
    - label: "Upload to S3 for team sharing"
      description: "Upload artifacts to S3 with retrieval command in commit"

AskUserQuestion:
  question: "Link this to an existing ADR or design spec?"
  header: "ADR Link"
  multiSelect: false
  options:
    - label: "No ADR link"
      description: "This is standalone or ADR doesn't exist yet"
    - label: "Specify ADR slug"
      description: "Link to an existing ADR (e.g., 2025-12-15-feature-name)"
    - label: "Create new ADR"
      description: "This finding warrants a new ADR"

/usr/bin/env bash << 'SCAN_EOF'
set -euo pipefail

CWD=$(pwd)
ENCODED_PATH=$(echo "$CWD" | tr '/' '-')
PROJECT_SESSIONS="$HOME/.claude/projects/$ENCODED_PATH"

if [[ ! -d "$PROJECT_SESSIONS" ]]; then
  echo "ERROR: Project sessions directory not found: $PROJECT_SESSIONS" >&2
  exit 1
fi

echo "=== Building Session Index ==="
MAIN_COUNT=0
AGENT_COUNT=0

undefined

{
  "session_contexts": [
    {
      "session_uuid": "8c821a19-e4f4-45d5-9338-be3a47ac81a3",
      "type": "main",
      "entries": 980,
      "timestamp_start": "2026-01-03T21:25:07.435Z",
      "description": "Primary session - research iterations, PR preparation"
    },
    {
      "session_uuid": "agent-a728ebe",
      "type": "subagent",
      "entries": 113,
      "timestamp_start": "2026-01-02T07:25:47.658Z",
      "description": "Explore agent - codebase analysis"
    }
  ]
}

/usr/bin/env bash << 'TRACE_EOF'
set -euo pipefail

trace_uuid_chain() {
  local uuid="$1"
  local session_file="$2"
  local depth=0
  local max_depth=100

  if [[ -z "$uuid" ]]; then
    echo "ERROR: UUID argument required" >&2
    return 1
  fi

  if [[ ! -f "$session_file" ]]; then
    echo "ERROR: Session file not found: $session_file" >&2
    return 1
  fi

  echo "Tracing UUID chain from: $uuid"

  while [[ -n "$uuid" && $depth -lt $max_depth ]]; do
    # Use jq with explicit error handling
    entry=$(jq -c "select(.uuid == \"$uuid\")" "$session_file" 2>&1) || {
      echo "ERROR: jq failed parsing $session_file" >&2
      return 1
    }

    if [[ -n "$entry" ]]; then
      parent=$(echo "$entry" | jq -r '.parentUuid // empty') || parent=""
      timestamp=$(echo "$entry" | jq -r '.timestamp // "unknown"') || timestamp="unknown"
      type=$(echo "$entry" | jq -r '.type // "unknown"') || type="unknown"

      echo "  [$depth] $uuid ($type) @ $timestamp"
      echo "       -> parent: ${parent:-<root>}"

      uuid="$parent"
      ((depth++)) || true
    else
      echo "  UUID $uuid not in current session, searching others..."
      found=false
      for session in "$PROJECT_SESSIONS"/*.jsonl; do
        [[ ! -f "$session" ]] && continue
        if grep -q "\"uuid\":\"$uuid\"" "$session"; then
          session_file="$session"
          echo "  ✓ Found in $(basename "$session")"
          found=true
          break
        fi
      done
      if [[ "$found" == "false" ]]; then
        echo "  WARNING: UUID chain broken - $uuid not found in any session" >&2
        break
      fi
    fi
  done

  if [[ $depth -ge $max_depth ]]; then
    echo "WARNING: Reached max chain depth ($max_depth) - chain may be incomplete" >&2
  fi

  echo "✓ Chain depth: $depth"
}
TRACE_EOF

{
  "id": "2026-01-01-multiyear-momentum",
  "type": "research_session",
  "title": "Multi-Year Cross-Sectional Momentum Strategy Validation",
  "project": "alpha-forge",
  "branch": "feat/2026-01-01-multiyear-cs-momentum-research",
  "created_at": "2026-01-03T01:00:00Z",
  "created_by": {
    "github_username": "terrylica",
    "model": "claude-opus-4-5-20251101",
    "session_uuid": "8c821a19-e4f4-45d5-9338-be3a47ac81a3"
  },
  "strategy_type": "cross_sectional_momentum",
  "date_range": { "start": "2022-01-01", "end": "2025-12-31" },
  "session_contexts": [
    {
      "session_uuid": "8c821a19-...",
      "type": "main",
      "entries": 1128,
      "description": "Primary session - research iterations, PR preparation"
    },
    {
      "session_uuid": "agent-a728ebe",
      "type": "subagent",
      "entries": 113,
      "timestamp_start": "2026-01-02T07:25:47.658Z",
      "description": "Explore agent - codebase analysis"
    }
  ],
  "metrics": {
    "sharpe_2bps": 1.05,
    "sharpe_13bps": 0.31,
    "max_drawdown": -0.18
  },
  "tags": ["momentum", "cross-sectional", "multi-year", "validated"],
  "artifacts": {
    "adr": "docs/adr/2026-01-02-multiyear-momentum-vs-ml.md",
    "strategy_config": "examples/02_strategies/cs_momentum_multiyear.yaml",
    "research_log": "outputs/research_sessions/2026-01-01-multiyear-momentum/research_log.md",
    "iteration_configs": "outputs/research_sessions/2026-01-01-multiyear-momentum/",
    "s3": "s3://eonlabs-findings/sessions/2026-01-01-multiyear-momentum/"
  },
  "status": "validated",
  "finding": "BiLSTM time-series models show no predictive edge (49.05% hit rate). Simple CS momentum outperforms.",
  "recommendation": "Deploy CS Momentum 120+240 strategy. Abandon ML-based approaches for this market regime."
}

{
  "id": "iter-001",
  "registry_id": "2026-01-01-multiyear-momentum",
  "type": "iteration",
  "created_at": "2026-01-01T10:00:00Z",
  "created_by": {
    "github_username": "terrylica",
    "model": "claude-opus-4-5-20251101",
    "session_uuid": "8c821a19-e4f4-45d5-9338-be3a47ac81a3"
  },
  "hypothesis": "Test BiLSTM with conservative clip",
  "config": { "strategy": "bilstm", "clip": 0.05 },
  "results": { "train_sharpe": 0.31, "test_sharpe": -1.15 },
  "finding": "BiLSTM shows no edge",
  "status": "FAILED"
}

/usr/bin/env bash << 'COMPRESS_EOF'
set -euo pipefail

undefined

feat(finding): <short description>

Session-Chronicle Provenance:
registry_id: <registry_id>
github_username: <github_username>
main_sessions: <count>
subagent_sessions: <count>
total_entries: <total>

Artifacts:
- findings/registry.jsonl
- findings/sessions/<id>/iterations.jsonl
- S3: s3://eonlabs-findings/sessions/<id>/

---

AskUserQuestion:
  question: "Ready to write to registry. Confirm the entry:"
  header: "Confirm"
  multiSelect: false
  options:
    - label: "Write to registry"
      description: "Append this entry to findings/registry.jsonl"
    - label: "Edit first"
      description: "Let me modify some fields before writing"
    - label: "Cancel"
      description: "Don't write anything"

undefined

---

1. PREFLIGHT
   ├── Verify session storage location
   ├── Find ALL sessions (main + subagent)
   └── Check required tools (jq, brotli)

2. ASK: TARGET TYPE
   └── AskUserQuestion: What to trace?

3. ASK: GITHUB ATTRIBUTION
   └── AskUserQuestion: Who created this?

4. ASK: SESSION SCOPE
   └── AskUserQuestion: Which sessions? (Default: ALL)

5. BUILD session_contexts ARRAY
   ├── Enumerate ALL main sessions
   ├── Enumerate ALL subagent sessions
   └── Collect metadata (entries, timestamps)

6. ASK: PREVIEW session_contexts
   └── AskUserQuestion: Review before writing

7. ASK: OUTPUT FORMAT
   └── AskUserQuestion: What to generate?

8. ASK: ADR LINK
   └── AskUserQuestion: Link to ADR?

9. GENERATE OUTPUTS
   ├── Build registry.jsonl entry (with iterations_path, iterations_count)
   ├── Build iterations.jsonl entries (if applicable)
   └── Prepare commit message

10. ASK: FINAL CONFIRMATION
    └── AskUserQuestion: Ready to write?

11. WRITE & VERIFY
    ├── Append to registry.jsonl
    ├── Append to sessions/<id>/iterations.jsonl
    └── Validate NDJSON format

12. (OPTIONAL) S3 UPLOAD
    └── Upload compressed archives