apply Ganymede review fixes: delete misplaced ops/db.py, correct diff log, fix stale_pr DB update

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

ops/diagnostics/CONSOLIDATION-DIFF-LOG.md

@@ -38,7 +38,9 @@
 - evolution.md — kept (documentation)
 - weekly/2026-03-25-week3.md — kept (report)
 - ops/sessions/*.json — kept (session data)
-- All .py files REMOVED from root diagnostics/
+- alerting.py, alerting_routes.py REMOVED by this consolidation
+- vitality.py, vitality_routes.py were already absent (moved in prior commit)
+- No .py files remain in root diagnostics/
 
 ## VPS .bak files inventory (30+ files)
 All in /opt/teleo-eval/diagnostics/. Git is the backup now. Safe to delete after consolidation verified.

ops/diagnostics/ops/db.py

@@ -1,655 +0,0 @@
-"""SQLite database — schema, migrations, connection management."""
-
-import json
-import logging
-import sqlite3
-from contextlib import contextmanager
-
-from . import config
-
-logger = logging.getLogger("pipeline.db")
-
-SCHEMA_VERSION = 16
-
-SCHEMA_SQL = """
-CREATE TABLE IF NOT EXISTS schema_version (
-    version INTEGER PRIMARY KEY,
-    applied_at TEXT DEFAULT (datetime('now'))
-);
-
-CREATE TABLE IF NOT EXISTS sources (
-    path TEXT PRIMARY KEY,
-    status TEXT NOT NULL DEFAULT 'unprocessed',
-    -- unprocessed, triaging, extracting, extracted, null_result,
-    -- needs_reextraction, error
-    priority TEXT DEFAULT 'medium',
-    -- critical, high, medium, low, skip
-    priority_log TEXT DEFAULT '[]',
-    -- JSON array: [{stage, priority, reasoning, ts}]
-    extraction_model TEXT,
-    claims_count INTEGER DEFAULT 0,
-    pr_number INTEGER,
-    transient_retries INTEGER DEFAULT 0,
-    substantive_retries INTEGER DEFAULT 0,
-    last_error TEXT,
-    feedback TEXT,
-    -- eval feedback for re-extraction (JSON)
-    cost_usd REAL DEFAULT 0,
-    created_at TEXT DEFAULT (datetime('now')),
-    updated_at TEXT DEFAULT (datetime('now'))
-);
-
-CREATE TABLE IF NOT EXISTS prs (
-    number INTEGER PRIMARY KEY,
-    source_path TEXT REFERENCES sources(path),
-    branch TEXT,
-    status TEXT NOT NULL DEFAULT 'open',
-    -- validating, open, reviewing, approved, merging, merged, closed, zombie, conflict
-    -- conflict: rebase failed or merge timed out — needs human intervention
-    domain TEXT,
-    agent TEXT,
-    commit_type TEXT CHECK(commit_type IS NULL OR commit_type IN ('extract', 'research', 'entity', 'decision', 'reweave', 'fix', 'challenge', 'enrich', 'synthesize', 'unknown')),
-    tier TEXT,
-    -- LIGHT, STANDARD, DEEP
-    tier0_pass INTEGER,
-    -- 0/1
-    leo_verdict TEXT DEFAULT 'pending',
-    -- pending, approve, request_changes, skipped, failed
-    domain_verdict TEXT DEFAULT 'pending',
-    domain_agent TEXT,
-    domain_model TEXT,
-    priority TEXT,
-    -- NULL = inherit from source. Set explicitly for human-submitted PRs.
-    -- Pipeline PRs: COALESCE(p.priority, s.priority, 'medium')
-    -- Human PRs: 'critical' (detected via missing source_path or non-agent author)
-    origin TEXT DEFAULT 'pipeline',
-    -- pipeline | human | external
-    transient_retries INTEGER DEFAULT 0,
-    substantive_retries INTEGER DEFAULT 0,
-    last_error TEXT,
-    last_attempt TEXT,
-    cost_usd REAL DEFAULT 0,
-    created_at TEXT DEFAULT (datetime('now')),
-    merged_at TEXT
-);
-
-CREATE TABLE IF NOT EXISTS costs (
-    date TEXT,
-    model TEXT,
-    stage TEXT,
-    calls INTEGER DEFAULT 0,
-    input_tokens INTEGER DEFAULT 0,
-    output_tokens INTEGER DEFAULT 0,
-    cost_usd REAL DEFAULT 0,
-    PRIMARY KEY (date, model, stage)
-);
-
-CREATE TABLE IF NOT EXISTS circuit_breakers (
-    name TEXT PRIMARY KEY,
-    state TEXT DEFAULT 'closed',
-    -- closed, open, halfopen
-    failures INTEGER DEFAULT 0,
-    successes INTEGER DEFAULT 0,
-    tripped_at TEXT,
-    last_success_at TEXT,
-    -- heartbeat: if now() - last_success_at > 2*interval, stage is stalled (Vida)
-    last_update TEXT DEFAULT (datetime('now'))
-);
-
-CREATE TABLE IF NOT EXISTS audit_log (
-    id INTEGER PRIMARY KEY AUTOINCREMENT,
-    timestamp TEXT DEFAULT (datetime('now')),
-    stage TEXT,
-    event TEXT,
-    detail TEXT
-);
-
-CREATE TABLE IF NOT EXISTS response_audit (
-    id INTEGER PRIMARY KEY AUTOINCREMENT,
-    timestamp TEXT NOT NULL DEFAULT (datetime('now')),
-    chat_id INTEGER,
-    user TEXT,
-    agent TEXT DEFAULT 'rio',
-    model TEXT,
-    query TEXT,
-    conversation_window TEXT,
-    -- JSON: prior N messages for context
-    -- NOTE: intentional duplication of transcript data for audit self-containment.
-    -- Transcripts live in /opt/teleo-eval/transcripts/ but audit rows need prompt
-    -- context inline for retrieval-quality diagnosis. Primary driver of row size —
-    -- target for cleanup when 90-day retention policy lands.
-    entities_matched TEXT,
-    -- JSON: [{name, path, score, used_in_response}]
-    claims_matched TEXT,
-    -- JSON: [{path, title, score, source, used_in_response}]
-    retrieval_layers_hit TEXT,
-    -- JSON: ["keyword","qdrant","graph"]
-    retrieval_gap TEXT,
-    -- What the KB was missing (if anything)
-    market_data TEXT,
-    -- JSON: injected token prices
-    research_context TEXT,
-    -- Haiku pre-pass results if any
-    kb_context_text TEXT,
-    -- Full context string sent to model
-    tool_calls TEXT,
-    -- JSON: ordered array [{tool, input, output, duration_ms, ts}]
-    raw_response TEXT,
-    display_response TEXT,
-    confidence_score REAL,
-    -- Model self-rated retrieval quality 0.0-1.0
-    response_time_ms INTEGER,
-    -- Eval pipeline columns (v10)
-    prompt_tokens INTEGER,
-    completion_tokens INTEGER,
-    generation_cost REAL,
-    embedding_cost REAL,
-    total_cost REAL,
-    blocked INTEGER DEFAULT 0,
-    block_reason TEXT,
-    query_type TEXT,
-    created_at TEXT DEFAULT (datetime('now'))
-);
-
-CREATE INDEX IF NOT EXISTS idx_sources_status ON sources(status);
-CREATE INDEX IF NOT EXISTS idx_prs_status ON prs(status);
-CREATE INDEX IF NOT EXISTS idx_prs_domain ON prs(domain);
-CREATE INDEX IF NOT EXISTS idx_costs_date ON costs(date);
-CREATE INDEX IF NOT EXISTS idx_audit_stage ON audit_log(stage);
-CREATE INDEX IF NOT EXISTS idx_response_audit_ts ON response_audit(timestamp);
-CREATE INDEX IF NOT EXISTS idx_response_audit_agent ON response_audit(agent);
-CREATE INDEX IF NOT EXISTS idx_response_audit_chat_ts ON response_audit(chat_id, timestamp);
-"""
-
-
-def get_connection(readonly: bool = False) -> sqlite3.Connection:
-    """Create a SQLite connection with WAL mode and proper settings."""
-    config.DB_PATH.parent.mkdir(parents=True, exist_ok=True)
-    conn = sqlite3.connect(
-        str(config.DB_PATH),
-        timeout=30,
-        isolation_level=None,  # autocommit — we manage transactions explicitly
-    )
-    conn.row_factory = sqlite3.Row
-    conn.execute("PRAGMA journal_mode=WAL")
-    conn.execute("PRAGMA busy_timeout=10000")
-    conn.execute("PRAGMA foreign_keys=ON")
-    if readonly:
-        conn.execute("PRAGMA query_only=ON")
-    return conn
-
-
-@contextmanager
-def transaction(conn: sqlite3.Connection):
-    """Context manager for explicit transactions."""
-    conn.execute("BEGIN")
-    try:
-        yield conn
-        conn.execute("COMMIT")
-    except Exception:
-        conn.execute("ROLLBACK")
-        raise
-
-
-# Branch prefix → (agent, commit_type) mapping.
-# Single source of truth — used by merge.py at INSERT time and migration v7 backfill.
-# Unknown prefixes → ('unknown', 'unknown') + warning log.
-BRANCH_PREFIX_MAP = {
-    "extract": ("pipeline", "extract"),
-    "ingestion": ("pipeline", "extract"),
-    "epimetheus": ("epimetheus", "extract"),
-    "rio": ("rio", "research"),
-    "theseus": ("theseus", "research"),
-    "astra": ("astra", "research"),
-    "vida": ("vida", "research"),
-    "clay": ("clay", "research"),
-    "leo": ("leo", "entity"),
-    "reweave": ("pipeline", "reweave"),
-    "fix": ("pipeline", "fix"),
-}
-
-
-def classify_branch(branch: str) -> tuple[str, str]:
-    """Derive (agent, commit_type) from branch prefix.
-
-    Returns ('unknown', 'unknown') and logs a warning for unrecognized prefixes.
-    """
-    prefix = branch.split("/", 1)[0] if "/" in branch else branch
-    result = BRANCH_PREFIX_MAP.get(prefix)
-    if result is None:
-        logger.warning("Unknown branch prefix %r in branch %r — defaulting to ('unknown', 'unknown')", prefix, branch)
-        return ("unknown", "unknown")
-    return result
-
-
-def migrate(conn: sqlite3.Connection):
-    """Run schema migrations."""
-    conn.executescript(SCHEMA_SQL)
-
-    # Check current version
-    try:
-        row = conn.execute("SELECT MAX(version) as v FROM schema_version").fetchone()
-        current = row["v"] if row and row["v"] else 0
-    except sqlite3.OperationalError:
-        current = 0
-
-    # --- Incremental migrations ---
-    if current < 2:
-        # Phase 2: add multiplayer columns to prs table
-        for stmt in [
-            "ALTER TABLE prs ADD COLUMN priority TEXT",
-            "ALTER TABLE prs ADD COLUMN origin TEXT DEFAULT 'pipeline'",
-            "ALTER TABLE prs ADD COLUMN last_error TEXT",
-        ]:
-            try:
-                conn.execute(stmt)
-            except sqlite3.OperationalError:
-                pass  # Column already exists (idempotent)
-        logger.info("Migration v2: added priority, origin, last_error to prs")
-
-    if current < 3:
-        # Phase 3: retry budget — track eval attempts and issue tags per PR
-        for stmt in [
-            "ALTER TABLE prs ADD COLUMN eval_attempts INTEGER DEFAULT 0",
-            "ALTER TABLE prs ADD COLUMN eval_issues TEXT DEFAULT '[]'",
-        ]:
-            try:
-                conn.execute(stmt)
-            except sqlite3.OperationalError:
-                pass  # Column already exists (idempotent)
-        logger.info("Migration v3: added eval_attempts, eval_issues to prs")
-
-    if current < 4:
-        # Phase 4: auto-fixer — track fix attempts per PR
-        for stmt in [
-            "ALTER TABLE prs ADD COLUMN fix_attempts INTEGER DEFAULT 0",
-        ]:
-            try:
-                conn.execute(stmt)
-            except sqlite3.OperationalError:
-                pass  # Column already exists (idempotent)
-        logger.info("Migration v4: added fix_attempts to prs")
-
-    if current < 5:
-        # Phase 5: contributor identity system — tracks who contributed what
-        # Aligned with schemas/attribution.md (5 roles) + Leo's tier system.
-        # CI is COMPUTED from raw counts × weights, never stored.
-        conn.executescript("""
-            CREATE TABLE IF NOT EXISTS contributors (
-                handle TEXT PRIMARY KEY,
-                display_name TEXT,
-                agent_id TEXT,
-                first_contribution TEXT,
-                last_contribution TEXT,
-                tier TEXT DEFAULT 'new',
-                -- new, contributor, veteran
-                sourcer_count INTEGER DEFAULT 0,
-                extractor_count INTEGER DEFAULT 0,
-                challenger_count INTEGER DEFAULT 0,
-                synthesizer_count INTEGER DEFAULT 0,
-                reviewer_count INTEGER DEFAULT 0,
-                claims_merged INTEGER DEFAULT 0,
-                challenges_survived INTEGER DEFAULT 0,
-                domains TEXT DEFAULT '[]',
-                highlights TEXT DEFAULT '[]',
-                identities TEXT DEFAULT '{}',
-                created_at TEXT DEFAULT (datetime('now')),
-                updated_at TEXT DEFAULT (datetime('now'))
-            );
-
-            CREATE INDEX IF NOT EXISTS idx_contributors_tier ON contributors(tier);
-        """)
-        logger.info("Migration v5: added contributors table")
-
-    if current < 6:
-        # Phase 6: analytics — time-series metrics snapshots for trending dashboard
-        conn.executescript("""
-            CREATE TABLE IF NOT EXISTS metrics_snapshots (
-                ts TEXT DEFAULT (datetime('now')),
-                throughput_1h INTEGER,
-                approval_rate REAL,
-                open_prs INTEGER,
-                merged_total INTEGER,
-                closed_total INTEGER,
-                conflict_total INTEGER,
-                evaluated_24h INTEGER,
-                fix_success_rate REAL,
-                rejection_broken_wiki_links INTEGER DEFAULT 0,
-                rejection_frontmatter_schema INTEGER DEFAULT 0,
-                rejection_near_duplicate INTEGER DEFAULT 0,
-                rejection_confidence INTEGER DEFAULT 0,
-                rejection_other INTEGER DEFAULT 0,
-                extraction_model TEXT,
-                eval_domain_model TEXT,
-                eval_leo_model TEXT,
-                prompt_version TEXT,
-                pipeline_version TEXT,
-                source_origin_agent INTEGER DEFAULT 0,
-                source_origin_human INTEGER DEFAULT 0,
-                source_origin_scraper INTEGER DEFAULT 0
-            );
-
-            CREATE INDEX IF NOT EXISTS idx_snapshots_ts ON metrics_snapshots(ts);
-        """)
-        logger.info("Migration v6: added metrics_snapshots table for analytics dashboard")
-
-    if current < 7:
-        # Phase 7: agent attribution + commit_type for dashboard
-        # commit_type column + backfill agent/commit_type from branch prefix
-        try:
-            conn.execute("ALTER TABLE prs ADD COLUMN commit_type TEXT CHECK(commit_type IS NULL OR commit_type IN ('extract', 'research', 'entity', 'decision', 'reweave', 'fix', 'unknown'))")
-        except sqlite3.OperationalError:
-            pass  # column already exists from CREATE TABLE
-        # Backfill agent and commit_type from branch prefix
-        rows = conn.execute("SELECT number, branch FROM prs WHERE branch IS NOT NULL").fetchall()
-        for row in rows:
-            agent, commit_type = classify_branch(row["branch"])
-            conn.execute(
-                "UPDATE prs SET agent = ?, commit_type = ? WHERE number = ? AND (agent IS NULL OR commit_type IS NULL)",
-                (agent, commit_type, row["number"]),
-            )
-        backfilled = len(rows)
-        logger.info("Migration v7: added commit_type column, backfilled %d PRs with agent/commit_type", backfilled)
-
-    if current < 8:
-        # Phase 8: response audit — full-chain visibility for agent response quality
-        # Captures: query → tool calls → retrieval → context → response → confidence
-        # Approved by Ganymede (architecture), Rio (agent needs), Rhea (ops)
-        conn.executescript("""
-            CREATE TABLE IF NOT EXISTS response_audit (
-                id INTEGER PRIMARY KEY AUTOINCREMENT,
-                timestamp TEXT NOT NULL DEFAULT (datetime('now')),
-                chat_id INTEGER,
-                user TEXT,
-                agent TEXT DEFAULT 'rio',
-                model TEXT,
-                query TEXT,
-                conversation_window TEXT,  -- intentional transcript duplication for audit self-containment
-                entities_matched TEXT,
-                claims_matched TEXT,
-                retrieval_layers_hit TEXT,
-                retrieval_gap TEXT,
-                market_data TEXT,
-                research_context TEXT,
-                kb_context_text TEXT,
-                tool_calls TEXT,
-                raw_response TEXT,
-                display_response TEXT,
-                confidence_score REAL,
-                response_time_ms INTEGER,
-                created_at TEXT DEFAULT (datetime('now'))
-            );
-
-            CREATE INDEX IF NOT EXISTS idx_response_audit_ts ON response_audit(timestamp);
-            CREATE INDEX IF NOT EXISTS idx_response_audit_agent ON response_audit(agent);
-            CREATE INDEX IF NOT EXISTS idx_response_audit_chat_ts ON response_audit(chat_id, timestamp);
-        """)
-        logger.info("Migration v8: added response_audit table for agent response auditing")
-
-    if current < 9:
-        # Phase 9: rebuild prs table to expand CHECK constraint on commit_type.
-        # SQLite cannot ALTER CHECK constraints in-place — must rebuild table.
-        # Old constraint (v7): extract,research,entity,decision,reweave,fix,unknown
-        # New constraint: adds challenge,enrich,synthesize
-        # Also re-derive commit_type from branch prefix for rows with invalid/NULL values.
-
-        # Step 1: Get all column names from existing table
-        cols_info = conn.execute("PRAGMA table_info(prs)").fetchall()
-        col_names = [c["name"] for c in cols_info]
-        col_list = ", ".join(col_names)
-
-        # Step 2: Create new table with expanded CHECK constraint
-        conn.executescript(f"""
-            CREATE TABLE prs_new (
-                number INTEGER PRIMARY KEY,
-                source_path TEXT REFERENCES sources(path),
-                branch TEXT,
-                status TEXT NOT NULL DEFAULT 'open',
-                domain TEXT,
-                agent TEXT,
-                commit_type TEXT CHECK(commit_type IS NULL OR commit_type IN ('extract','research','entity','decision','reweave','fix','challenge','enrich','synthesize','unknown')),
-                tier TEXT,
-                tier0_pass INTEGER,
-                leo_verdict TEXT DEFAULT 'pending',
-                domain_verdict TEXT DEFAULT 'pending',
-                domain_agent TEXT,
-                domain_model TEXT,
-                priority TEXT,
-                origin TEXT DEFAULT 'pipeline',
-                transient_retries INTEGER DEFAULT 0,
-                substantive_retries INTEGER DEFAULT 0,
-                last_error TEXT,
-                last_attempt TEXT,
-                cost_usd REAL DEFAULT 0,
-                created_at TEXT DEFAULT (datetime('now')),
-                merged_at TEXT
-            );
-            INSERT INTO prs_new ({col_list}) SELECT {col_list} FROM prs;
-            DROP TABLE prs;
-            ALTER TABLE prs_new RENAME TO prs;
-        """)
-        logger.info("Migration v9: rebuilt prs table with expanded commit_type CHECK constraint")
-
-        # Step 3: Re-derive commit_type from branch prefix for invalid/NULL values
-        rows = conn.execute(
-            """SELECT number, branch FROM prs
-               WHERE branch IS NOT NULL
-                 AND (commit_type IS NULL
-                      OR commit_type NOT IN ('extract','research','entity','decision','reweave','fix','challenge','enrich','synthesize','unknown'))"""
-        ).fetchall()
-        fixed = 0
-        for row in rows:
-            agent, commit_type = classify_branch(row["branch"])
-            conn.execute(
-                "UPDATE prs SET agent = COALESCE(agent, ?), commit_type = ? WHERE number = ?",
-                (agent, commit_type, row["number"]),
-            )
-            fixed += 1
-        conn.commit()
-        logger.info("Migration v9: re-derived commit_type for %d PRs with invalid/NULL values", fixed)
-
-    if current < 10:
-        # Add eval pipeline columns to response_audit
-        # VPS may already be at v10/v11 from prior (incomplete) deploys — use IF NOT EXISTS pattern
-        for col_def in [
-            ("prompt_tokens", "INTEGER"),
-            ("completion_tokens", "INTEGER"),
-            ("generation_cost", "REAL"),
-            ("embedding_cost", "REAL"),
-            ("total_cost", "REAL"),
-            ("blocked", "INTEGER DEFAULT 0"),
-            ("block_reason", "TEXT"),
-            ("query_type", "TEXT"),
-        ]:
-            try:
-                conn.execute(f"ALTER TABLE response_audit ADD COLUMN {col_def[0]} {col_def[1]}")
-            except sqlite3.OperationalError:
-                pass  # Column already exists
-        conn.commit()
-        logger.info("Migration v10: added eval pipeline columns to response_audit")
-
-
-    if current < 11:
-        # Phase 11: compute tracking — extended costs table columns
-        # (May already exist on VPS from manual deploy — idempotent ALTERs)
-        for col_def in [
-            ("duration_ms", "INTEGER DEFAULT 0"),
-            ("cache_read_tokens", "INTEGER DEFAULT 0"),
-            ("cache_write_tokens", "INTEGER DEFAULT 0"),
-            ("cost_estimate_usd", "REAL DEFAULT 0"),
-        ]:
-            try:
-                conn.execute(f"ALTER TABLE costs ADD COLUMN {col_def[0]} {col_def[1]}")
-            except sqlite3.OperationalError:
-                pass  # Column already exists
-        conn.commit()
-        logger.info("Migration v11: added compute tracking columns to costs")
-
-    if current < 12:
-        # Phase 12: structured review records — captures all evaluation outcomes
-        # including rejections, disagreements, and approved-with-changes.
-        # Schema locked with Leo (2026-04-01).
-        conn.executescript("""
-            CREATE TABLE IF NOT EXISTS review_records (
-                id INTEGER PRIMARY KEY AUTOINCREMENT,
-                pr_number INTEGER NOT NULL,
-                claim_path TEXT,
-                domain TEXT,
-                agent TEXT,
-                reviewer TEXT NOT NULL,
-                reviewer_model TEXT,
-                outcome TEXT NOT NULL
-                    CHECK (outcome IN ('approved', 'approved-with-changes', 'rejected')),
-                rejection_reason TEXT
-                    CHECK (rejection_reason IS NULL OR rejection_reason IN (
-                        'fails-standalone-test', 'duplicate', 'scope-mismatch',
-                        'evidence-insufficient', 'framing-poor', 'other'
-                    )),
-                disagreement_type TEXT
-                    CHECK (disagreement_type IS NULL OR disagreement_type IN (
-                        'factual', 'scope', 'framing', 'evidence'
-                    )),
-                notes TEXT,
-                batch_id TEXT,
-                claims_in_batch INTEGER DEFAULT 1,
-                reviewed_at TEXT DEFAULT (datetime('now'))
-            );
-            CREATE INDEX IF NOT EXISTS idx_review_records_pr ON review_records(pr_number);
-            CREATE INDEX IF NOT EXISTS idx_review_records_outcome ON review_records(outcome);
-            CREATE INDEX IF NOT EXISTS idx_review_records_domain ON review_records(domain);
-            CREATE INDEX IF NOT EXISTS idx_review_records_reviewer ON review_records(reviewer);
-        """)
-        logger.info("Migration v12: created review_records table")
-
-    if current < 16:
-        # Phase 16: trace_id on audit_log — queryable provenance chain.
-        # Auto-extracted from detail JSON's "pr" field by audit().
-        # Backfill existing rows from their detail JSON.
-        try:
-            conn.execute("ALTER TABLE audit_log ADD COLUMN trace_id TEXT")
-        except sqlite3.OperationalError:
-            pass  # Column already exists
-        conn.execute("""
-            UPDATE audit_log
-            SET trace_id = json_extract(detail, '$.pr')
-            WHERE trace_id IS NULL
-              AND detail IS NOT NULL
-              AND json_extract(detail, '$.pr') IS NOT NULL
-        """)
-        conn.execute("CREATE INDEX IF NOT EXISTS idx_audit_log_trace ON audit_log(trace_id)")
-        conn.commit()
-        logger.info("Migration v16: added trace_id to audit_log + backfilled from detail JSON")
-
-    if current < SCHEMA_VERSION:
-        conn.execute(
-            "INSERT OR REPLACE INTO schema_version (version) VALUES (?)",
-            (SCHEMA_VERSION,),
-        )
-        conn.commit()  # Explicit commit — executescript auto-commits DDL but not subsequent DML
-        logger.info("Database migrated to schema version %d", SCHEMA_VERSION)
-    else:
-        logger.debug("Database at schema version %d", current)
-
-
-def audit(conn: sqlite3.Connection, stage: str, event: str, detail: str = None, *, trace_id: str = None):
-    """Write an audit log entry.
-
-    trace_id is auto-extracted from detail JSON's "pr" field if not provided.
-    This gives every audit row a queryable trace without changing any call site.
-    """
-    if trace_id is None and detail:
-        try:
-            trace_id = str(json.loads(detail).get("pr", ""))
-        except (json.JSONDecodeError, TypeError, AttributeError):
-            pass
-        if trace_id == "":
-            trace_id = None
-    conn.execute(
-        "INSERT INTO audit_log (stage, event, detail, trace_id) VALUES (?, ?, ?, ?)",
-        (stage, event, detail, trace_id),
-    )
-
-
-
-
-def record_review(conn, pr_number: int, reviewer: str, outcome: str, *,
-                  claim_path: str = None, domain: str = None, agent: str = None,
-                  reviewer_model: str = None, rejection_reason: str = None,
-                  disagreement_type: str = None, notes: str = None,
-                  claims_in_batch: int = 1):
-    """Record a structured review outcome.
-
-    Called from evaluate stage after Leo/domain reviewer returns a verdict.
-    outcome must be: approved, approved-with-changes, or rejected.
-    """
-    batch_id = str(pr_number)
-    conn.execute(
-        """INSERT INTO review_records
-           (pr_number, claim_path, domain, agent, reviewer, reviewer_model,
-            outcome, rejection_reason, disagreement_type, notes,
-            batch_id, claims_in_batch)
-           VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)""",
-        (pr_number, claim_path, domain, agent, reviewer, reviewer_model,
-         outcome, rejection_reason, disagreement_type, notes,
-         batch_id, claims_in_batch),
-    )
-
-def append_priority_log(conn: sqlite3.Connection, path: str, stage: str, priority: str, reasoning: str):
-    """Append a priority assessment to a source's priority_log.
-
-    NOTE: This does NOT update the source's priority column. The priority column
-    is the authoritative priority, set only by initial triage or human override.
-    The priority_log records each stage's opinion for offline calibration analysis.
-    (Bug caught by Theseus — original version overwrote priority with each stage's opinion.)
-    (Race condition fix per Vida — read-then-write wrapped in transaction.)
-    """
-    conn.execute("BEGIN")
-    try:
-        row = conn.execute("SELECT priority_log FROM sources WHERE path = ?", (path,)).fetchone()
-        if not row:
-            conn.execute("ROLLBACK")
-            return
-        log = json.loads(row["priority_log"] or "[]")
-        log.append({"stage": stage, "priority": priority, "reasoning": reasoning})
-        conn.execute(
-            "UPDATE sources SET priority_log = ?, updated_at = datetime('now') WHERE path = ?",
-            (json.dumps(log), path),
-        )
-        conn.execute("COMMIT")
-    except Exception:
-        conn.execute("ROLLBACK")
-        raise
-
-
-def insert_response_audit(conn: sqlite3.Connection, **kwargs):
-    """Insert a response audit record. All fields optional except query."""
-    cols = [
-        "timestamp", "chat_id", "user", "agent", "model", "query",
-        "conversation_window", "entities_matched", "claims_matched",
-        "retrieval_layers_hit", "retrieval_gap", "market_data",
-        "research_context", "kb_context_text", "tool_calls",
-        "raw_response", "display_response", "confidence_score",
-        "response_time_ms",
-        # Eval pipeline columns (v10)
-        "prompt_tokens", "completion_tokens", "generation_cost",
-        "embedding_cost", "total_cost", "blocked", "block_reason",
-        "query_type",
-    ]
-    present = {k: v for k, v in kwargs.items() if k in cols and v is not None}
-    if not present:
-        return
-    col_names = ", ".join(present.keys())
-    placeholders = ", ".join("?" for _ in present)
-    conn.execute(
-        f"INSERT INTO response_audit ({col_names}) VALUES ({placeholders})",
-        tuple(present.values()),
-    )
-
-
-def set_priority(conn: sqlite3.Connection, path: str, priority: str, reason: str = "human override"):
-    """Set a source's authoritative priority. Used for human overrides and initial triage."""
-    conn.execute(
-        "UPDATE sources SET priority = ?, updated_at = datetime('now') WHERE path = ?",
-        (priority, path),
-    )
-    append_priority_log(conn, path, "override", priority, reason)

ops/pipeline-v2/lib/stale_pr.py

@@ -20,7 +20,7 @@ from .forgejo import api, repo_path
 
 logger = logging.getLogger("pipeline.stale_pr")
 
-STALE_THRESHOLD_MINUTES = 30
+STALE_THRESHOLD_MINUTES = 45
 
 
 async def check_stale_prs(conn) -> tuple[int, int]: