laminark 2.21.9 → 2.22.1

package/plugin/dist/tool-registry-Bi1Zdqkm.mjs.map

@@ -0,0 +1 @@
+{"version":3,"file":"tool-registry-Bi1Zdqkm.mjs","names":["up","graphTablesDDL","projectHashIndexDDL"],"sources":["../../src/shared/debug.ts","../../src/storage/migrations.ts","../../src/storage/database.ts","../../src/shared/types.ts","../../src/storage/observations.ts","../../src/storage/sessions.ts","../../src/storage/search.ts","../../src/search/hybrid.ts","../../src/shared/similarity.ts","../../src/hooks/save-guard.ts","../../src/graph/migrations/001-graph-tables.ts","../../src/graph/migrations/002-project-hash-index.ts","../../src/graph/schema.ts","../../src/graph/staleness.ts","../../src/config/hygiene-config.ts","../../src/graph/hygiene-analyzer.ts","../../src/hooks/tool-name-parser.ts","../../src/branches/branch-repository.ts","../../src/storage/research-buffer.ts","../../src/storage/notifications.ts","../../src/paths/schema.ts","../../src/paths/path-repository.ts","../../src/storage/tool-registry.ts"],"sourcesContent":["import { isDebugEnabled } from './config.js';\n\n/**\n * Internal cached state for debug mode.\n * Resolved on first call and never changes (debug mode is process-lifetime).\n */\nlet _enabled: boolean | null = null;\n\nfunction enabled(): boolean {\n  if (_enabled === null) {\n    _enabled = isDebugEnabled();\n  }\n  return _enabled;\n}\n\n/**\n * Logs a debug message to stderr when debug mode is active.\n *\n * When debug is disabled (the default), this is a near-zero-cost no-op after the\n * first call -- the cached flag short-circuits immediately.\n *\n * Format: `[ISO_TIMESTAMP] [LAMINARK:category] message {json_data}`\n *\n * @param category - Debug category (e.g., 'db', 'obs', 'search', 'session')\n * @param message - Human-readable log message\n * @param data - Optional structured data to include (keep lightweight -- no large payloads)\n */\nexport function debug(\n  category: string,\n  message: string,\n  data?: Record<string, unknown>,\n): void {\n  if (!enabled()) {\n    return;\n  }\n\n  const timestamp = new Date().toISOString();\n  let line = `[${timestamp}] [LAMINARK:${category}] ${message}`;\n  if (data !== undefined) {\n    line += ` ${JSON.stringify(data)}`;\n  }\n  process.stderr.write(line + '\\n');\n}\n\n/**\n * Wraps a synchronous function with timing instrumentation.\n *\n * When debug is disabled, calls `fn()` directly with zero overhead --\n * no timing measurement, no wrapping.\n *\n * @param category - Debug category for the log line\n * @param message - Description of the operation being timed\n * @param fn - Synchronous function to execute and time\n * @returns The return value of `fn()`\n */\nexport function debugTimed<T>(\n  category: string,\n  message: string,\n  fn: () => T,\n): T {\n  if (!enabled()) {\n    return fn();\n  }\n\n  const start = performance.now();\n  const result = fn();\n  const duration = (performance.now() - start).toFixed(2);\n  debug(category, `${message} (${duration}ms)`);\n  return result;\n}\n","import type BetterSqlite3 from 'better-sqlite3';\n\n/**\n * A versioned schema migration.\n * Migrations are applied in order and tracked in the _migrations table.\n */\nexport interface Migration {\n  version: number;\n  name: string;\n  up: string | ((db: BetterSqlite3.Database) => void); // SQL string or function\n}\n\n/**\n * All schema migrations in order.\n *\n * Migration 001: Observations table with INTEGER PRIMARY KEY AUTOINCREMENT\n *   (critical for FTS5 content_rowid stability across VACUUM).\n * Migration 002: Sessions table for session lifecycle tracking.\n * Migration 003: FTS5 external content table with porter+unicode61 tokenizer\n *   and three sync triggers (INSERT, UPDATE, DELETE).\n * Migration 004: sqlite-vec vec0 table for 384-dim embeddings (conditional).\n * Migration 005: Add title column to observations and rebuild FTS5 with\n *   title+content dual-column indexing.\n * Migration 006: Recreate vec0 table with cosine distance metric (conditional).\n * Migration 007: Context stashes table for topic detection thread snapshots.\n * Migration 008: Threshold history table for EWMA adaptive threshold seeding.\n * Migration 009: Shift decisions table for topic shift decision logging.\n * Migration 010: Project metadata table for project selector UI.\n * Migration 011: Add project_hash to graph tables and backfill from observations.\n * Migration 012: Add classification and classified_at columns for LLM-based observation classification.\n * Migration 013: Research buffer table for exploration tool event buffering.\n * Migration 014: Add kind column to observations with backfill from source field.\n * Migration 015: Update graph taxonomy -- remove Tool/Person nodes, tighten CHECK constraints.\n * Migration 016: Tool registry table for discovered tools with scope-aware uniqueness.\n * Migration 017: Tool usage events table for per-event temporal tracking.\n * Migration 018: Tool registry FTS5 + vec0 tables for hybrid search on tool descriptions.\n * Migration 019: Add status column (active/stale/demoted) to tool_registry for staleness management.\n * Migration 020: Debug path tables (debug_paths + path_waypoints) for resolution path tracking.\n * Migration 021: Thought branch tables for coherent work unit tracking.\n * Migration 022: Add trigger_hints column to tool_registry for proactive suggestion matching.\n */\nexport const MIGRATIONS: Migration[] = [\n  {\n    version: 1,\n    name: 'create_observations',\n    up: `\n      CREATE TABLE observations (\n        rowid INTEGER PRIMARY KEY AUTOINCREMENT,\n        id TEXT NOT NULL UNIQUE DEFAULT (lower(hex(randomblob(16)))),\n        project_hash TEXT NOT NULL,\n        content TEXT NOT NULL,\n        source TEXT NOT NULL DEFAULT 'unknown',\n        session_id TEXT,\n        embedding BLOB,\n        embedding_model TEXT,\n        embedding_version TEXT,\n        created_at TEXT NOT NULL DEFAULT (datetime('now')),\n        updated_at TEXT NOT NULL DEFAULT (datetime('now')),\n        deleted_at TEXT\n      );\n\n      CREATE INDEX idx_observations_project ON observations(project_hash);\n      CREATE INDEX idx_observations_session ON observations(session_id);\n      CREATE INDEX idx_observations_created ON observations(created_at);\n      CREATE INDEX idx_observations_deleted ON observations(deleted_at) WHERE deleted_at IS NOT NULL;\n    `,\n  },\n  {\n    version: 2,\n    name: 'create_sessions',\n    up: `\n      CREATE TABLE sessions (\n        id TEXT PRIMARY KEY,\n        project_hash TEXT NOT NULL,\n        started_at TEXT NOT NULL DEFAULT (datetime('now')),\n        ended_at TEXT,\n        summary TEXT\n      );\n\n      CREATE INDEX idx_sessions_project ON sessions(project_hash);\n      CREATE INDEX idx_sessions_started ON sessions(started_at);\n    `,\n  },\n  {\n    version: 3,\n    name: 'create_fts5_observations',\n    up: `\n      CREATE VIRTUAL TABLE observations_fts USING fts5(\n        content,\n        content='observations',\n        content_rowid='rowid',\n        tokenize='porter unicode61'\n      );\n\n      -- Sync trigger: INSERT\n      CREATE TRIGGER observations_ai AFTER INSERT ON observations BEGIN\n        INSERT INTO observations_fts(rowid, content)\n          VALUES (new.rowid, new.content);\n      END;\n\n      -- Sync trigger: UPDATE (delete old entry, insert new)\n      CREATE TRIGGER observations_au AFTER UPDATE ON observations BEGIN\n        INSERT INTO observations_fts(observations_fts, rowid, content)\n          VALUES('delete', old.rowid, old.content);\n        INSERT INTO observations_fts(rowid, content)\n          VALUES (new.rowid, new.content);\n      END;\n\n      -- Sync trigger: DELETE\n      CREATE TRIGGER observations_ad AFTER DELETE ON observations BEGIN\n        INSERT INTO observations_fts(observations_fts, rowid, content)\n          VALUES('delete', old.rowid, old.content);\n      END;\n    `,\n  },\n  {\n    version: 4,\n    name: 'create_vec0_embeddings',\n    up: `\n      CREATE VIRTUAL TABLE IF NOT EXISTS observation_embeddings USING vec0(\n        observation_id TEXT PRIMARY KEY,\n        embedding float[384]\n      );\n    `,\n  },\n  {\n    version: 5,\n    name: 'add_observation_title',\n    up: `\n      ALTER TABLE observations ADD COLUMN title TEXT;\n\n      DROP TRIGGER observations_ai;\n      DROP TRIGGER observations_au;\n      DROP TRIGGER observations_ad;\n      DROP TABLE observations_fts;\n\n      CREATE VIRTUAL TABLE observations_fts USING fts5(\n        title,\n        content,\n        content='observations',\n        content_rowid='rowid',\n        tokenize='porter unicode61'\n      );\n\n      CREATE TRIGGER observations_ai AFTER INSERT ON observations BEGIN\n        INSERT INTO observations_fts(rowid, title, content)\n          VALUES (new.rowid, new.title, new.content);\n      END;\n\n      CREATE TRIGGER observations_au AFTER UPDATE ON observations BEGIN\n        INSERT INTO observations_fts(observations_fts, rowid, title, content)\n          VALUES('delete', old.rowid, old.title, old.content);\n        INSERT INTO observations_fts(rowid, title, content)\n          VALUES (new.rowid, new.title, new.content);\n      END;\n\n      CREATE TRIGGER observations_ad AFTER DELETE ON observations BEGIN\n        INSERT INTO observations_fts(observations_fts, rowid, title, content)\n          VALUES('delete', old.rowid, old.title, old.content);\n      END;\n\n      INSERT INTO observations_fts(observations_fts) VALUES('rebuild');\n    `,\n  },\n  {\n    version: 6,\n    name: 'recreate_vec0_cosine_distance',\n    up: `\n      DROP TABLE IF EXISTS observation_embeddings;\n      CREATE VIRTUAL TABLE IF NOT EXISTS observation_embeddings USING vec0(\n        observation_id TEXT PRIMARY KEY,\n        embedding float[384] distance_metric=cosine\n      );\n    `,\n  },\n  {\n    version: 7,\n    name: 'create_context_stashes',\n    up: `\n      CREATE TABLE context_stashes (\n        id TEXT PRIMARY KEY,\n        project_id TEXT NOT NULL,\n        session_id TEXT NOT NULL,\n        topic_label TEXT NOT NULL,\n        summary TEXT NOT NULL,\n        observation_snapshots TEXT NOT NULL,\n        observation_ids TEXT NOT NULL,\n        status TEXT NOT NULL DEFAULT 'stashed',\n        created_at TEXT NOT NULL DEFAULT (datetime('now')),\n        resumed_at TEXT\n      );\n\n      CREATE INDEX idx_stashes_project_status_created\n        ON context_stashes(project_id, status, created_at DESC);\n\n      CREATE INDEX idx_stashes_session\n        ON context_stashes(session_id);\n    `,\n  },\n  {\n    version: 8,\n    name: 'create_threshold_history',\n    up: `\n      CREATE TABLE threshold_history (\n        id INTEGER PRIMARY KEY AUTOINCREMENT,\n        project_id TEXT NOT NULL,\n        session_id TEXT NOT NULL,\n        final_ewma_distance REAL NOT NULL,\n        final_ewma_variance REAL NOT NULL,\n        observation_count INTEGER NOT NULL,\n        created_at TEXT NOT NULL DEFAULT (datetime('now'))\n      );\n\n      CREATE INDEX idx_threshold_history_project\n        ON threshold_history(project_id, created_at DESC);\n    `,\n  },\n  {\n    version: 9,\n    name: 'create_shift_decisions',\n    up: `\n      CREATE TABLE shift_decisions (\n        id TEXT PRIMARY KEY,\n        project_id TEXT NOT NULL,\n        session_id TEXT NOT NULL,\n        observation_id TEXT,\n        distance REAL NOT NULL,\n        threshold REAL NOT NULL,\n        ewma_distance REAL,\n        ewma_variance REAL,\n        sensitivity_multiplier REAL,\n        shifted INTEGER NOT NULL,\n        confidence REAL,\n        stash_id TEXT,\n        created_at TEXT NOT NULL DEFAULT (datetime('now'))\n      );\n\n      CREATE INDEX idx_shift_decisions_session\n        ON shift_decisions(project_id, session_id, created_at DESC);\n\n      CREATE INDEX idx_shift_decisions_shifted\n        ON shift_decisions(shifted, created_at DESC);\n    `,\n  },\n  {\n    version: 10,\n    name: 'create_project_metadata',\n    up: `\n      CREATE TABLE IF NOT EXISTS project_metadata (\n        project_hash TEXT PRIMARY KEY,\n        project_path TEXT NOT NULL,\n        display_name TEXT,\n        last_seen_at TEXT NOT NULL DEFAULT (datetime('now'))\n      );\n    `,\n  },\n  {\n    version: 11,\n    name: 'add_project_hash_to_graph_tables',\n    up: (db: BetterSqlite3.Database) => {\n      // Graph tables are created by initGraphSchema() (separate from main migrations).\n      // They may or may not exist, and may or may not already have project_hash.\n      const tableExists = (name: string) =>\n        !!db.prepare(\"SELECT 1 FROM sqlite_master WHERE type='table' AND name=?\").get(name);\n\n      const columnExists = (table: string, column: string) => {\n        const cols = db.prepare(`PRAGMA table_info('${table}')`).all() as Array<{ name: string }>;\n        return cols.some(c => c.name === column);\n      };\n\n      if (tableExists('graph_nodes') && !columnExists('graph_nodes', 'project_hash')) {\n        db.exec('ALTER TABLE graph_nodes ADD COLUMN project_hash TEXT');\n\n        // Backfill from linked observations\n        db.exec(`\n          UPDATE graph_nodes SET project_hash = (\n            SELECT o.project_hash FROM observations o\n            WHERE o.id IN (\n              SELECT value FROM json_each(graph_nodes.observation_ids)\n            )\n            LIMIT 1\n          ) WHERE project_hash IS NULL\n        `);\n      }\n\n      if (tableExists('graph_edges') && !columnExists('graph_edges', 'project_hash')) {\n        db.exec('ALTER TABLE graph_edges ADD COLUMN project_hash TEXT');\n\n        // Backfill from source node\n        db.exec(`\n          UPDATE graph_edges SET project_hash = (\n            SELECT gn.project_hash FROM graph_nodes gn\n            WHERE gn.id = graph_edges.source_id\n          ) WHERE project_hash IS NULL\n        `);\n      }\n\n      // Indexes are safe with IF NOT EXISTS\n      if (tableExists('graph_nodes')) {\n        db.exec('CREATE INDEX IF NOT EXISTS idx_graph_nodes_project ON graph_nodes(project_hash)');\n      }\n      if (tableExists('graph_edges')) {\n        db.exec('CREATE INDEX IF NOT EXISTS idx_graph_edges_project ON graph_edges(project_hash)');\n      }\n    },\n  },\n  {\n    version: 12,\n    name: 'add_observation_classification',\n    up: `\n      ALTER TABLE observations ADD COLUMN classification TEXT;\n      ALTER TABLE observations ADD COLUMN classified_at TEXT;\n      CREATE INDEX idx_observations_classification\n        ON observations(classification) WHERE classification IS NOT NULL;\n    `,\n  },\n  {\n    version: 13,\n    name: 'create_research_buffer',\n    up: `\n      CREATE TABLE research_buffer (\n        id INTEGER PRIMARY KEY AUTOINCREMENT,\n        project_hash TEXT NOT NULL,\n        session_id TEXT,\n        tool_name TEXT NOT NULL,\n        target TEXT NOT NULL,\n        created_at TEXT NOT NULL DEFAULT (datetime('now'))\n      );\n      CREATE INDEX idx_research_buffer_session ON research_buffer(session_id, created_at DESC);\n    `,\n  },\n  {\n    version: 14,\n    name: 'add_observation_kind',\n    up: (db: BetterSqlite3.Database) => {\n      // Add kind column\n      db.exec(\"ALTER TABLE observations ADD COLUMN kind TEXT DEFAULT 'finding'\");\n\n      // Backfill from source field\n      db.exec(`\n        UPDATE observations SET kind = 'change'\n        WHERE source LIKE 'hook:Write' OR source LIKE 'hook:Edit'\n      `);\n      db.exec(`\n        UPDATE observations SET kind = 'verification'\n        WHERE source LIKE 'hook:Bash'\n      `);\n      db.exec(`\n        UPDATE observations SET kind = 'reference'\n        WHERE source LIKE 'hook:WebFetch' OR source LIKE 'hook:WebSearch'\n      `);\n      db.exec(`\n        UPDATE observations SET kind = 'finding'\n        WHERE source IN ('mcp:save_memory', 'manual', 'slash:remember')\n          AND kind = 'finding'\n      `);\n\n      // Soft-delete old noise observations from Read/Glob/Grep hooks\n      db.exec(`\n        UPDATE observations\n        SET deleted_at = datetime('now'), updated_at = datetime('now')\n        WHERE (source LIKE 'hook:Read' OR source LIKE 'hook:Glob' OR source LIKE 'hook:Grep')\n          AND deleted_at IS NULL\n      `);\n\n      // Index for kind-based queries\n      db.exec('CREATE INDEX idx_observations_kind ON observations(kind)');\n    },\n  },\n  {\n    version: 15,\n    name: 'update_graph_taxonomy',\n    up: (db: BetterSqlite3.Database) => {\n      // Check if graph tables exist\n      const tableExists = (name: string) =>\n        !!db.prepare(\"SELECT 1 FROM sqlite_master WHERE type='table' AND name=?\").get(name);\n\n      if (!tableExists('graph_nodes')) return;\n\n      // Delete old Tool and Person nodes (and their connected edges via CASCADE)\n      db.exec(\"DELETE FROM graph_nodes WHERE type IN ('Tool', 'Person')\");\n\n      // Delete old relationship types that no longer exist\n      db.exec(\"DELETE FROM graph_edges WHERE type IN ('uses', 'depends_on', 'decided_by', 'part_of')\");\n\n      // Recreate graph_nodes with updated CHECK constraint\n      db.exec(`\n        CREATE TABLE graph_nodes_new (\n          id TEXT PRIMARY KEY,\n          type TEXT NOT NULL CHECK(type IN ('Project','File','Decision','Problem','Solution','Reference')),\n          name TEXT NOT NULL,\n          metadata TEXT DEFAULT '{}',\n          observation_ids TEXT DEFAULT '[]',\n          project_hash TEXT,\n          created_at TEXT NOT NULL DEFAULT (datetime('now')),\n          updated_at TEXT NOT NULL DEFAULT (datetime('now'))\n        );\n\n        INSERT INTO graph_nodes_new SELECT * FROM graph_nodes;\n\n        DROP TABLE graph_nodes;\n        ALTER TABLE graph_nodes_new RENAME TO graph_nodes;\n\n        CREATE INDEX idx_graph_nodes_type ON graph_nodes(type);\n        CREATE INDEX idx_graph_nodes_name ON graph_nodes(name);\n        CREATE INDEX IF NOT EXISTS idx_graph_nodes_project ON graph_nodes(project_hash);\n      `);\n\n      // Recreate graph_edges with updated CHECK constraint\n      db.exec(`\n        CREATE TABLE graph_edges_new (\n          id TEXT PRIMARY KEY,\n          source_id TEXT NOT NULL REFERENCES graph_nodes(id) ON DELETE CASCADE,\n          target_id TEXT NOT NULL REFERENCES graph_nodes(id) ON DELETE CASCADE,\n          type TEXT NOT NULL CHECK(type IN ('related_to','solved_by','caused_by','modifies','informed_by','references','verified_by','preceded_by')),\n          weight REAL NOT NULL DEFAULT 1.0 CHECK(weight >= 0.0 AND weight <= 1.0),\n          metadata TEXT DEFAULT '{}',\n          project_hash TEXT,\n          created_at TEXT NOT NULL DEFAULT (datetime('now'))\n        );\n\n        INSERT INTO graph_edges_new SELECT * FROM graph_edges;\n\n        DROP TABLE graph_edges;\n        ALTER TABLE graph_edges_new RENAME TO graph_edges;\n\n        CREATE INDEX idx_graph_edges_source ON graph_edges(source_id);\n        CREATE INDEX idx_graph_edges_target ON graph_edges(target_id);\n        CREATE INDEX idx_graph_edges_type ON graph_edges(type);\n        CREATE UNIQUE INDEX idx_graph_edges_unique ON graph_edges(source_id, target_id, type);\n        CREATE INDEX IF NOT EXISTS idx_graph_edges_project ON graph_edges(project_hash);\n      `);\n    },\n  },\n  {\n    version: 16,\n    name: 'create_tool_registry',\n    up: `\n      CREATE TABLE tool_registry (\n        id INTEGER PRIMARY KEY AUTOINCREMENT,\n        name TEXT NOT NULL,\n        tool_type TEXT NOT NULL,\n        scope TEXT NOT NULL,\n        source TEXT NOT NULL,\n        project_hash TEXT,\n        description TEXT,\n        server_name TEXT,\n        usage_count INTEGER NOT NULL DEFAULT 0,\n        last_used_at TEXT,\n        discovered_at TEXT NOT NULL DEFAULT (datetime('now')),\n        updated_at TEXT NOT NULL DEFAULT (datetime('now'))\n      );\n\n      CREATE UNIQUE INDEX idx_tool_registry_name_project\n        ON tool_registry(name, COALESCE(project_hash, ''));\n      CREATE INDEX idx_tool_registry_scope\n        ON tool_registry(scope);\n      CREATE INDEX idx_tool_registry_project\n        ON tool_registry(project_hash) WHERE project_hash IS NOT NULL;\n      CREATE INDEX idx_tool_registry_usage\n        ON tool_registry(usage_count DESC, last_used_at DESC);\n    `,\n  },\n  {\n    version: 17,\n    name: 'create_tool_usage_events',\n    up: `\n      CREATE TABLE tool_usage_events (\n        id INTEGER PRIMARY KEY AUTOINCREMENT,\n        tool_name TEXT NOT NULL,\n        session_id TEXT,\n        project_hash TEXT,\n        success INTEGER NOT NULL DEFAULT 1,\n        created_at TEXT NOT NULL DEFAULT (datetime('now'))\n      );\n\n      CREATE INDEX idx_tool_usage_events_tool\n        ON tool_usage_events(tool_name, created_at DESC);\n      CREATE INDEX idx_tool_usage_events_session\n        ON tool_usage_events(session_id) WHERE session_id IS NOT NULL;\n      CREATE INDEX idx_tool_usage_events_project_time\n        ON tool_usage_events(project_hash, created_at DESC);\n    `,\n  },\n  {\n    version: 18,\n    name: 'create_tool_registry_search',\n    up: (db: BetterSqlite3.Database) => {\n      // FTS5 external content table for tool registry (always created)\n      db.exec(`\n        CREATE VIRTUAL TABLE tool_registry_fts USING fts5(\n          name,\n          description,\n          content='tool_registry',\n          content_rowid='id',\n          tokenize='porter unicode61'\n        );\n\n        -- Sync trigger: INSERT\n        CREATE TRIGGER tool_registry_ai AFTER INSERT ON tool_registry BEGIN\n          INSERT INTO tool_registry_fts(rowid, name, description)\n            VALUES (new.id, new.name, new.description);\n        END;\n\n        -- Sync trigger: UPDATE (delete old entry, insert new)\n        CREATE TRIGGER tool_registry_au AFTER UPDATE ON tool_registry BEGIN\n          INSERT INTO tool_registry_fts(tool_registry_fts, rowid, name, description)\n            VALUES('delete', old.id, old.name, old.description);\n          INSERT INTO tool_registry_fts(rowid, name, description)\n            VALUES (new.id, new.name, new.description);\n        END;\n\n        -- Sync trigger: DELETE\n        CREATE TRIGGER tool_registry_ad AFTER DELETE ON tool_registry BEGIN\n          INSERT INTO tool_registry_fts(tool_registry_fts, rowid, name, description)\n            VALUES('delete', old.id, old.name, old.description);\n        END;\n\n        -- Rebuild to index existing tool_registry rows\n        INSERT INTO tool_registry_fts(tool_registry_fts) VALUES('rebuild');\n      `);\n\n      // vec0 table for tool embeddings (conditional on sqlite-vec availability)\n      try {\n        db.exec(`\n          CREATE VIRTUAL TABLE IF NOT EXISTS tool_registry_embeddings USING vec0(\n            tool_id INTEGER PRIMARY KEY,\n            embedding float[384] distance_metric=cosine\n          );\n        `);\n      } catch {\n        // sqlite-vec not available -- skip silently, vector search will degrade gracefully\n      }\n    },\n  },\n  {\n    version: 19,\n    name: 'add_tool_registry_status',\n    up: `\n      ALTER TABLE tool_registry ADD COLUMN status TEXT NOT NULL DEFAULT 'active';\n      CREATE INDEX idx_tool_registry_status ON tool_registry(status);\n    `,\n  },\n  {\n    version: 20,\n    name: 'create_debug_path_tables',\n    up: `\n      CREATE TABLE IF NOT EXISTS debug_paths (\n        id TEXT PRIMARY KEY,\n        status TEXT NOT NULL DEFAULT 'active' CHECK(status IN ('active', 'resolved', 'abandoned')),\n        trigger_summary TEXT NOT NULL,\n        resolution_summary TEXT,\n        kiss_summary TEXT,\n        started_at TEXT NOT NULL DEFAULT (datetime('now')),\n        resolved_at TEXT,\n        project_hash TEXT NOT NULL\n      );\n\n      CREATE TABLE IF NOT EXISTS path_waypoints (\n        id TEXT PRIMARY KEY,\n        path_id TEXT NOT NULL REFERENCES debug_paths(id) ON DELETE CASCADE,\n        observation_id TEXT,\n        waypoint_type TEXT NOT NULL CHECK(waypoint_type IN ('error', 'attempt', 'failure', 'success', 'pivot', 'revert', 'discovery', 'resolution')),\n        sequence_order INTEGER NOT NULL,\n        summary TEXT NOT NULL,\n        created_at TEXT NOT NULL DEFAULT (datetime('now'))\n      );\n\n      CREATE INDEX IF NOT EXISTS idx_debug_paths_project_status\n        ON debug_paths(project_hash, status);\n\n      CREATE INDEX IF NOT EXISTS idx_debug_paths_started\n        ON debug_paths(started_at DESC);\n\n      CREATE INDEX IF NOT EXISTS idx_path_waypoints_path_order\n        ON path_waypoints(path_id, sequence_order);\n    `,\n  },\n  {\n    version: 21,\n    name: 'create_thought_branch_tables',\n    up: `\n      CREATE TABLE IF NOT EXISTS thought_branches (\n        id TEXT PRIMARY KEY,\n        project_hash TEXT NOT NULL,\n        session_id TEXT,\n        status TEXT NOT NULL DEFAULT 'active'\n          CHECK(status IN ('active', 'completed', 'abandoned', 'merged')),\n        branch_type TEXT NOT NULL DEFAULT 'unknown'\n          CHECK(branch_type IN ('investigation', 'bug_fix', 'feature', 'refactor', 'research', 'unknown')),\n        arc_stage TEXT NOT NULL DEFAULT 'investigation'\n          CHECK(arc_stage IN ('investigation', 'diagnosis', 'planning', 'execution', 'verification', 'completed')),\n        title TEXT,\n        summary TEXT,\n        parent_branch_id TEXT REFERENCES thought_branches(id),\n        linked_debug_path_id TEXT,\n        trigger_source TEXT,\n        trigger_observation_id TEXT,\n        observation_count INTEGER NOT NULL DEFAULT 0,\n        tool_pattern TEXT DEFAULT '{}',\n        started_at TEXT NOT NULL DEFAULT (datetime('now')),\n        ended_at TEXT,\n        created_at TEXT NOT NULL DEFAULT (datetime('now'))\n      );\n\n      CREATE TABLE IF NOT EXISTS branch_observations (\n        branch_id TEXT NOT NULL REFERENCES thought_branches(id) ON DELETE CASCADE,\n        observation_id TEXT NOT NULL,\n        sequence_order INTEGER NOT NULL,\n        tool_name TEXT,\n        arc_stage_at_add TEXT,\n        created_at TEXT NOT NULL DEFAULT (datetime('now')),\n        PRIMARY KEY (branch_id, observation_id)\n      );\n\n      CREATE INDEX IF NOT EXISTS idx_thought_branches_project_status\n        ON thought_branches(project_hash, status);\n      CREATE INDEX IF NOT EXISTS idx_thought_branches_session\n        ON thought_branches(session_id);\n      CREATE INDEX IF NOT EXISTS idx_thought_branches_started\n        ON thought_branches(started_at DESC);\n      CREATE INDEX IF NOT EXISTS idx_branch_observations_obs\n        ON branch_observations(observation_id);\n    `,\n  },\n  {\n    version: 22,\n    name: 'add_tool_registry_trigger_hints',\n    up: `\n      ALTER TABLE tool_registry ADD COLUMN trigger_hints TEXT;\n    `,\n  },\n];\n\n/**\n * Applies unapplied schema migrations in order.\n *\n * Creates a _migrations tracking table if it does not exist, then applies\n * each migration whose version exceeds the current max applied version.\n * Each migration runs inside a transaction for atomicity.\n *\n * Migrations 004 and 006 (vec0 tables) are only applied when hasVectorSupport\n * is true. If sqlite-vec is not available, they are silently skipped and will\n * be applied on a future run when the extension becomes available.\n *\n * @param db - An open better-sqlite3 database connection\n * @param hasVectorSupport - Whether sqlite-vec loaded successfully\n */\nexport function runMigrations(\n  db: BetterSqlite3.Database,\n  hasVectorSupport: boolean,\n): void {\n  // Create tracking table\n  db.exec(`\n    CREATE TABLE IF NOT EXISTS _migrations (\n      version INTEGER PRIMARY KEY,\n      name TEXT NOT NULL,\n      applied_at TEXT NOT NULL DEFAULT (datetime('now'))\n    )\n  `);\n\n  // Get current max applied version\n  const maxVersion = db.prepare(\n    'SELECT COALESCE(MAX(version), 0) FROM _migrations',\n  ).pluck().get() as number;\n\n  // Prepare insert statement\n  const insertMigration = db.prepare(\n    'INSERT INTO _migrations (version, name) VALUES (?, ?)',\n  );\n\n  // Apply each unapplied migration in a transaction\n  const applyMigration = db.transaction((m: Migration) => {\n    if (typeof m.up === 'function') {\n      m.up(db);\n    } else {\n      db.exec(m.up);\n    }\n    insertMigration.run(m.version, m.name);\n  });\n\n  for (const migration of MIGRATIONS) {\n    if (migration.version <= maxVersion) {\n      continue;\n    }\n\n    // Skip vec0 migrations if sqlite-vec is not available\n    if ((migration.version === 4 || migration.version === 6) && !hasVectorSupport) {\n      continue;\n    }\n\n    applyMigration(migration);\n  }\n}\n","import Database from 'better-sqlite3';\nimport * as sqliteVec from 'sqlite-vec';\nimport { mkdirSync } from 'node:fs';\nimport { dirname } from 'node:path';\n\nimport { debug } from '../shared/debug.js';\nimport type { DatabaseConfig } from '../shared/types.js';\nimport { runMigrations } from './migrations.js';\n\n/**\n * Wrapper around a configured better-sqlite3 database instance.\n * Provides lifecycle methods (close, checkpoint) and tracks whether\n * the sqlite-vec extension loaded successfully.\n */\nexport interface LaminarkDatabase {\n  db: Database.Database;\n  hasVectorSupport: boolean;\n  close(): void;\n  checkpoint(): void;\n}\n\n/**\n * Opens a SQLite database with WAL mode, correct PRAGMA order,\n * optional sqlite-vec extension loading, and schema migrations.\n *\n * Single connection per process by design -- better-sqlite3 is synchronous,\n * so connection pooling adds zero benefit.\n *\n * @param config - Database path and busy timeout configuration\n * @returns A configured LaminarkDatabase instance\n */\nexport function openDatabase(config: DatabaseConfig): LaminarkDatabase {\n  // 1. Ensure directory exists\n  mkdirSync(dirname(config.dbPath), { recursive: true });\n\n  // 2. Create connection\n  const db = new Database(config.dbPath);\n\n  // 3. Set PRAGMAs in correct order (order matters per research)\n  //    WAL mode MUST be first -- synchronous = NORMAL is only safe with WAL\n  const journalMode = db.pragma('journal_mode = WAL', {\n    simple: true,\n  }) as string;\n  if (journalMode !== 'wal') {\n    console.warn(\n      `WARNING: WAL mode not active (got '${journalMode}'). ` +\n        'Database may be on a read-only filesystem or otherwise restricted.',\n    );\n  }\n\n  // busy_timeout -- per-connection, must set every time\n  db.pragma(`busy_timeout = ${config.busyTimeout}`);\n\n  // synchronous NORMAL -- safe ONLY with WAL, faster than FULL\n  db.pragma('synchronous = NORMAL');\n\n  // cache_size -- negative = KiB (64MB)\n  db.pragma('cache_size = -64000');\n\n  // foreign_keys -- per-connection, not persistent\n  db.pragma('foreign_keys = ON');\n\n  // temp_store -- temp tables in memory\n  db.pragma('temp_store = MEMORY');\n\n  // wal_autocheckpoint -- explicit default, prevents WAL growth\n  db.pragma('wal_autocheckpoint = 1000');\n\n  debug('db', 'PRAGMAs configured', { journalMode, busyTimeout: config.busyTimeout });\n\n  // 4. Load sqlite-vec with graceful degradation\n  let hasVectorSupport = false;\n  try {\n    sqliteVec.load(db);\n    hasVectorSupport = true;\n  } catch {\n    // Vector search unavailable -- keyword-only mode\n  }\n\n  debug('db', hasVectorSupport ? 'sqlite-vec loaded' : 'sqlite-vec unavailable, keyword-only mode');\n\n  // 5. Run migrations\n  runMigrations(db, hasVectorSupport);\n\n  debug('db', 'Database opened', { path: config.dbPath, hasVectorSupport });\n\n  // 6. Return LaminarkDatabase\n  return {\n    db,\n    hasVectorSupport,\n\n    close(): void {\n      try {\n        // Flush WAL before shutdown\n        db.pragma('wal_checkpoint(PASSIVE)');\n      } catch {\n        // If checkpoint fails (e.g., locked), still close\n      }\n      debug('db', 'Database closed');\n      db.close();\n    },\n\n    checkpoint(): void {\n      db.pragma('wal_checkpoint(PASSIVE)');\n    },\n  };\n}\n","import { z } from 'zod';\n\n// =============================================================================\n// Project Hash Reference (cross-project isolation)\n// =============================================================================\n\n/**\n * Mutable reference to the active project hash.\n *\n * The MCP server's process.cwd() returns the plugin install path, NOT the\n * user's project directory.  The correct hash is only known after the\n * SessionStart hook writes to `project_metadata`.  This ref auto-refreshes\n * from the database so that tool handlers always resolve the current project.\n */\nexport interface ProjectHashRef {\n  /** Current project hash — reads may trigger a DB refresh. */\n  readonly current: string;\n}\n\n// =============================================================================\n// Database Layer Types (snake_case, matches SQL columns)\n// =============================================================================\n\n/**\n * ObservationRow -- the raw database row shape.\n * Uses snake_case to match SQL column names directly.\n * rowid is INTEGER PRIMARY KEY AUTOINCREMENT for FTS5 content_rowid compatibility.\n */\nexport const ObservationRowSchema = z.object({\n  rowid: z.number(),\n  id: z.string(),\n  project_hash: z.string(),\n  content: z.string(),\n  title: z.string().nullable(),\n  source: z.string(),\n  session_id: z.string().nullable(),\n  embedding: z.instanceof(Buffer).nullable(),\n  embedding_model: z.string().nullable(),\n  embedding_version: z.string().nullable(),\n  kind: z.string().default('finding'),\n  classification: z.string().nullable(),\n  classified_at: z.string().nullable(),\n  created_at: z.string(),\n  updated_at: z.string(),\n  deleted_at: z.string().nullable(),\n});\n\nexport type ObservationRow = z.infer<typeof ObservationRowSchema>;\n\n// =============================================================================\n// Application Layer Types (camelCase)\n// =============================================================================\n\n/**\n * Observation -- the application-layer shape.\n * Uses camelCase for idiomatic TypeScript.\n * embedding is Float32Array (converted from Buffer during mapping).\n */\nexport type ObservationClassification = 'discovery' | 'problem' | 'solution' | 'noise';\n\nexport type ObservationKind = 'change' | 'reference' | 'finding' | 'decision' | 'verification';\n\nexport interface Observation {\n  rowid: number;\n  id: string;\n  projectHash: string;\n  content: string;\n  title: string | null;\n  source: string;\n  sessionId: string | null;\n  kind: ObservationKind;\n  embedding: Float32Array | null;\n  embeddingModel: string | null;\n  embeddingVersion: string | null;\n  classification: ObservationClassification | null;\n  classifiedAt: string | null;\n  createdAt: string;\n  updatedAt: string;\n  deletedAt: string | null;\n}\n\n// =============================================================================\n// Input Types (validated with Zod)\n// =============================================================================\n\n/**\n * ObservationInsert -- input for creating observations.\n * Validated at runtime via Zod schema.\n */\nexport const ObservationInsertSchema = z.object({\n  content: z.string().min(1).max(100_000),\n  title: z.string().max(200).nullable().default(null),\n  source: z.string().default('unknown'),\n  kind: z.string().default('finding'),\n  sessionId: z.string().nullable().default(null),\n  embedding: z.instanceof(Float32Array).nullable().default(null),\n  embeddingModel: z.string().nullable().default(null),\n  embeddingVersion: z.string().nullable().default(null),\n});\n\nexport type ObservationInsert = z.input<typeof ObservationInsertSchema>;\n\n// =============================================================================\n// Session Types\n// =============================================================================\n\nexport interface Session {\n  id: string;\n  projectHash: string;\n  startedAt: string;\n  endedAt: string | null;\n  summary: string | null;\n}\n\n// =============================================================================\n// Search Types\n// =============================================================================\n\nexport interface SearchResult {\n  observation: Observation;\n  score: number;\n  matchType: 'fts' | 'vector' | 'hybrid';\n  snippet: string;\n}\n\n// =============================================================================\n// Configuration Types\n// =============================================================================\n\nexport interface DatabaseConfig {\n  dbPath: string;\n  busyTimeout: number;\n}\n\n// =============================================================================\n// Mapping Helpers\n// =============================================================================\n\n/**\n * Maps a snake_case ObservationRow (from SQLite) to a camelCase Observation.\n * Converts embedding Buffer to Float32Array for application use.\n */\nexport function rowToObservation(row: ObservationRow): Observation {\n  return {\n    rowid: row.rowid,\n    id: row.id,\n    projectHash: row.project_hash,\n    content: row.content,\n    title: row.title,\n    source: row.source,\n    sessionId: row.session_id,\n    kind: (row.kind ?? 'finding') as ObservationKind,\n    embedding: row.embedding\n      ? new Float32Array(\n          row.embedding.buffer,\n          row.embedding.byteOffset,\n          row.embedding.byteLength / 4,\n        )\n      : null,\n    embeddingModel: row.embedding_model,\n    embeddingVersion: row.embedding_version,\n    classification: row.classification as ObservationClassification | null,\n    classifiedAt: row.classified_at,\n    createdAt: row.created_at,\n    updatedAt: row.updated_at,\n    deletedAt: row.deleted_at,\n  };\n}\n","import type BetterSqlite3 from 'better-sqlite3';\nimport { randomBytes } from 'node:crypto';\n\nimport { debug } from '../shared/debug.js';\nimport {\n  ObservationInsertSchema,\n  rowToObservation,\n  type Observation,\n  type ObservationClassification,\n  type ObservationInsert,\n  type ObservationRow,\n} from '../shared/types.js';\n\n/**\n * Repository for observation CRUD operations.\n *\n * Every query is scoped to the projectHash provided at construction time.\n * Callers cannot accidentally query the wrong project -- project isolation\n * is baked into every prepared statement.\n *\n * All SQL statements are prepared once in the constructor and reused for\n * every call (better-sqlite3 performance best practice).\n */\nexport class ObservationRepository {\n  private readonly db: BetterSqlite3.Database;\n  private readonly projectHash: string;\n\n  // Prepared statements (prepared once, reused for every call)\n  private readonly stmtInsert: BetterSqlite3.Statement;\n  private readonly stmtGetById: BetterSqlite3.Statement;\n  private readonly stmtGetByIdIncludingDeleted: BetterSqlite3.Statement;\n  private readonly stmtSoftDelete: BetterSqlite3.Statement;\n  private readonly stmtRestore: BetterSqlite3.Statement;\n  private readonly stmtCount: BetterSqlite3.Statement;\n\n  constructor(db: BetterSqlite3.Database, projectHash: string) {\n    this.db = db;\n    this.projectHash = projectHash;\n\n    this.stmtInsert = db.prepare(`\n      INSERT INTO observations (id, project_hash, content, title, source, kind, session_id, embedding, embedding_model, embedding_version)\n      VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?)\n    `);\n\n    this.stmtGetById = db.prepare(`\n      SELECT * FROM observations\n      WHERE id = ? AND project_hash = ? AND deleted_at IS NULL\n    `);\n\n    this.stmtGetByIdIncludingDeleted = db.prepare(`\n      SELECT * FROM observations\n      WHERE id = ? AND project_hash = ?\n    `);\n\n    this.stmtSoftDelete = db.prepare(`\n      UPDATE observations\n      SET deleted_at = datetime('now'), updated_at = datetime('now')\n      WHERE id = ? AND project_hash = ? AND deleted_at IS NULL\n    `);\n\n    this.stmtRestore = db.prepare(`\n      UPDATE observations\n      SET deleted_at = NULL, updated_at = datetime('now')\n      WHERE id = ? AND project_hash = ?\n    `);\n\n    this.stmtCount = db.prepare(`\n      SELECT COUNT(*) AS count FROM observations\n      WHERE project_hash = ? AND deleted_at IS NULL\n    `);\n\n    debug('obs', 'ObservationRepository initialized', { projectHash });\n  }\n\n  /**\n   * Creates a new observation scoped to this repository's project.\n   * Validates input with Zod at runtime.\n   */\n  create(input: ObservationInsert): Observation {\n    const validated = ObservationInsertSchema.parse(input);\n\n    const id = randomBytes(16).toString('hex');\n    const embeddingBuffer = validated.embedding\n      ? Buffer.from(\n          validated.embedding.buffer,\n          validated.embedding.byteOffset,\n          validated.embedding.byteLength,\n        )\n      : null;\n\n    debug('obs', 'Creating observation', { source: validated.source, contentLength: validated.content.length });\n\n    this.stmtInsert.run(\n      id,\n      this.projectHash,\n      validated.content,\n      validated.title,\n      validated.source,\n      validated.kind,\n      validated.sessionId,\n      embeddingBuffer,\n      validated.embeddingModel,\n      validated.embeddingVersion,\n    );\n\n    // Fetch the created row (includes generated timestamps and rowid)\n    const row = this.stmtGetById.get(id, this.projectHash) as\n      | ObservationRow\n      | undefined;\n\n    if (!row) {\n      throw new Error('Failed to retrieve newly created observation');\n    }\n\n    debug('obs', 'Observation created', { id });\n\n    return rowToObservation(row);\n  }\n\n  /**\n   * Resolves a full or prefix ID to the full 32-char ID.\n   * Observation IDs are 32-char hex strings. Search results display only the\n   * first 8 chars via shortId(). This method allows callers to pass either\n   * a full ID or an 8-char (or any-length) prefix and get the full ID back.\n   * Returns null if no unique match is found.\n   */\n  private resolveId(id: string): string | null {\n    const FULL_ID_LENGTH = 32;\n    if (id.length === FULL_ID_LENGTH) {\n      return id; // Already a full ID, no prefix resolution needed\n    }\n    // Prefix search: find observations whose ID starts with the given prefix\n    const rows = this.db\n      .prepare(\n        \"SELECT id FROM observations WHERE project_hash = ? AND id LIKE ? ESCAPE '\\\\' LIMIT 2\",\n      )\n      .all(this.projectHash, id.replace(/[%_\\\\]/g, '\\\\$&') + '%') as { id: string }[];\n    if (rows.length === 1) {\n      return rows[0].id;\n    }\n    if (rows.length > 1) {\n      debug('obs', 'Ambiguous ID prefix - multiple matches', { prefix: id, count: rows.length });\n    }\n    return null;\n  }\n\n  /**\n   * Gets an observation by ID, scoped to this project.\n   * Accepts full 32-char IDs or shorter prefix strings (e.g. the 8-char\n   * display IDs shown in search results).\n   * Returns null if not found or soft-deleted.\n   */\n  getById(id: string): Observation | null {\n    const resolvedId = this.resolveId(id);\n    if (!resolvedId) return null;\n    const row = this.stmtGetById.get(resolvedId, this.projectHash) as\n      | ObservationRow\n      | undefined;\n    return row ? rowToObservation(row) : null;\n  }\n\n  /**\n   * Lists observations for this project, ordered by created_at DESC.\n   * Excludes soft-deleted observations.\n   */\n  list(options?: {\n    limit?: number;\n    offset?: number;\n    sessionId?: string;\n    since?: string;\n    kind?: string;\n    includeUnclassified?: boolean;\n  }): Observation[] {\n    debug('obs', 'Listing observations', { ...options });\n\n    const limit = options?.limit ?? 50;\n    const offset = options?.offset ?? 0;\n    const includeUnclassified = options?.includeUnclassified ?? false;\n\n    let sql =\n      'SELECT * FROM observations WHERE project_hash = ? AND deleted_at IS NULL';\n    const params: unknown[] = [this.projectHash];\n\n    if (!includeUnclassified) {\n      sql += \" AND ((classification IS NOT NULL AND classification != 'noise') OR created_at >= datetime('now', '-60 seconds'))\";\n    }\n\n    if (options?.kind) {\n      sql += ' AND kind = ?';\n      params.push(options.kind);\n    }\n\n    if (options?.sessionId) {\n      sql += ' AND session_id = ?';\n      params.push(options.sessionId);\n    }\n\n    if (options?.since) {\n      sql += ' AND created_at >= ?';\n      params.push(options.since);\n    }\n\n    sql += ' ORDER BY created_at DESC, rowid DESC LIMIT ? OFFSET ?';\n    params.push(limit, offset);\n\n    const rows = this.db.prepare(sql).all(...params) as ObservationRow[];\n\n    debug('obs', 'Listed observations', { count: rows.length });\n\n    return rows.map(rowToObservation);\n  }\n\n  /**\n   * Updates an observation's content, embedding fields, or both.\n   * Always sets updated_at to current time.\n   * Scoped to this project; returns null if not found or soft-deleted.\n   */\n  update(\n    id: string,\n    updates: Partial<\n      Pick<\n        Observation,\n        'content' | 'embedding' | 'embeddingModel' | 'embeddingVersion'\n      >\n    >,\n  ): Observation | null {\n    debug('obs', 'Updating observation', { id });\n\n    const setClauses: string[] = [\"updated_at = datetime('now')\"];\n    const params: unknown[] = [];\n\n    if (updates.content !== undefined) {\n      setClauses.push('content = ?');\n      params.push(updates.content);\n    }\n\n    if (updates.embedding !== undefined) {\n      setClauses.push('embedding = ?');\n      params.push(\n        updates.embedding\n          ? Buffer.from(\n              updates.embedding.buffer,\n              updates.embedding.byteOffset,\n              updates.embedding.byteLength,\n            )\n          : null,\n      );\n    }\n\n    if (updates.embeddingModel !== undefined) {\n      setClauses.push('embedding_model = ?');\n      params.push(updates.embeddingModel);\n    }\n\n    if (updates.embeddingVersion !== undefined) {\n      setClauses.push('embedding_version = ?');\n      params.push(updates.embeddingVersion);\n    }\n\n    params.push(id, this.projectHash);\n\n    const sql = `UPDATE observations SET ${setClauses.join(', ')} WHERE id = ? AND project_hash = ? AND deleted_at IS NULL`;\n    const result = this.db.prepare(sql).run(...params);\n\n    if (result.changes === 0) {\n      debug('obs', 'Observation not found for update', { id });\n      return null;\n    }\n\n    debug('obs', 'Observation updated', { id });\n\n    return this.getById(id);\n  }\n\n  /**\n   * Soft-deletes an observation by setting deleted_at.\n   * Accepts full 32-char IDs or shorter prefix strings (e.g. the 8-char\n   * display IDs shown in search results).\n   * Returns true if the observation was found and deleted.\n   */\n  softDelete(id: string): boolean {\n    debug('obs', 'Soft-deleting observation', { id });\n    const resolvedId = this.resolveId(id) ?? id;\n    const result = this.stmtSoftDelete.run(resolvedId, this.projectHash);\n    debug('obs', result.changes > 0 ? 'Observation soft-deleted' : 'Observation not found for delete', { id: resolvedId });\n    return result.changes > 0;\n  }\n\n  /**\n   * Restores a soft-deleted observation by clearing deleted_at.\n   * Accepts full 32-char IDs or shorter prefix strings (e.g. the 8-char\n   * display IDs shown in search results).\n   * Returns true if the observation was found and restored.\n   */\n  restore(id: string): boolean {\n    const resolvedId = this.resolveId(id) ?? id;\n    const result = this.stmtRestore.run(resolvedId, this.projectHash);\n    return result.changes > 0;\n  }\n\n  /**\n   * Updates the classification of an observation.\n   * Sets classified_at to current time. Returns true if found and updated.\n   */\n  updateClassification(\n    id: string,\n    classification: ObservationClassification,\n  ): boolean {\n    debug('obs', 'Updating classification', { id, classification });\n    const sql = `\n      UPDATE observations\n      SET classification = ?, classified_at = datetime('now'), updated_at = datetime('now')\n      WHERE id = ? AND project_hash = ? AND deleted_at IS NULL\n    `;\n    const result = this.db.prepare(sql).run(classification, id, this.projectHash);\n    return result.changes > 0;\n  }\n\n  /**\n   * Creates an observation with an initial classification (bypasses classifier).\n   * Used for explicit user saves that should be immediately visible.\n   */\n  createClassified(input: ObservationInsert, classification: ObservationClassification): Observation {\n    const obs = this.create(input);\n    this.updateClassification(obs.id, classification);\n    // Re-fetch to get the updated classification fields\n    return this.getById(obs.id)!;\n  }\n\n  /**\n   * Fetches unclassified observations for the background classifier.\n   * Returns observations ordered by created_at ASC (oldest first).\n   */\n  listUnclassified(limit: number = 20): Observation[] {\n    const sql = `\n      SELECT * FROM observations\n      WHERE project_hash = ? AND classification IS NULL AND deleted_at IS NULL\n      ORDER BY created_at ASC\n      LIMIT ?\n    `;\n    const rows = this.db.prepare(sql).all(this.projectHash, limit) as ObservationRow[];\n    return rows.map(rowToObservation);\n  }\n\n  /**\n   * Lists unclassified observations across ALL projects.\n   * Used by HaikuProcessor to avoid missing observations from other projects.\n   */\n  static listAllUnclassified(db: import('better-sqlite3').Database, limit: number = 20): Observation[] {\n    const sql = `\n      SELECT * FROM observations\n      WHERE classification IS NULL AND deleted_at IS NULL\n      ORDER BY created_at ASC\n      LIMIT ?\n    `;\n    const rows = db.prepare(sql).all(limit) as ObservationRow[];\n    return rows.map(rowToObservation);\n  }\n\n  /**\n   * Fetches observations surrounding a given timestamp for classification context.\n   * Returns observations regardless of classification status.\n   */\n  listContext(aroundTime: string, windowSize: number = 5): Observation[] {\n    // Get N observations before\n    const beforeSql = `\n      SELECT * FROM observations\n      WHERE project_hash = ? AND deleted_at IS NULL AND created_at <= ?\n      ORDER BY created_at DESC, rowid DESC\n      LIMIT ?\n    `;\n    const beforeRows = this.db.prepare(beforeSql).all(\n      this.projectHash, aroundTime, windowSize + 1,\n    ) as ObservationRow[];\n\n    // Get N observations after\n    const afterSql = `\n      SELECT * FROM observations\n      WHERE project_hash = ? AND deleted_at IS NULL AND created_at > ?\n      ORDER BY created_at ASC, rowid ASC\n      LIMIT ?\n    `;\n    const afterRows = this.db.prepare(afterSql).all(\n      this.projectHash, aroundTime, windowSize,\n    ) as ObservationRow[];\n\n    // Combine in chronological order (before is DESC, so reverse it)\n    const allRows = [...beforeRows.reverse(), ...afterRows];\n    // Deduplicate by id\n    const seen = new Set<string>();\n    const unique = allRows.filter(r => {\n      if (seen.has(r.id)) return false;\n      seen.add(r.id);\n      return true;\n    });\n    return unique.map(rowToObservation);\n  }\n\n  /**\n   * Counts non-deleted observations for this project.\n   */\n  count(): number {\n    const row = this.stmtCount.get(this.projectHash) as { count: number };\n    return row.count;\n  }\n\n  /**\n   * Gets an observation by ID, including soft-deleted observations.\n   * Accepts full 32-char IDs or shorter prefix strings (e.g. the 8-char\n   * display IDs shown in search results).\n   * Used by the recall tool for restore operations (must find purged items).\n   */\n  getByIdIncludingDeleted(id: string): Observation | null {\n    debug('obs', 'Getting observation including deleted', { id });\n    // resolveId only queries non-deleted; for deleted items we need a wider search\n    const FULL_ID_LENGTH = 32;\n    let resolvedId: string;\n    if (id.length === FULL_ID_LENGTH) {\n      resolvedId = id;\n    } else {\n      const rows = this.db\n        .prepare(\n          \"SELECT id FROM observations WHERE project_hash = ? AND id LIKE ? ESCAPE '\\\\' LIMIT 2\",\n        )\n        .all(this.projectHash, id.replace(/[%_\\\\]/g, '\\\\$&') + '%') as { id: string }[];\n      if (rows.length === 0) return null;\n      if (rows.length > 1) {\n        debug('obs', 'Ambiguous ID prefix for getByIdIncludingDeleted', { prefix: id, count: rows.length });\n        return null;\n      }\n      resolvedId = rows[0].id;\n    }\n    const row = this.stmtGetByIdIncludingDeleted.get(resolvedId, this.projectHash) as\n      | ObservationRow\n      | undefined;\n    return row ? rowToObservation(row) : null;\n  }\n\n  /**\n   * Lists observations for this project, including soft-deleted ones.\n   * Used by recall with include_purged: true to show all items.\n   */\n  listIncludingDeleted(options?: {\n    limit?: number;\n    offset?: number;\n  }): Observation[] {\n    const limit = options?.limit ?? 50;\n    const offset = options?.offset ?? 0;\n\n    debug('obs', 'Listing observations including deleted', { limit, offset });\n\n    const sql =\n      'SELECT * FROM observations WHERE project_hash = ? ORDER BY created_at DESC, rowid DESC LIMIT ? OFFSET ?';\n    const rows = this.db\n      .prepare(sql)\n      .all(this.projectHash, limit, offset) as ObservationRow[];\n\n    debug('obs', 'Listed observations including deleted', {\n      count: rows.length,\n    });\n\n    return rows.map(rowToObservation);\n  }\n\n  /**\n   * Searches observations by title substring (partial match via LIKE).\n   * Optionally includes soft-deleted items.\n   */\n  getByTitle(\n    title: string,\n    options?: { limit?: number; includePurged?: boolean },\n  ): Observation[] {\n    const limit = options?.limit ?? 20;\n    const includePurged = options?.includePurged ?? false;\n\n    debug('obs', 'Searching by title', { title, limit, includePurged });\n\n    let sql = 'SELECT * FROM observations WHERE project_hash = ? AND title LIKE ?';\n    if (!includePurged) {\n      sql += ' AND deleted_at IS NULL';\n    }\n    sql += \" AND classification IS NOT NULL AND classification != 'noise'\";\n    sql += ' ORDER BY created_at DESC, rowid DESC LIMIT ?';\n\n    const rows = this.db\n      .prepare(sql)\n      .all(this.projectHash, `%${title}%`, limit) as ObservationRow[];\n\n    debug('obs', 'Title search completed', { count: rows.length });\n\n    return rows.map(rowToObservation);\n  }\n}\n","import type BetterSqlite3 from 'better-sqlite3';\n\nimport { debug } from '../shared/debug.js';\nimport type { Session } from '../shared/types.js';\n\n/**\n * Raw session row from SQLite (snake_case column names).\n */\ninterface SessionRow {\n  id: string;\n  project_hash: string;\n  started_at: string;\n  ended_at: string | null;\n  summary: string | null;\n}\n\n/**\n * Maps a snake_case SessionRow to a camelCase Session interface.\n */\nfunction rowToSession(row: SessionRow): Session {\n  return {\n    id: row.id,\n    projectHash: row.project_hash,\n    startedAt: row.started_at,\n    endedAt: row.ended_at,\n    summary: row.summary,\n  };\n}\n\n/**\n * Repository for session lifecycle management.\n *\n * Every query is scoped to the projectHash provided at construction time.\n * All SQL statements are prepared once in the constructor.\n */\nexport class SessionRepository {\n  private readonly db: BetterSqlite3.Database;\n  private readonly projectHash: string;\n\n  // Prepared statements\n  private readonly stmtCreate: BetterSqlite3.Statement;\n  private readonly stmtGetById: BetterSqlite3.Statement;\n  private readonly stmtGetActive: BetterSqlite3.Statement;\n\n  constructor(db: BetterSqlite3.Database, projectHash: string) {\n    this.db = db;\n    this.projectHash = projectHash;\n\n    this.stmtCreate = db.prepare(`\n      INSERT INTO sessions (id, project_hash)\n      VALUES (?, ?)\n    `);\n\n    this.stmtGetById = db.prepare(`\n      SELECT * FROM sessions\n      WHERE id = ? AND project_hash = ?\n    `);\n\n    this.stmtGetActive = db.prepare(`\n      SELECT * FROM sessions\n      WHERE ended_at IS NULL AND project_hash = ?\n      ORDER BY started_at DESC\n      LIMIT 1\n    `);\n\n    debug('session', 'SessionRepository initialized', { projectHash });\n  }\n\n  /**\n   * Creates a new session with the given ID, scoped to this project.\n   */\n  create(id: string): Session {\n    this.stmtCreate.run(id, this.projectHash);\n\n    const row = this.stmtGetById.get(id, this.projectHash) as\n      | SessionRow\n      | undefined;\n\n    if (!row) {\n      throw new Error('Failed to retrieve newly created session');\n    }\n\n    debug('session', 'Session created', { id });\n\n    return rowToSession(row);\n  }\n\n  /**\n   * Ends a session by setting ended_at and optionally a summary.\n   * Returns the updated session or null if not found.\n   */\n  end(id: string, summary?: string): Session | null {\n    const setClauses = [\"ended_at = datetime('now')\"];\n    const params: unknown[] = [];\n\n    if (summary !== undefined) {\n      setClauses.push('summary = ?');\n      params.push(summary);\n    }\n\n    params.push(id, this.projectHash);\n\n    const sql = `UPDATE sessions SET ${setClauses.join(', ')} WHERE id = ? AND project_hash = ?`;\n    const result = this.db.prepare(sql).run(...params);\n\n    if (result.changes === 0) {\n      return null;\n    }\n\n    debug('session', 'Session ended', { id, hasSummary: !!summary });\n\n    return this.getById(id);\n  }\n\n  /**\n   * Gets a session by ID, scoped to this project.\n   */\n  getById(id: string): Session | null {\n    const row = this.stmtGetById.get(id, this.projectHash) as\n      | SessionRow\n      | undefined;\n    return row ? rowToSession(row) : null;\n  }\n\n  /**\n   * Gets the most recent sessions for this project, ordered by started_at DESC.\n   */\n  getLatest(limit?: number): Session[] {\n    const effectiveLimit = limit ?? 10;\n    const rows = this.db\n      .prepare(\n        `SELECT * FROM sessions WHERE project_hash = ? ORDER BY started_at DESC, rowid DESC LIMIT ?`,\n      )\n      .all(this.projectHash, effectiveLimit) as SessionRow[];\n    return rows.map(rowToSession);\n  }\n\n  /**\n   * Gets the currently active (not ended) session for this project.\n   * Returns the most recently started active session, or null if none.\n   */\n  getActive(): Session | null {\n    const row = this.stmtGetActive.get(this.projectHash) as\n      | SessionRow\n      | undefined;\n    return row ? rowToSession(row) : null;\n  }\n\n  /**\n   * Updates the summary column on an existing session row.\n   * Sets updated_at (via ended_at preservation) to track when the summary was written.\n   *\n   * Used by the curation module after compressing session observations.\n   */\n  updateSessionSummary(sessionId: string, summary: string): void {\n    const result = this.db\n      .prepare(\n        `UPDATE sessions SET summary = ? WHERE id = ? AND project_hash = ?`,\n      )\n      .run(summary, sessionId, this.projectHash);\n\n    if (result.changes === 0) {\n      debug('session', 'Session not found for summary update', {\n        sessionId,\n      });\n      return;\n    }\n\n    debug('session', 'Session summary updated', {\n      sessionId,\n      summaryLength: summary.length,\n    });\n  }\n}\n","import type BetterSqlite3 from 'better-sqlite3';\n\nimport { debug, debugTimed } from '../shared/debug.js';\nimport {\n  rowToObservation,\n  type ObservationRow,\n  type SearchResult,\n} from '../shared/types.js';\n\n/**\n * FTS5 search engine with BM25 ranking, snippet extraction, and strict project scoping.\n *\n * All queries are scoped to the projectHash provided at construction time.\n * Queries are sanitized to prevent FTS5 syntax errors and injection.\n */\nexport class SearchEngine {\n  private readonly db: BetterSqlite3.Database;\n  private readonly projectHash: string;\n\n  constructor(db: BetterSqlite3.Database, projectHash: string) {\n    this.db = db;\n    this.projectHash = projectHash;\n  }\n\n  /**\n   * Full-text search with BM25 ranking and snippet extraction.\n   *\n   * bm25() returns NEGATIVE values where more negative = more relevant.\n   * ORDER BY rank (ascending) puts best matches first.\n   *\n   * @param query - User's search query (sanitized for FTS5 safety)\n   * @param options - Optional limit and sessionId filter\n   * @returns SearchResult[] ordered by relevance (best match first)\n   */\n  searchKeyword(\n    query: string,\n    options?: { limit?: number; sessionId?: string },\n  ): SearchResult[] {\n    const sanitized = this.sanitizeQuery(query);\n    if (!sanitized) {\n      return [];\n    }\n\n    const limit = options?.limit ?? 20;\n\n    let sql = `\n      SELECT\n        o.*,\n        bm25(observations_fts, 2.0, 1.0) AS rank,\n        snippet(observations_fts, 1, '<mark>', '</mark>', '...', 32) AS snippet\n      FROM observations_fts\n      JOIN observations o ON o.rowid = observations_fts.rowid\n      WHERE observations_fts MATCH ?\n        AND o.project_hash = ?\n        AND o.deleted_at IS NULL\n        AND (o.classification IS NULL OR o.classification != 'noise')\n    `;\n    const params: unknown[] = [sanitized, this.projectHash];\n\n    if (options?.sessionId) {\n      sql += ' AND o.session_id = ?';\n      params.push(options.sessionId);\n    }\n\n    sql += ' ORDER BY rank LIMIT ?';\n    params.push(limit);\n\n    const results = debugTimed('search', 'FTS5 keyword search', () => {\n      const rows = this.db.prepare(sql).all(...params) as (ObservationRow & {\n        rank: number;\n        snippet: string;\n      })[];\n\n      return rows.map((row) => ({\n        observation: rowToObservation(row),\n        score: Math.abs(row.rank),\n        matchType: 'fts' as const,\n        snippet: row.snippet,\n      }));\n    });\n\n    debug('search', 'Keyword search completed', { query: sanitized, resultCount: results.length });\n\n    return results;\n  }\n\n  /**\n   * Prefix search for autocomplete-style matching.\n   * Appends `*` to each word for prefix matching.\n   */\n  searchByPrefix(prefix: string, limit?: number): SearchResult[] {\n    const words = prefix.trim().split(/\\s+/).filter(Boolean);\n    if (words.length === 0) {\n      return [];\n    }\n\n    // Sanitize each word and append * for prefix matching\n    const sanitizedWords = words\n      .map((w) => this.sanitizeWord(w))\n      .filter(Boolean);\n    if (sanitizedWords.length === 0) {\n      return [];\n    }\n\n    const ftsQuery = sanitizedWords.map((w) => `${w}*`).join(' ');\n    const effectiveLimit = limit ?? 20;\n\n    const sql = `\n      SELECT\n        o.*,\n        bm25(observations_fts, 2.0, 1.0) AS rank,\n        snippet(observations_fts, 1, '<mark>', '</mark>', '...', 32) AS snippet\n      FROM observations_fts\n      JOIN observations o ON o.rowid = observations_fts.rowid\n      WHERE observations_fts MATCH ?\n        AND o.project_hash = ?\n        AND o.deleted_at IS NULL\n        AND (o.classification IS NULL OR o.classification != 'noise')\n      ORDER BY rank\n      LIMIT ?\n    `;\n\n    const results = debugTimed('search', 'FTS5 prefix search', () => {\n      const rows = this.db\n        .prepare(sql)\n        .all(ftsQuery, this.projectHash, effectiveLimit) as (ObservationRow & {\n        rank: number;\n        snippet: string;\n      })[];\n\n      return rows.map((row) => ({\n        observation: rowToObservation(row),\n        score: Math.abs(row.rank),\n        matchType: 'fts' as const,\n        snippet: row.snippet,\n      }));\n    });\n\n    debug('search', 'Prefix search completed', { prefix, resultCount: results.length });\n\n    return results;\n  }\n\n  /**\n   * Rebuild the FTS5 index if it gets out of sync.\n   */\n  rebuildIndex(): void {\n    debug('search', 'Rebuilding FTS5 index');\n    this.db.exec(\n      \"INSERT INTO observations_fts(observations_fts) VALUES('rebuild')\",\n    );\n  }\n\n  /**\n   * Sanitizes a user query for safe FTS5 MATCH usage.\n   * Removes FTS5 operators and special characters.\n   * Returns null if the query is empty after sanitization.\n   */\n  private sanitizeQuery(query: string): string | null {\n    const words = query.trim().split(/\\s+/).filter(Boolean);\n    if (words.length === 0) {\n      return null;\n    }\n\n    const sanitizedWords = words\n      .map((w) => this.sanitizeWord(w))\n      .filter(Boolean);\n\n    if (sanitizedWords.length === 0) {\n      return null;\n    }\n\n    // FTS5 defaults to implicit AND for space-separated words\n    return sanitizedWords.join(' ');\n  }\n\n  /**\n   * Sanitizes a single word for FTS5 safety.\n   * Removes quotes, parentheses, asterisks, and FTS5 operator keywords.\n   */\n  private sanitizeWord(word: string): string {\n    // Remove FTS5 special characters\n    let cleaned = word.replace(/[\"*()^{}[\\]]/g, '');\n\n    // Remove FTS5 operator keywords (case-insensitive, only when the whole word is an operator)\n    if (/^(NEAR|OR|AND|NOT)$/i.test(cleaned)) {\n      return '';\n    }\n\n    // Remove any remaining non-alphanumeric characters except hyphens and underscores\n    cleaned = cleaned.replace(/[^\\w\\-]/g, '');\n\n    return cleaned;\n  }\n}\n","/**\n * Hybrid search combining FTS5 keyword results and vec0 vector results\n * using reciprocal rank fusion (RRF).\n *\n * When both keyword and vector results are available, RRF merges the two\n * ranked lists into a single score-sorted list. When only keyword results\n * are available (worker not ready, no embeddings), falls back transparently.\n */\n\nimport { debug, debugTimed } from '../shared/debug.js';\nimport type { SearchResult } from '../shared/types.js';\nimport type { SearchEngine } from '../storage/search.js';\nimport type { EmbeddingStore, EmbeddingSearchResult } from '../storage/embeddings.js';\nimport type { AnalysisWorker } from '../analysis/worker-bridge.js';\nimport { ObservationRepository } from '../storage/observations.js';\n\n// ---------------------------------------------------------------------------\n// Types\n// ---------------------------------------------------------------------------\n\ninterface RankedItem {\n  id: string;\n  [key: string]: unknown;\n}\n\ninterface FusedResult {\n  id: string;\n  fusedScore: number;\n}\n\nexport interface HybridSearchParams {\n  searchEngine: SearchEngine;\n  embeddingStore: EmbeddingStore;\n  worker: AnalysisWorker | null;\n  query: string;\n  db: import('better-sqlite3').Database;\n  projectHash: string;\n  options?: { limit?: number; sessionId?: string };\n}\n\n// ---------------------------------------------------------------------------\n// Reciprocal Rank Fusion\n// ---------------------------------------------------------------------------\n\n/**\n * Merges multiple ranked lists into a single fused ranking using RRF.\n *\n * For each document across all lists, computes:\n *   fusedScore = sum(1 / (k + rank + 1))\n * where rank is the 0-based position in each list.\n *\n * @param rankedLists - Arrays of ranked items, each with an `id` field\n * @param k - Smoothing constant (default 60, standard RRF value)\n * @returns Fused results sorted by fusedScore descending\n */\nexport function reciprocalRankFusion(\n  rankedLists: Array<Array<RankedItem>>,\n  k = 60,\n): FusedResult[] {\n  const scores = new Map<string, number>();\n\n  for (const list of rankedLists) {\n    for (let rank = 0; rank < list.length; rank++) {\n      const item = list[rank];\n      const current = scores.get(item.id) ?? 0;\n      scores.set(item.id, current + 1 / (k + rank + 1));\n    }\n  }\n\n  const results: FusedResult[] = [];\n  for (const [id, fusedScore] of scores) {\n    results.push({ id, fusedScore });\n  }\n\n  results.sort((a, b) => b.fusedScore - a.fusedScore);\n  return results;\n}\n\n// ---------------------------------------------------------------------------\n// Hybrid Search\n// ---------------------------------------------------------------------------\n\n/**\n * Combines FTS5 keyword search and vec0 vector search using RRF.\n *\n * Falls back to keyword-only when:\n * - Worker is null or not ready\n * - Query embedding fails\n * - No vector results returned\n *\n * @returns SearchResult[] with matchType indicating source(s)\n */\nexport async function hybridSearch(\n  params: HybridSearchParams,\n): Promise<SearchResult[]> {\n  const { searchEngine, embeddingStore, worker, query, db, projectHash, options } = params;\n  const limit = options?.limit ?? 20;\n\n  return debugTimed('search', 'Hybrid search', async () => {\n    // Step 1: Always run keyword search\n    const keywordResults = searchEngine.searchKeyword(query, {\n      limit,\n      sessionId: options?.sessionId,\n    });\n\n    debug('search', 'Keyword results', { count: keywordResults.length });\n\n    // Step 2: Attempt vector search if worker is available\n    let vectorResults: EmbeddingSearchResult[] = [];\n\n    if (worker && worker.isReady()) {\n      const queryEmbedding = await worker.embed(query);\n\n      if (queryEmbedding) {\n        // Fetch more vector results than limit to improve fusion quality\n        vectorResults = embeddingStore.search(queryEmbedding, limit * 2);\n        debug('search', 'Vector results', { count: vectorResults.length });\n      } else {\n        debug('search', 'Query embedding failed, keyword-only');\n      }\n    } else {\n      debug('search', 'Worker not ready, keyword-only');\n    }\n\n    // Step 3: Keyword-only fallback\n    if (vectorResults.length === 0) {\n      debug('search', 'Returning keyword-only results', { count: keywordResults.length });\n      return keywordResults;\n    }\n\n    // Step 4: Fuse keyword + vector results with RRF\n    const keywordRanked: RankedItem[] = keywordResults.map((r) => ({\n      id: r.observation.id,\n    }));\n\n    const vectorRanked: RankedItem[] = vectorResults.map((r) => ({\n      id: r.observationId,\n    }));\n\n    const fused = reciprocalRankFusion([keywordRanked, vectorRanked]);\n\n    // Build lookup maps\n    const keywordMap = new Map<string, SearchResult>();\n    for (const r of keywordResults) {\n      keywordMap.set(r.observation.id, r);\n    }\n\n    const vectorIdSet = new Set(vectorResults.map((r) => r.observationId));\n\n    // We need an ObservationRepository to look up vector-only observations\n    const obsRepo = new ObservationRepository(db, projectHash);\n\n    // Merge results\n    const merged: SearchResult[] = [];\n\n    for (const item of fused) {\n      if (merged.length >= limit) break;\n\n      const fromKeyword = keywordMap.get(item.id);\n      const fromVector = vectorIdSet.has(item.id);\n\n      if (fromKeyword && fromVector) {\n        // In both: hybrid match, use keyword snippet\n        merged.push({\n          observation: fromKeyword.observation,\n          score: item.fusedScore,\n          matchType: 'hybrid',\n          snippet: fromKeyword.snippet,\n        });\n      } else if (fromKeyword) {\n        // Keyword only\n        merged.push({\n          observation: fromKeyword.observation,\n          score: item.fusedScore,\n          matchType: 'fts',\n          snippet: fromKeyword.snippet,\n        });\n      } else if (fromVector) {\n        // Vector only -- need to load observation\n        const obs = obsRepo.getById(item.id);\n        if (obs) {\n          const snippet = (obs.content ?? '').replace(/\\n/g, ' ').slice(0, 100);\n          merged.push({\n            observation: obs,\n            score: item.fusedScore,\n            matchType: 'vector',\n            snippet,\n          });\n        }\n      }\n    }\n\n    debug('search', 'Hybrid search complete', {\n      keyword: keywordResults.length,\n      vector: vectorResults.length,\n      fused: merged.length,\n      hybrid: merged.filter((r) => r.matchType === 'hybrid').length,\n    });\n\n    return merged;\n  });\n}\n","/**\n * Text similarity utilities shared across modules.\n */\n\n/**\n * Computes Jaccard similarity between two texts based on tokenized words.\n * Words are lowercased and split on whitespace/punctuation.\n */\nexport function jaccardSimilarity(textA: string, textB: string): number {\n  const tokenize = (t: string): Set<string> =>\n    new Set(\n      t\n        .toLowerCase()\n        .split(/[\\s,.!?;:'\"()\\[\\]{}<>\\/\\\\|@#$%^&*+=~`]+/)\n        .filter((w) => w.length > 0),\n    );\n\n  const setA = tokenize(textA);\n  const setB = tokenize(textB);\n\n  if (setA.size === 0 && setB.size === 0) return 1;\n  if (setA.size === 0 || setB.size === 0) return 0;\n\n  let intersection = 0;\n  for (const w of setA) {\n    if (setB.has(w)) intersection++;\n  }\n\n  const union = setA.size + setB.size - intersection;\n  return union === 0 ? 0 : intersection / union;\n}\n","/**\n * Pre-save gate for duplicate detection.\n *\n * Two operating modes:\n * - Fast (hook path): Jaccard text similarity against recent observations. <5ms.\n * - Full (MCP path): Embedding-based KNN via EmbeddingStore.search() + text fallback. <100ms.\n *\n * Prevents database bloat by rejecting near-duplicate observations\n * before they hit storage, across both the hook auto-capture and MCP save_memory paths.\n *\n * Relevance scoring is handled by the background ObservationClassifier (LLM-based).\n */\n\nimport type BetterSqlite3 from 'better-sqlite3';\nimport type { AnalysisWorker } from '../analysis/worker-bridge.js';\nimport type { EmbeddingStore } from '../storage/embeddings.js';\nimport { ObservationRepository } from '../storage/observations.js';\nimport { jaccardSimilarity } from '../shared/similarity.js';\nimport { debug } from '../shared/debug.js';\n\nexport interface SaveDecision {\n  save: boolean;\n  reason?: string;\n  duplicateOf?: string;\n}\n\nexport interface SaveGuardOptions {\n  worker?: AnalysisWorker | null;\n  embeddingStore?: EmbeddingStore | null;\n  duplicateThreshold?: number;\n  vectorDistanceThreshold?: number;\n  recentWindow?: number;\n}\n\nexport class SaveGuard {\n  private readonly obsRepo: ObservationRepository;\n  private readonly worker: AnalysisWorker | null;\n  private readonly embeddingStore: EmbeddingStore | null;\n  private readonly duplicateThreshold: number;\n  private readonly vectorDistanceThreshold: number;\n  private readonly recentWindow: number;\n\n  /**\n   * Construct from db + projectHash (creates internal ObservationRepository),\n   * or from an existing ObservationRepository.\n   */\n  constructor(\n    dbOrRepo: BetterSqlite3.Database | ObservationRepository,\n    projectHashOrOpts?: string | SaveGuardOptions,\n    opts?: SaveGuardOptions,\n  ) {\n    if (dbOrRepo instanceof ObservationRepository) {\n      this.obsRepo = dbOrRepo;\n      const resolvedOpts = (projectHashOrOpts as SaveGuardOptions | undefined) ?? {};\n      this.worker = resolvedOpts.worker ?? null;\n      this.embeddingStore = resolvedOpts.embeddingStore ?? null;\n      this.duplicateThreshold = resolvedOpts.duplicateThreshold ?? 0.85;\n      this.vectorDistanceThreshold = resolvedOpts.vectorDistanceThreshold ?? 0.08;\n      this.recentWindow = resolvedOpts.recentWindow ?? 20;\n    } else {\n      this.obsRepo = new ObservationRepository(dbOrRepo, projectHashOrOpts as string);\n      this.worker = opts?.worker ?? null;\n      this.embeddingStore = opts?.embeddingStore ?? null;\n      this.duplicateThreshold = opts?.duplicateThreshold ?? 0.85;\n      this.vectorDistanceThreshold = opts?.vectorDistanceThreshold ?? 0.08;\n      this.recentWindow = opts?.recentWindow ?? 20;\n    }\n  }\n\n  /**\n   * Synchronous evaluation for the hook path (text-only, no embeddings).\n   * Only checks for duplicates — relevance is handled by the background classifier.\n   */\n  evaluateSync(content: string, _source: string): SaveDecision {\n    const dupResult = this.checkTextDuplicates(content);\n    if (dupResult) return dupResult;\n    return { save: true, reason: 'ok' };\n  }\n\n  /**\n   * Async evaluation for the MCP path (embeddings + text fallback).\n   * Only checks for duplicates — relevance is handled by the background classifier.\n   */\n  async evaluate(content: string, _source: string): Promise<SaveDecision> {\n    // 1a. Vector duplicate detection (if worker + embeddingStore available)\n    if (this.worker?.isReady() && this.embeddingStore) {\n      const embedding = await this.worker.embed(content);\n      if (embedding) {\n        const results = this.embeddingStore.search(embedding, 5);\n        for (const result of results) {\n          if (result.distance < this.vectorDistanceThreshold) {\n            debug('save-guard', 'Vector duplicate detected', {\n              distance: result.distance,\n              duplicateOf: result.observationId,\n            });\n            return {\n              save: false,\n              reason: 'duplicate',\n              duplicateOf: result.observationId,\n            };\n          }\n        }\n      }\n    }\n\n    // 1b. Text-based fallback\n    const dupResult = this.checkTextDuplicates(content);\n    if (dupResult) return dupResult;\n\n    return { save: true, reason: 'ok' };\n  }\n\n  private checkTextDuplicates(content: string): SaveDecision | null {\n    const recent = this.obsRepo.list({ limit: this.recentWindow, includeUnclassified: true });\n\n    for (const obs of recent) {\n      const sim = jaccardSimilarity(content, obs.content);\n      if (sim >= this.duplicateThreshold) {\n        debug('save-guard', 'Text duplicate detected', {\n          similarity: sim,\n          duplicateOf: obs.id,\n        });\n        return {\n          save: false,\n          reason: 'duplicate',\n          duplicateOf: obs.id,\n        };\n      }\n    }\n\n    return null;\n  }\n}\n","/**\n * Migration 001: Create graph_nodes and graph_edges tables.\n *\n * Graph tables are managed separately from the main observation/session tables\n * because the knowledge graph is a distinct subsystem that operates\n * on extracted entities rather than raw observations.\n *\n * Tables:\n *   - graph_nodes: entities with type-checked taxonomy (6 types)\n *   - graph_edges: directed relationships with type-checked taxonomy (8 types),\n *     weight confidence, and unique constraint on (source_id, target_id, type)\n *\n * Indexes:\n *   - Nodes: type, name\n *   - Edges: source_id, target_id, type, unique(source_id, target_id, type)\n */\n\nexport const up = `\n  CREATE TABLE IF NOT EXISTS graph_nodes (\n    id TEXT PRIMARY KEY,\n    type TEXT NOT NULL CHECK(type IN ('Project','File','Decision','Problem','Solution','Reference')),\n    name TEXT NOT NULL,\n    metadata TEXT DEFAULT '{}',\n    observation_ids TEXT DEFAULT '[]',\n    project_hash TEXT,\n    created_at TEXT NOT NULL DEFAULT (datetime('now')),\n    updated_at TEXT NOT NULL DEFAULT (datetime('now'))\n  );\n\n  CREATE TABLE IF NOT EXISTS graph_edges (\n    id TEXT PRIMARY KEY,\n    source_id TEXT NOT NULL REFERENCES graph_nodes(id) ON DELETE CASCADE,\n    target_id TEXT NOT NULL REFERENCES graph_nodes(id) ON DELETE CASCADE,\n    type TEXT NOT NULL CHECK(type IN ('related_to','solved_by','caused_by','modifies','informed_by','references','verified_by','preceded_by')),\n    weight REAL NOT NULL DEFAULT 1.0 CHECK(weight >= 0.0 AND weight <= 1.0),\n    metadata TEXT DEFAULT '{}',\n    project_hash TEXT,\n    created_at TEXT NOT NULL DEFAULT (datetime('now'))\n  );\n\n  CREATE INDEX IF NOT EXISTS idx_graph_nodes_type ON graph_nodes(type);\n  CREATE INDEX IF NOT EXISTS idx_graph_nodes_name ON graph_nodes(name);\n  CREATE INDEX IF NOT EXISTS idx_graph_edges_source ON graph_edges(source_id);\n  CREATE INDEX IF NOT EXISTS idx_graph_edges_target ON graph_edges(target_id);\n  CREATE INDEX IF NOT EXISTS idx_graph_edges_type ON graph_edges(type);\n  CREATE UNIQUE INDEX IF NOT EXISTS idx_graph_edges_unique ON graph_edges(source_id, target_id, type);\n`;\n\nexport const down = `\n  DROP INDEX IF EXISTS idx_graph_edges_unique;\n  DROP INDEX IF EXISTS idx_graph_edges_type;\n  DROP INDEX IF EXISTS idx_graph_edges_target;\n  DROP INDEX IF EXISTS idx_graph_edges_source;\n  DROP INDEX IF EXISTS idx_graph_nodes_name;\n  DROP INDEX IF EXISTS idx_graph_nodes_type;\n  DROP TABLE IF EXISTS graph_edges;\n  DROP TABLE IF EXISTS graph_nodes;\n`;\n","/**\n * Migration 002: Add indexes on project_hash for graph tables.\n *\n * Supports project-scoped queries that filter by project_hash.\n */\n\nexport const up = `\n  CREATE INDEX IF NOT EXISTS idx_graph_nodes_project ON graph_nodes(project_hash);\n  CREATE INDEX IF NOT EXISTS idx_graph_edges_project ON graph_edges(project_hash);\n`;\n\nexport const down = `\n  DROP INDEX IF EXISTS idx_graph_edges_project;\n  DROP INDEX IF EXISTS idx_graph_nodes_project;\n`;\n","/**\n * Knowledge graph schema initialization and query builders.\n *\n * All functions accept a better-sqlite3 Database handle and use prepared\n * statements for performance. Metadata and observation_ids are stored as\n * JSON TEXT in SQLite and parsed on read.\n *\n * Traversal uses recursive CTEs for efficient subgraph extraction up to\n * a configurable depth.\n */\n\nimport type BetterSqlite3 from 'better-sqlite3';\nimport { randomBytes } from 'node:crypto';\n\nimport type {\n  EntityType,\n  RelationshipType,\n  GraphNode,\n  GraphEdge,\n} from './types.js';\nimport { up as graphTablesDDL } from './migrations/001-graph-tables.js';\nimport { up as projectHashIndexDDL } from './migrations/002-project-hash-index.js';\n\n// =============================================================================\n// Raw Row Types (snake_case, matches SQL columns)\n// =============================================================================\n\ninterface NodeRow {\n  id: string;\n  type: string;\n  name: string;\n  metadata: string; // JSON string\n  observation_ids: string; // JSON string\n  created_at: string;\n  updated_at: string;\n}\n\ninterface EdgeRow {\n  id: string;\n  source_id: string;\n  target_id: string;\n  type: string;\n  weight: number;\n  metadata: string; // JSON string\n  created_at: string;\n}\n\ninterface TraversalRow {\n  // Node columns (prefixed n_)\n  n_id: string;\n  n_type: string;\n  n_name: string;\n  n_metadata: string;\n  n_observation_ids: string;\n  n_created_at: string;\n  n_updated_at: string;\n  // Edge columns (prefixed e_) -- nullable for starting node\n  e_id: string | null;\n  e_source_id: string | null;\n  e_target_id: string | null;\n  e_type: string | null;\n  e_weight: number | null;\n  e_metadata: string | null;\n  e_created_at: string | null;\n  // Traversal depth\n  depth: number;\n}\n\n// =============================================================================\n// Row Mapping\n// =============================================================================\n\nfunction rowToNode(row: NodeRow): GraphNode {\n  return {\n    id: row.id,\n    type: row.type as EntityType,\n    name: row.name,\n    metadata: JSON.parse(row.metadata) as Record<string, unknown>,\n    observation_ids: JSON.parse(row.observation_ids) as string[],\n    created_at: row.created_at,\n    updated_at: row.updated_at,\n  };\n}\n\nfunction rowToEdge(row: EdgeRow): GraphEdge {\n  return {\n    id: row.id,\n    source_id: row.source_id,\n    target_id: row.target_id,\n    type: row.type as RelationshipType,\n    weight: row.weight,\n    metadata: JSON.parse(row.metadata) as Record<string, unknown>,\n    created_at: row.created_at,\n  };\n}\n\n// =============================================================================\n// Traversal Result\n// =============================================================================\n\nexport interface TraversalResult {\n  node: GraphNode;\n  edge: GraphEdge | null;\n  depth: number;\n}\n\n// =============================================================================\n// Schema Initialization\n// =============================================================================\n\n/**\n * Initializes graph tables if they do not exist.\n * Uses CREATE TABLE IF NOT EXISTS so it is safe to call multiple times.\n */\nexport function initGraphSchema(db: BetterSqlite3.Database): void {\n  db.exec(graphTablesDDL);\n  db.exec(projectHashIndexDDL);\n}\n\n// =============================================================================\n// Traversal Queries\n// =============================================================================\n\n/**\n * Traverses the graph from a starting node using a recursive CTE.\n *\n * Supports directional traversal:\n *   - 'outgoing': follows edges where source_id matches (default)\n *   - 'incoming': follows edges where target_id matches\n *   - 'both': follows edges in either direction\n *\n * Returns nodes and the edges that connect them, up to the specified depth.\n * The starting node itself is NOT included in results (depth > 0 filter).\n *\n * @param db - better-sqlite3 Database handle\n * @param nodeId - starting node ID\n * @param opts - traversal options (depth, edgeTypes, direction)\n * @returns Array of { node, edge, depth } for each reachable node\n */\nexport function traverseFrom(\n  db: BetterSqlite3.Database,\n  nodeId: string,\n  opts: {\n    depth?: number;\n    edgeTypes?: RelationshipType[];\n    direction?: 'outgoing' | 'incoming' | 'both';\n    projectHash: string | null;\n  },\n): TraversalResult[] {\n  const maxDepth = opts.depth ?? 2;\n  const direction = opts.direction ?? 'outgoing';\n\n  // Build edge type filter clause\n  let edgeTypeFilter = '';\n\n  if (opts.edgeTypes && opts.edgeTypes.length > 0) {\n    const placeholders = opts.edgeTypes.map(() => '?').join(', ');\n    edgeTypeFilter = `AND e.type IN (${placeholders})`;\n  }\n\n  // Project isolation: filter edges by project_hash to prevent cross-project traversal\n  const projectFilter = opts.projectHash ? 'AND e.project_hash = ?' : '';\n\n  // Build the recursive step based on direction\n  let recursiveStep: string;\n\n  if (direction === 'outgoing') {\n    recursiveStep = `\n      SELECT e.target_id, t.depth + 1, e.id\n      FROM graph_edges e\n      JOIN traverse t ON e.source_id = t.node_id\n      WHERE t.depth < ?\n      ${edgeTypeFilter}\n      ${projectFilter}\n    `;\n  } else if (direction === 'incoming') {\n    recursiveStep = `\n      SELECT e.source_id, t.depth + 1, e.id\n      FROM graph_edges e\n      JOIN traverse t ON e.target_id = t.node_id\n      WHERE t.depth < ?\n      ${edgeTypeFilter}\n      ${projectFilter}\n    `;\n  } else {\n    // both directions\n    recursiveStep = `\n      SELECT e.target_id, t.depth + 1, e.id\n      FROM graph_edges e\n      JOIN traverse t ON e.source_id = t.node_id\n      WHERE t.depth < ?\n      ${edgeTypeFilter}\n      ${projectFilter}\n      UNION ALL\n      SELECT e.source_id, t.depth + 1, e.id\n      FROM graph_edges e\n      JOIN traverse t ON e.target_id = t.node_id\n      WHERE t.depth < ?\n      ${edgeTypeFilter}\n      ${projectFilter}\n    `;\n  }\n\n  const sql = `\n    WITH RECURSIVE traverse(node_id, depth, edge_id) AS (\n      SELECT ?, 0, NULL\n      UNION ALL\n      ${recursiveStep}\n    )\n    SELECT DISTINCT\n      n.id AS n_id, n.type AS n_type, n.name AS n_name,\n      n.metadata AS n_metadata, n.observation_ids AS n_observation_ids,\n      n.created_at AS n_created_at, n.updated_at AS n_updated_at,\n      e.id AS e_id, e.source_id AS e_source_id, e.target_id AS e_target_id,\n      e.type AS e_type, e.weight AS e_weight, e.metadata AS e_metadata,\n      e.created_at AS e_created_at,\n      t.depth\n    FROM traverse t\n    JOIN graph_nodes n ON n.id = t.node_id\n    LEFT JOIN graph_edges e ON e.id = t.edge_id\n    WHERE t.depth > 0\n  `;\n\n  // Helper to push params for one recursive branch\n  const pushBranchParams = (params: unknown[]) => {\n    params.push(maxDepth);\n    if (opts.edgeTypes) params.push(...opts.edgeTypes);\n    if (opts.projectHash) params.push(opts.projectHash);\n  };\n\n  // Build parameter list depending on direction\n  const queryParams: unknown[] = [nodeId]; // initial SELECT ?\n\n  if (direction === 'both') {\n    pushBranchParams(queryParams);\n    pushBranchParams(queryParams);\n  } else {\n    pushBranchParams(queryParams);\n  }\n\n  const rows = db.prepare(sql).all(...queryParams) as TraversalRow[];\n\n  return rows.map((row) => ({\n    node: {\n      id: row.n_id,\n      type: row.n_type as EntityType,\n      name: row.n_name,\n      metadata: JSON.parse(row.n_metadata) as Record<string, unknown>,\n      observation_ids: JSON.parse(row.n_observation_ids) as string[],\n      created_at: row.n_created_at,\n      updated_at: row.n_updated_at,\n    },\n    edge: row.e_id\n      ? {\n          id: row.e_id,\n          source_id: row.e_source_id!,\n          target_id: row.e_target_id!,\n          type: row.e_type as RelationshipType,\n          weight: row.e_weight!,\n          metadata: JSON.parse(row.e_metadata!) as Record<string, unknown>,\n          created_at: row.e_created_at!,\n        }\n      : null,\n    depth: row.depth,\n  }));\n}\n\n// =============================================================================\n// Node Queries\n// =============================================================================\n\n/**\n * Returns all nodes of a given entity type.\n */\nexport function getNodesByType(\n  db: BetterSqlite3.Database,\n  type: EntityType,\n  projectHash: string | null,\n): GraphNode[] {\n  if (projectHash) {\n    const rows = db\n      .prepare('SELECT * FROM graph_nodes WHERE type = ? AND project_hash = ?')\n      .all(type, projectHash) as NodeRow[];\n    return rows.map(rowToNode);\n  }\n  const rows = db\n    .prepare('SELECT * FROM graph_nodes WHERE type = ?')\n    .all(type) as NodeRow[];\n  return rows.map(rowToNode);\n}\n\n/**\n * Looks up a node by name and type (composite natural key).\n * Returns null if no matching node exists.\n */\nexport function getNodeByNameAndType(\n  db: BetterSqlite3.Database,\n  name: string,\n  type: EntityType,\n  projectHash: string | null,\n): GraphNode | null {\n  if (projectHash) {\n    const row = db\n      .prepare('SELECT * FROM graph_nodes WHERE name = ? AND type = ? AND project_hash = ?')\n      .get(name, type, projectHash) as NodeRow | undefined;\n    return row ? rowToNode(row) : null;\n  }\n  const row = db\n    .prepare('SELECT * FROM graph_nodes WHERE name = ? AND type = ?')\n    .get(name, type) as NodeRow | undefined;\n  return row ? rowToNode(row) : null;\n}\n\n// =============================================================================\n// Edge Queries\n// =============================================================================\n\n/**\n * Returns edges connected to a node, filtered by direction.\n *\n * @param direction - 'outgoing' (source), 'incoming' (target), or 'both' (default: 'both')\n */\nexport function getEdgesForNode(\n  db: BetterSqlite3.Database,\n  nodeId: string,\n  opts: { direction?: 'outgoing' | 'incoming' | 'both'; projectHash: string | null },\n): GraphEdge[] {\n  const direction = opts.direction ?? 'both';\n  const pFilter = opts.projectHash ? ' AND project_hash = ?' : '';\n\n  let sql: string;\n  let params: unknown[];\n\n  if (direction === 'outgoing') {\n    sql = `SELECT * FROM graph_edges WHERE source_id = ?${pFilter}`;\n    params = opts.projectHash ? [nodeId, opts.projectHash] : [nodeId];\n  } else if (direction === 'incoming') {\n    sql = `SELECT * FROM graph_edges WHERE target_id = ?${pFilter}`;\n    params = opts.projectHash ? [nodeId, opts.projectHash] : [nodeId];\n  } else {\n    sql = `SELECT * FROM graph_edges WHERE (source_id = ? OR target_id = ?)${pFilter}`;\n    params = opts.projectHash ? [nodeId, nodeId, opts.projectHash] : [nodeId, nodeId];\n  }\n\n  const rows = db.prepare(sql).all(...params) as EdgeRow[];\n  return rows.map(rowToEdge);\n}\n\n/**\n * Returns the total number of edges connected to a node (both directions).\n * Used for degree enforcement (MAX_NODE_DEGREE constraint).\n */\nexport function countEdgesForNode(\n  db: BetterSqlite3.Database,\n  nodeId: string,\n  projectHash: string | null,\n): number {\n  if (projectHash) {\n    const result = db\n      .prepare(\n        'SELECT COUNT(*) as cnt FROM graph_edges WHERE (source_id = ? OR target_id = ?) AND project_hash = ?',\n      )\n      .get(nodeId, nodeId, projectHash) as { cnt: number };\n    return result.cnt;\n  }\n  const result = db\n    .prepare(\n      'SELECT COUNT(*) as cnt FROM graph_edges WHERE source_id = ? OR target_id = ?',\n    )\n    .get(nodeId, nodeId) as { cnt: number };\n  return result.cnt;\n}\n\n// =============================================================================\n// Mutations\n// =============================================================================\n\n/**\n * Inserts or updates a node by name+type composite key.\n *\n * If a node with the same name and type already exists, updates its metadata\n * and merges observation_ids. Otherwise, inserts a new node with a generated UUID.\n *\n * @returns The upserted GraphNode\n */\nexport function upsertNode(\n  db: BetterSqlite3.Database,\n  node: Omit<GraphNode, 'id' | 'created_at' | 'updated_at'> & { id?: string; project_hash: string | null },\n): GraphNode {\n  const existing = getNodeByNameAndType(db, node.name, node.type, node.project_hash);\n\n  if (existing) {\n    // Merge observation_ids (deduplicated)\n    const mergedObsIds = [\n      ...new Set([...existing.observation_ids, ...node.observation_ids]),\n    ];\n\n    // Merge metadata (new values override existing)\n    const mergedMetadata = { ...existing.metadata, ...node.metadata };\n\n    db.prepare(\n      `UPDATE graph_nodes\n       SET metadata = ?, observation_ids = ?, updated_at = datetime('now')\n       WHERE id = ?`,\n    ).run(\n      JSON.stringify(mergedMetadata),\n      JSON.stringify(mergedObsIds),\n      existing.id,\n    );\n\n    const updated = db\n      .prepare('SELECT * FROM graph_nodes WHERE id = ?')\n      .get(existing.id) as NodeRow;\n    return rowToNode(updated);\n  }\n\n  // Insert new node\n  const id = node.id ?? randomBytes(16).toString('hex');\n  db.prepare(\n    `INSERT INTO graph_nodes (id, type, name, metadata, observation_ids, project_hash)\n     VALUES (?, ?, ?, ?, ?, ?)`,\n  ).run(\n    id,\n    node.type,\n    node.name,\n    JSON.stringify(node.metadata),\n    JSON.stringify(node.observation_ids),\n    node.project_hash,\n  );\n\n  const inserted = db\n    .prepare('SELECT * FROM graph_nodes WHERE id = ?')\n    .get(id) as NodeRow;\n  return rowToNode(inserted);\n}\n\n/**\n * Inserts an edge. On conflict (same source_id, target_id, type),\n * updates the weight to the maximum of existing and new values.\n *\n * @returns The inserted or updated GraphEdge\n */\nexport function insertEdge(\n  db: BetterSqlite3.Database,\n  edge: Omit<GraphEdge, 'id' | 'created_at'> & { id?: string; project_hash: string | null },\n): GraphEdge {\n  const id = edge.id ?? randomBytes(16).toString('hex');\n\n  db.prepare(\n    `INSERT INTO graph_edges (id, source_id, target_id, type, weight, metadata, project_hash)\n     VALUES (?, ?, ?, ?, ?, ?, ?)\n     ON CONFLICT (source_id, target_id, type) DO UPDATE SET\n       weight = MAX(graph_edges.weight, excluded.weight),\n       metadata = excluded.metadata`,\n  ).run(\n    id,\n    edge.source_id,\n    edge.target_id,\n    edge.type,\n    edge.weight,\n    JSON.stringify(edge.metadata),\n    edge.project_hash,\n  );\n\n  // Retrieve the actual row (may be the existing row if conflict occurred)\n  const inserted = db\n    .prepare(\n      'SELECT * FROM graph_edges WHERE source_id = ? AND target_id = ? AND type = ?',\n    )\n    .get(edge.source_id, edge.target_id, edge.type) as EdgeRow;\n  return rowToEdge(inserted);\n}\n","/**\n * Staleness detection for the knowledge graph.\n *\n * Detects contradictions between observations linked to the same entity\n * using pattern matching (negation, replacement, status change). Stale\n * observations are FLAGGED but NEVER deleted -- the system surfaces both\n * observations and lets the user decide.\n *\n * This module is detection-only on the read path (detectStaleness) and\n * provides advisory flagging on the write path (flagStaleObservation).\n */\n\nimport type BetterSqlite3 from 'better-sqlite3';\n\nimport type { Observation, ObservationRow } from '../shared/types.js';\nimport { rowToObservation } from '../shared/types.js';\nimport type { EntityType } from './types.js';\n\n// =============================================================================\n// Types\n// =============================================================================\n\n/**\n * A staleness report documenting a detected contradiction between\n * two observations about the same entity.\n */\nexport interface StalenessReport {\n  entityId: string;\n  entityName: string;\n  entityType: EntityType;\n  newerObservation: { id: string; text: string; created_at: string };\n  olderObservation: { id: string; text: string; created_at: string };\n  reason: string;\n  detectedAt: string;\n}\n\n/**\n * A flagged stale observation with its staleness metadata.\n */\nexport interface StalenessFlag {\n  observation_id: string;\n  flagged_at: string;\n  reason: string;\n  resolved: boolean;\n}\n\n// =============================================================================\n// Staleness Detection Patterns\n// =============================================================================\n\n/**\n * Negation patterns: newer observation negates older one.\n * Matches when newer text contains negation keywords absent in older text\n * and both discuss similar subjects.\n */\nconst NEGATION_KEYWORDS = [\n  'not',\n  \"don't\",\n  'no longer',\n  'stopped',\n  'never',\n  \"doesn't\",\n  \"won't\",\n  \"isn't\",\n  \"aren't\",\n  'discontinued',\n] as const;\n\n/**\n * Replacement patterns: newer observation explicitly replaces older approach.\n */\nconst REPLACEMENT_PATTERNS = [\n  /switched\\s+(?:from\\s+\\S+\\s+)?to\\b/i,\n  /migrated\\s+(?:from\\s+\\S+\\s+)?to\\b/i,\n  /replaced\\s+(?:\\S+\\s+)?with\\b/i,\n  /changed\\s+from\\b/i,\n  /moved\\s+(?:from\\s+\\S+\\s+)?to\\b/i,\n  /upgraded\\s+(?:from\\s+\\S+\\s+)?to\\b/i,\n  /swapped\\s+(?:\\S+\\s+)?(?:for|with)\\b/i,\n] as const;\n\n/**\n * Status change patterns: newer observation marks something as inactive.\n */\nconst STATUS_CHANGE_KEYWORDS = [\n  'removed',\n  'deleted',\n  'deprecated',\n  'archived',\n  'dropped',\n  'disabled',\n  'decommissioned',\n  'sunset',\n  'abandoned',\n] as const;\n\n// =============================================================================\n// Schema Initialization\n// =============================================================================\n\n/**\n * Creates the staleness_flags table if it doesn't exist.\n * Uses a separate table rather than modifying the observations table,\n * keeping staleness metadata decoupled from core observation storage.\n */\nexport function initStalenessSchema(db: BetterSqlite3.Database): void {\n  db.exec(`\n    CREATE TABLE IF NOT EXISTS staleness_flags (\n      observation_id TEXT PRIMARY KEY,\n      flagged_at TEXT NOT NULL DEFAULT (datetime('now')),\n      reason TEXT NOT NULL,\n      resolved INTEGER NOT NULL DEFAULT 0\n    );\n    CREATE INDEX IF NOT EXISTS idx_staleness_resolved ON staleness_flags(resolved);\n  `);\n}\n\n// =============================================================================\n// Detection\n// =============================================================================\n\n/**\n * Detects potential staleness (contradictions) between observations\n * linked to a specific entity.\n *\n * Compares consecutive observation pairs chronologically and checks for:\n * 1. Negation patterns (newer negates older)\n * 2. Replacement patterns (newer replaces older approach)\n * 3. Status change patterns (newer marks something as inactive)\n *\n * This is DETECTION ONLY -- no data is modified.\n *\n * @param db - better-sqlite3 Database handle\n * @param entityId - Graph node ID to check observations for\n * @returns Array of StalenessReport for each detected contradiction\n */\nexport function detectStaleness(\n  db: BetterSqlite3.Database,\n  entityId: string,\n): StalenessReport[] {\n  // Get entity info\n  const node = db\n    .prepare('SELECT id, name, type, observation_ids FROM graph_nodes WHERE id = ?')\n    .get(entityId) as\n    | { id: string; name: string; type: string; observation_ids: string }\n    | undefined;\n\n  if (!node) return [];\n\n  const obsIds = JSON.parse(node.observation_ids) as string[];\n  if (obsIds.length < 2) return [];\n\n  // Fetch observations and sort by created_at\n  const placeholders = obsIds.map(() => '?').join(', ');\n  const rows = db\n    .prepare(\n      `SELECT * FROM observations WHERE id IN (${placeholders}) AND deleted_at IS NULL ORDER BY created_at ASC`,\n    )\n    .all(...obsIds) as ObservationRow[];\n\n  const observations = rows.map(rowToObservation);\n  if (observations.length < 2) return [];\n\n  const reports: StalenessReport[] = [];\n  const now = new Date().toISOString();\n\n  // Compare consecutive pairs\n  for (let i = 0; i < observations.length - 1; i++) {\n    const older = observations[i];\n    const newer = observations[i + 1];\n\n    const reason = detectContradiction(older.content, newer.content);\n    if (reason) {\n      reports.push({\n        entityId: node.id,\n        entityName: node.name,\n        entityType: node.type as EntityType,\n        newerObservation: {\n          id: newer.id,\n          text: newer.content,\n          created_at: newer.createdAt,\n        },\n        olderObservation: {\n          id: older.id,\n          text: older.content,\n          created_at: older.createdAt,\n        },\n        reason,\n        detectedAt: now,\n      });\n    }\n  }\n\n  return reports;\n}\n\n/**\n * Detects contradiction between two observation texts.\n * Returns a human-readable reason string, or null if no contradiction found.\n */\nfunction detectContradiction(\n  olderText: string,\n  newerText: string,\n): string | null {\n  const olderLower = olderText.toLowerCase();\n  const newerLower = newerText.toLowerCase();\n\n  // Check negation patterns\n  const negationResult = detectNegation(olderLower, newerLower);\n  if (negationResult) return negationResult;\n\n  // Check replacement patterns\n  const replacementResult = detectReplacement(newerLower);\n  if (replacementResult) return replacementResult;\n\n  // Check status change patterns\n  const statusResult = detectStatusChange(olderLower, newerLower);\n  if (statusResult) return statusResult;\n\n  return null;\n}\n\n/**\n * Detects negation: newer text contains negation keywords that are absent\n * in the older text, suggesting the newer observation contradicts the older.\n */\nfunction detectNegation(\n  olderLower: string,\n  newerLower: string,\n): string | null {\n  for (const keyword of NEGATION_KEYWORDS) {\n    if (newerLower.includes(keyword) && !olderLower.includes(keyword)) {\n      return `Newer observation contains negation (\"${keyword}\") not present in older observation`;\n    }\n  }\n  return null;\n}\n\n/**\n * Detects replacement: newer text explicitly mentions switching/replacing.\n */\nfunction detectReplacement(newerLower: string): string | null {\n  for (const pattern of REPLACEMENT_PATTERNS) {\n    const match = newerLower.match(pattern);\n    if (match) {\n      return `Newer observation indicates replacement (\"${match[0].trim()}\")`;\n    }\n  }\n  return null;\n}\n\n/**\n * Detects status change: newer text marks something as removed/deprecated\n * when the older text described it as active/present.\n */\nfunction detectStatusChange(\n  olderLower: string,\n  newerLower: string,\n): string | null {\n  for (const keyword of STATUS_CHANGE_KEYWORDS) {\n    if (newerLower.includes(keyword) && !olderLower.includes(keyword)) {\n      return `Newer observation indicates status change (\"${keyword}\")`;\n    }\n  }\n  return null;\n}\n\n// =============================================================================\n// Flagging\n// =============================================================================\n\n/**\n * Flags an observation as stale with an advisory reason.\n *\n * This flag is advisory -- search can use it to deprioritize but never hide\n * the observation. The observation remains fully queryable.\n *\n * Uses INSERT OR REPLACE to allow re-flagging with an updated reason.\n *\n * @param db - better-sqlite3 Database handle\n * @param observationId - ID of the observation to flag\n * @param reason - Human-readable explanation of why it's stale\n */\nexport function flagStaleObservation(\n  db: BetterSqlite3.Database,\n  observationId: string,\n  reason: string,\n): void {\n  initStalenessSchema(db);\n\n  db.prepare(\n    `INSERT OR REPLACE INTO staleness_flags (observation_id, reason, resolved)\n     VALUES (?, ?, 0)`,\n  ).run(observationId, reason);\n}\n\n// =============================================================================\n// Querying Flagged Observations\n// =============================================================================\n\n/**\n * Retrieves observations that have been flagged as stale.\n *\n * Optionally filtered by entity (via graph_nodes.observation_ids) or\n * resolution status.\n *\n * @param db - better-sqlite3 Database handle\n * @param opts - Filter options: entityId, resolved status\n * @returns Array of observation + staleness report pairs\n */\nexport function getStaleObservations(\n  db: BetterSqlite3.Database,\n  opts?: { entityId?: string; resolved?: boolean },\n): Array<{ observation: Observation; flag: StalenessFlag }> {\n  initStalenessSchema(db);\n\n  // Get candidate observation IDs (optionally scoped to entity)\n  let candidateIds: string[] | null = null;\n  if (opts?.entityId) {\n    const node = db\n      .prepare('SELECT observation_ids FROM graph_nodes WHERE id = ?')\n      .get(opts.entityId) as { observation_ids: string } | undefined;\n\n    if (!node) return [];\n    candidateIds = JSON.parse(node.observation_ids) as string[];\n    if (candidateIds.length === 0) return [];\n  }\n\n  // Build query\n  const conditions: string[] = [];\n  const params: unknown[] = [];\n\n  if (candidateIds) {\n    const placeholders = candidateIds.map(() => '?').join(', ');\n    conditions.push(`sf.observation_id IN (${placeholders})`);\n    params.push(...candidateIds);\n  }\n\n  if (opts?.resolved !== undefined) {\n    conditions.push('sf.resolved = ?');\n    params.push(opts.resolved ? 1 : 0);\n  }\n\n  const whereClause =\n    conditions.length > 0 ? `WHERE ${conditions.join(' AND ')}` : '';\n\n  const sql = `\n    SELECT o.*, sf.observation_id AS sf_observation_id, sf.flagged_at AS sf_flagged_at,\n           sf.reason AS sf_reason, sf.resolved AS sf_resolved\n    FROM staleness_flags sf\n    JOIN observations o ON o.id = sf.observation_id\n    ${whereClause}\n    ORDER BY sf.flagged_at DESC\n  `;\n\n  interface StaleRow extends ObservationRow {\n    sf_observation_id: string;\n    sf_flagged_at: string;\n    sf_reason: string;\n    sf_resolved: number;\n  }\n\n  const rows = db.prepare(sql).all(...params) as StaleRow[];\n\n  return rows.map((row) => ({\n    observation: rowToObservation(row),\n    flag: {\n      observation_id: row.sf_observation_id,\n      flagged_at: row.sf_flagged_at,\n      reason: row.sf_reason,\n      resolved: row.sf_resolved === 1,\n    },\n  }));\n}\n","/**\n * Database Hygiene Configuration\n *\n * Controls signal weights and tier thresholds used by the hygiene\n * analyzer to score observations for deletion candidacy.\n *\n * Configuration is loaded from .laminark/hygiene.json with\n * a 5-second cache to avoid repeated disk reads.\n */\n\nimport { readFileSync, writeFileSync } from 'node:fs';\nimport { join } from 'node:path';\n\nimport { debug } from '../shared/debug.js';\nimport { getConfigDir } from '../shared/config.js';\n\nexport interface AutoCleanupConfig {\n  enabled: boolean;\n  tier: 'high' | 'medium' | 'all';\n  maxOrphanNodes: number;\n}\n\nexport interface HygieneConfig {\n  signalWeights: {\n    orphaned: number;\n    islandNode: number;\n    noiseClassified: number;\n    shortContent: number;\n    autoCaptured: number;\n    stale: number;\n  };\n  tierThresholds: {\n    high: number;\n    medium: number;\n  };\n  shortContentThreshold: number;\n  autoCleanup: AutoCleanupConfig;\n}\n\nconst DEFAULT_AUTO_CLEANUP: AutoCleanupConfig = {\n  enabled: true,\n  tier: 'high',\n  maxOrphanNodes: 500,\n};\n\nconst DEFAULTS: HygieneConfig = {\n  signalWeights: {\n    orphaned: 0.30,\n    islandNode: 0.25,\n    noiseClassified: 0.25,\n    shortContent: 0.10,\n    autoCaptured: 0.10,\n    stale: 0.10,\n  },\n  tierThresholds: {\n    high: 0.70,\n    medium: 0.50,\n  },\n  shortContentThreshold: 50,\n  autoCleanup: { ...DEFAULT_AUTO_CLEANUP },\n};\n\nconst CACHE_TTL_MS = 5000;\n\nlet cachedConfig: HygieneConfig | null = null;\nlet cachedAt = 0;\n\nfunction clamp(value: number, min: number, max: number): number {\n  return Math.max(min, Math.min(max, value));\n}\n\nfunction validate(raw: Record<string, unknown>): HygieneConfig {\n  const config = { ...DEFAULTS };\n\n  if (raw.signalWeights && typeof raw.signalWeights === 'object' && !Array.isArray(raw.signalWeights)) {\n    const sw = raw.signalWeights as Record<string, unknown>;\n    const weights = { ...DEFAULTS.signalWeights };\n    for (const key of Object.keys(DEFAULTS.signalWeights) as (keyof typeof DEFAULTS.signalWeights)[]) {\n      if (typeof sw[key] === 'number') {\n        weights[key] = clamp(sw[key] as number, 0, 1);\n      }\n    }\n    config.signalWeights = weights;\n  }\n\n  if (raw.tierThresholds && typeof raw.tierThresholds === 'object' && !Array.isArray(raw.tierThresholds)) {\n    const tt = raw.tierThresholds as Record<string, unknown>;\n    let high = typeof tt.high === 'number' ? clamp(tt.high as number, 0, 1) : DEFAULTS.tierThresholds.high;\n    let medium = typeof tt.medium === 'number' ? clamp(tt.medium as number, 0, 1) : DEFAULTS.tierThresholds.medium;\n    // Enforce medium < high\n    if (medium >= high) {\n      medium = Math.max(0, high - 0.1);\n    }\n    config.tierThresholds = { high, medium };\n  }\n\n  if (typeof raw.shortContentThreshold === 'number') {\n    config.shortContentThreshold = Math.max(0, Math.round(raw.shortContentThreshold as number));\n  }\n\n  if (raw.autoCleanup && typeof raw.autoCleanup === 'object' && !Array.isArray(raw.autoCleanup)) {\n    const ac = raw.autoCleanup as Record<string, unknown>;\n    const cleanup = { ...DEFAULT_AUTO_CLEANUP };\n    if (typeof ac.enabled === 'boolean') cleanup.enabled = ac.enabled;\n    if (ac.tier === 'high' || ac.tier === 'medium' || ac.tier === 'all') cleanup.tier = ac.tier;\n    if (typeof ac.maxOrphanNodes === 'number') cleanup.maxOrphanNodes = Math.max(0, Math.round(ac.maxOrphanNodes));\n    config.autoCleanup = cleanup;\n  }\n\n  return config;\n}\n\n/**\n * Loads hygiene configuration from disk with a 5-second cache.\n */\nexport function loadHygieneConfig(): HygieneConfig {\n  const now = Date.now();\n  if (cachedConfig && now - cachedAt < CACHE_TTL_MS) {\n    return cachedConfig;\n  }\n\n  const configPath = join(getConfigDir(), 'hygiene.json');\n  try {\n    const content = readFileSync(configPath, 'utf-8');\n    const raw = JSON.parse(content) as Record<string, unknown>;\n    cachedConfig = validate(raw);\n    debug('config', 'Loaded hygiene config', { ...cachedConfig });\n  } catch {\n    cachedConfig = { ...DEFAULTS, signalWeights: { ...DEFAULTS.signalWeights }, tierThresholds: { ...DEFAULTS.tierThresholds } };\n  }\n\n  cachedAt = now;\n  return cachedConfig;\n}\n\n/**\n * Saves hygiene configuration to disk and invalidates cache.\n */\nexport function saveHygieneConfig(config: HygieneConfig): void {\n  const configPath = join(getConfigDir(), 'hygiene.json');\n  writeFileSync(configPath, JSON.stringify(config, null, 2), 'utf-8');\n  cachedConfig = config;\n  cachedAt = Date.now();\n}\n\n/**\n * Resets hygiene config to defaults by invalidating cache.\n */\nexport function resetHygieneConfig(): HygieneConfig {\n  cachedConfig = null;\n  cachedAt = 0;\n  return { ...DEFAULTS, signalWeights: { ...DEFAULTS.signalWeights }, tierThresholds: { ...DEFAULTS.tierThresholds }, autoCleanup: { ...DEFAULT_AUTO_CLEANUP } };\n}\n","/**\n * Database hygiene analyzer.\n *\n * Scores observations on multiple deletion signals and produces a\n * simulation report of candidates for cleanup. No side effects in\n * analyze mode — purging is handled by the MCP tool layer.\n */\n\nimport type BetterSqlite3 from 'better-sqlite3';\n\nimport type { HygieneConfig, AutoCleanupConfig } from '../config/hygiene-config.js';\nimport { loadHygieneConfig } from '../config/hygiene-config.js';\nimport { debug } from '../shared/debug.js';\nimport { initStalenessSchema } from './staleness.js';\n\n// =============================================================================\n// Types\n// =============================================================================\n\nexport interface HygieneCandidate {\n  id: string;\n  shortId: string;\n  sessionId: string | null;\n  kind: string;\n  source: string;\n  contentPreview: string;\n  createdAt: string;\n  signals: {\n    orphaned: boolean;\n    islandNode: boolean;\n    noiseClassified: boolean;\n    shortContent: boolean;\n    autoCaptured: boolean;\n    stale: boolean;\n  };\n  confidence: number;\n  tier: 'high' | 'medium' | 'low';\n}\n\nexport interface OrphanNode {\n  id: string;\n  type: string;\n  name: string;\n  reason: string;\n}\n\nexport interface HygieneReport {\n  analyzedAt: string;\n  totalObservations: number;\n  candidates: HygieneCandidate[];\n  orphanNodes: OrphanNode[];\n  summary: {\n    high: number;\n    medium: number;\n    low: number;\n    orphanNodeCount: number;\n  };\n}\n\nexport interface FindAnalysisReport {\n  total: number;\n  bySignal: {\n    orphaned: number;\n    islandNode: number;\n    noiseClassified: number;\n    shortContent: number;\n    autoCaptured: number;\n    stale: number;\n  };\n  distribution: { range: string; count: number }[];\n  islandNodes: {\n    total: number;\n    minConfidence: number;\n    maxConfidence: number;\n    medianConfidence: number;\n    capturedAtCurrentThresholds: { high: number; medium: number; all: number };\n  };\n}\n\n// =============================================================================\n// Internal Row Types\n// =============================================================================\n\ninterface ObsRow {\n  id: string;\n  content: string;\n  title: string | null;\n  source: string;\n  kind: string;\n  session_id: string | null;\n  classification: string | null;\n  created_at: string;\n}\n\ninterface GraphNodeRow {\n  id: string;\n  type: string;\n  name: string;\n  observation_ids: string; // JSON array\n}\n\n// =============================================================================\n// Shared: build signal lookups\n// =============================================================================\n\ninterface SignalLookups {\n  linkedObsIds: Set<string>;\n  islandObsIds: Set<string>;\n  staleIds: Set<string>;\n  allNodes: GraphNodeRow[];\n  edgeCounts: Map<string, number>;\n}\n\nfunction buildSignalLookups(db: BetterSqlite3.Database, projectHash: string | null): SignalLookups {\n  const linkedObsIds = new Set<string>();\n  const islandObsIds = new Set<string>();\n\n  const allNodes = projectHash\n    ? db.prepare(\n        'SELECT id, type, name, observation_ids FROM graph_nodes WHERE project_hash = ?',\n      ).all(projectHash) as GraphNodeRow[]\n    : db.prepare(\n        'SELECT id, type, name, observation_ids FROM graph_nodes',\n      ).all() as GraphNodeRow[];\n\n  const edgeCounts = new Map<string, number>();\n  const edgeRows = projectHash\n    ? db.prepare(\n        `SELECT source_id AS nid, COUNT(*) AS cnt FROM graph_edges WHERE project_hash = ? GROUP BY source_id\n         UNION ALL\n         SELECT target_id AS nid, COUNT(*) AS cnt FROM graph_edges WHERE project_hash = ? GROUP BY target_id`,\n      ).all(projectHash, projectHash) as { nid: string; cnt: number }[]\n    : db.prepare(\n        `SELECT source_id AS nid, COUNT(*) AS cnt FROM graph_edges GROUP BY source_id\n         UNION ALL\n         SELECT target_id AS nid, COUNT(*) AS cnt FROM graph_edges GROUP BY target_id`,\n      ).all() as { nid: string; cnt: number }[];\n  for (const row of edgeRows) {\n    edgeCounts.set(row.nid, (edgeCounts.get(row.nid) ?? 0) + row.cnt);\n  }\n\n  for (const node of allNodes) {\n    let obsIds: string[];\n    try {\n      obsIds = JSON.parse(node.observation_ids) as string[];\n    } catch {\n      continue;\n    }\n\n    const degree = edgeCounts.get(node.id) ?? 0;\n\n    for (const oid of obsIds) {\n      linkedObsIds.add(oid);\n      if (degree === 0) {\n        islandObsIds.add(oid);\n      }\n    }\n  }\n\n  const staleIds = new Set<string>();\n  try {\n    initStalenessSchema(db);\n    const staleRows = db.prepare(\n      'SELECT observation_id FROM staleness_flags WHERE resolved = 0',\n    ).all() as { observation_id: string }[];\n    for (const row of staleRows) {\n      staleIds.add(row.observation_id);\n    }\n  } catch {\n    // staleness_flags may not exist\n  }\n\n  return { linkedObsIds, islandObsIds, staleIds, allNodes, edgeCounts };\n}\n\nfunction scoreObservation(\n  obs: ObsRow,\n  lookups: SignalLookups,\n  config: HygieneConfig,\n): { signals: HygieneCandidate['signals']; confidence: number; tier: 'high' | 'medium' | 'low' } {\n  const weights = config.signalWeights;\n  const thresholds = config.tierThresholds;\n\n  const signals = {\n    orphaned: !lookups.linkedObsIds.has(obs.id),\n    islandNode: lookups.islandObsIds.has(obs.id),\n    noiseClassified: obs.classification === 'noise',\n    shortContent: obs.content.length < config.shortContentThreshold,\n    autoCaptured: obs.source.startsWith('hook:'),\n    stale: lookups.staleIds.has(obs.id),\n  };\n\n  const confidence =\n    (signals.orphaned ? weights.orphaned : 0) +\n    (signals.islandNode ? weights.islandNode : 0) +\n    (signals.noiseClassified ? weights.noiseClassified : 0) +\n    (signals.shortContent ? weights.shortContent : 0) +\n    (signals.autoCaptured ? weights.autoCaptured : 0) +\n    (signals.stale ? weights.stale : 0);\n\n  const tier: 'high' | 'medium' | 'low' =\n    confidence >= thresholds.high ? 'high' : confidence >= thresholds.medium ? 'medium' : 'low';\n\n  return { signals, confidence: Math.round(confidence * 100) / 100, tier };\n}\n\n// =============================================================================\n// Analysis\n// =============================================================================\n\nexport interface AnalyzeOptions {\n  sessionId?: string;\n  limit?: number;\n  minTier?: 'high' | 'medium' | 'low';\n  config?: HygieneConfig;\n}\n\n/**\n * Analyzes all active observations and scores each on deletion signals.\n * Pure read-only — no data is modified.\n */\nexport function analyzeObservations(\n  db: BetterSqlite3.Database,\n  projectHash: string,\n  opts?: AnalyzeOptions,\n): HygieneReport {\n  const limit = opts?.limit ?? 50;\n  const minTier = opts?.minTier ?? 'medium';\n  const config = opts?.config ?? loadHygieneConfig();\n\n  debug('hygiene', 'Starting analysis', { projectHash, sessionId: opts?.sessionId });\n\n  // 1. Fetch all active observations for this project\n  let obsSql = `\n    SELECT id, content, title, source, kind, session_id, classification, created_at\n    FROM observations\n    WHERE project_hash = ? AND deleted_at IS NULL\n  `;\n  const obsParams: unknown[] = [projectHash];\n\n  if (opts?.sessionId) {\n    obsSql += ' AND session_id = ?';\n    obsParams.push(opts.sessionId);\n  }\n\n  obsSql += ' ORDER BY created_at DESC';\n  const observations = db.prepare(obsSql).all(...obsParams) as ObsRow[];\n\n  // 2. Build lookup sets for signal detection\n  const lookups = buildSignalLookups(db, projectHash);\n\n  // 3. Score each observation\n  const allCandidates: HygieneCandidate[] = [];\n\n  for (const obs of observations) {\n    const { signals, confidence, tier } = scoreObservation(obs, lookups, config);\n\n    // Filter by minimum tier\n    if (minTier === 'high' && tier !== 'high') continue;\n    if (minTier === 'medium' && tier === 'low') continue;\n\n    const preview = obs.content.length > 80\n      ? obs.content.substring(0, 80) + '...'\n      : obs.content;\n\n    allCandidates.push({\n      id: obs.id,\n      shortId: obs.id.substring(0, 8),\n      sessionId: obs.session_id,\n      kind: obs.kind,\n      source: obs.source,\n      contentPreview: preview,\n      createdAt: obs.created_at,\n      signals,\n      confidence,\n      tier,\n    });\n  }\n\n  // Sort by confidence descending\n  allCandidates.sort((a, b) => b.confidence - a.confidence);\n\n  // 4. Find orphan graph nodes (zero edges AND all observation refs dead/missing)\n  const activeObsIds = new Set(observations.map(o => o.id));\n  const orphanNodes: OrphanNode[] = [];\n\n  for (const node of lookups.allNodes) {\n    const degree = lookups.edgeCounts.get(node.id) ?? 0;\n    if (degree > 0) continue;\n\n    let obsIds: string[];\n    try {\n      obsIds = JSON.parse(node.observation_ids) as string[];\n    } catch {\n      continue;\n    }\n\n    // Zero-edge nodes are island nodes — they add no graph connectivity.\n    // Flag them all as orphans regardless of whether observation refs are alive.\n    const allDead = obsIds.length === 0 || obsIds.every(oid => !activeObsIds.has(oid));\n    orphanNodes.push({\n      id: node.id,\n      type: node.type,\n      name: node.name,\n      reason: allDead ? 'zero edges, dead observation refs' : 'zero edges (island node)',\n    });\n  }\n\n  // 5. Build summary\n  const limited = allCandidates.slice(0, limit);\n  const highCount = allCandidates.filter(c => c.tier === 'high').length;\n  const mediumCount = allCandidates.filter(c => c.tier === 'medium').length;\n  const lowCount = allCandidates.filter(c => c.tier === 'low').length;\n\n  debug('hygiene', 'Analysis complete', {\n    total: observations.length,\n    high: highCount,\n    medium: mediumCount,\n    orphanNodes: orphanNodes.length,\n  });\n\n  return {\n    analyzedAt: new Date().toISOString(),\n    totalObservations: observations.length,\n    candidates: limited,\n    orphanNodes: orphanNodes.slice(0, limit),\n    summary: {\n      high: highCount,\n      medium: mediumCount,\n      low: lowCount,\n      orphanNodeCount: orphanNodes.length,\n    },\n  };\n}\n\n// =============================================================================\n// Find Analysis\n// =============================================================================\n\n/**\n * Produces a score distribution report across all observations.\n * Shows signal counts, confidence histogram, and island node summary\n * so users can tune thresholds to catch the right candidates.\n */\nexport function findAnalysis(\n  db: BetterSqlite3.Database,\n  projectHash: string,\n  config?: HygieneConfig,\n): FindAnalysisReport {\n  const cfg = config ?? loadHygieneConfig();\n\n  const observations = db.prepare(`\n    SELECT id, content, title, source, kind, session_id, classification, created_at\n    FROM observations\n    WHERE project_hash = ? AND deleted_at IS NULL\n    ORDER BY created_at DESC\n  `).all(projectHash) as ObsRow[];\n\n  const lookups = buildSignalLookups(db, projectHash);\n\n  const bySignal = {\n    orphaned: 0,\n    islandNode: 0,\n    noiseClassified: 0,\n    shortContent: 0,\n    autoCaptured: 0,\n    stale: 0,\n  };\n\n  // 10 histogram buckets: 0.0-0.1, 0.1-0.2, ... 0.9-1.0\n  const buckets = new Array(10).fill(0) as number[];\n\n  // Track island-linked observation confidences\n  const islandConfidences: number[] = [];\n\n  for (const obs of observations) {\n    const { signals, confidence } = scoreObservation(obs, lookups, cfg);\n\n    if (signals.orphaned) bySignal.orphaned++;\n    if (signals.islandNode) bySignal.islandNode++;\n    if (signals.noiseClassified) bySignal.noiseClassified++;\n    if (signals.shortContent) bySignal.shortContent++;\n    if (signals.autoCaptured) bySignal.autoCaptured++;\n    if (signals.stale) bySignal.stale++;\n\n    const bucketIdx = Math.min(Math.floor(confidence * 10), 9);\n    buckets[bucketIdx]++;\n\n    if (signals.islandNode) {\n      islandConfidences.push(confidence);\n    }\n  }\n\n  const distribution = buckets.map((count, i) => ({\n    range: `${(i / 10).toFixed(1)}-${((i + 1) / 10).toFixed(1)}`,\n    count,\n  }));\n\n  // Island node summary\n  islandConfidences.sort((a, b) => a - b);\n  const islandTotal = islandConfidences.length;\n  const minConf = islandTotal > 0 ? islandConfidences[0] : 0;\n  const maxConf = islandTotal > 0 ? islandConfidences[islandTotal - 1] : 0;\n  const medianConf = islandTotal > 0\n    ? islandConfidences[Math.floor(islandTotal / 2)]\n    : 0;\n\n  const capturedHigh = islandConfidences.filter(c => c >= cfg.tierThresholds.high).length;\n  const capturedMedium = islandConfidences.filter(c => c >= cfg.tierThresholds.medium).length;\n\n  return {\n    total: observations.length,\n    bySignal,\n    distribution,\n    islandNodes: {\n      total: islandTotal,\n      minConfidence: Math.round(minConf * 100) / 100,\n      maxConfidence: Math.round(maxConf * 100) / 100,\n      medianConfidence: Math.round(medianConf * 100) / 100,\n      capturedAtCurrentThresholds: {\n        high: capturedHigh,\n        medium: capturedMedium,\n        all: islandTotal,\n      },\n    },\n  };\n}\n\n// =============================================================================\n// Purge Execution\n// =============================================================================\n\nexport interface PurgeResult {\n  observationsPurged: number;\n  orphanNodesRemoved: number;\n}\n\n/**\n * Soft-deletes observations matching the given tier threshold and removes\n * dead orphan graph nodes. Returns counts of affected records.\n */\nexport interface AutoCleanupResult {\n  skipped: boolean;\n  reason?: string;\n  observationsPurged: number;\n  orphanNodesRemoved: number;\n}\n\n/**\n * Runs automatic hygiene cleanup at session end.\n *\n * Analyzes observations and purges candidates matching the configured tier.\n * Orphan graph node removal is capped by autoCleanup.maxOrphanNodes.\n * Safe to call on every session end — skips quickly if disabled.\n */\nexport function runAutoCleanup(\n  db: BetterSqlite3.Database,\n  projectHash: string,\n  config?: HygieneConfig,\n): AutoCleanupResult {\n  const cfg = config ?? loadHygieneConfig();\n  const auto = cfg.autoCleanup;\n\n  if (!auto.enabled) {\n    return { skipped: true, reason: 'disabled', observationsPurged: 0, orphanNodesRemoved: 0 };\n  }\n\n  debug('hygiene', 'Auto-cleanup starting', { tier: auto.tier, maxOrphanNodes: auto.maxOrphanNodes });\n\n  const minTier = auto.tier === 'all' ? 'low' as const : auto.tier;\n  const report = analyzeObservations(db, projectHash, {\n    limit: 200,\n    minTier,\n    config: cfg,\n  });\n\n  // Cap orphan node removal\n  if (report.orphanNodes.length > auto.maxOrphanNodes) {\n    report.orphanNodes = report.orphanNodes.slice(0, auto.maxOrphanNodes);\n  }\n\n  const totalWork = report.candidates.length + report.orphanNodes.length;\n  if (totalWork === 0) {\n    debug('hygiene', 'Auto-cleanup: nothing to clean');\n    return { skipped: false, observationsPurged: 0, orphanNodesRemoved: 0 };\n  }\n\n  const result = executePurge(db, projectHash, report, auto.tier);\n\n  debug('hygiene', 'Auto-cleanup complete', {\n    observationsPurged: result.observationsPurged,\n    orphanNodesRemoved: result.orphanNodesRemoved,\n  });\n\n  return { skipped: false, ...result };\n}\n\nexport function executePurge(\n  db: BetterSqlite3.Database,\n  projectHash: string,\n  report: HygieneReport,\n  tier: 'high' | 'medium' | 'all',\n): PurgeResult {\n  const candidateIds = report.candidates\n    .filter(c => {\n      if (tier === 'high') return c.tier === 'high';\n      if (tier === 'medium') return c.tier === 'high' || c.tier === 'medium';\n      return true; // 'all'\n    })\n    .map(c => c.id);\n\n  debug('hygiene', 'Executing purge', { tier, candidates: candidateIds.length });\n\n  let observationsPurged = 0;\n\n  // Soft-delete observations in batches\n  const softDeleteStmt = db.prepare(`\n    UPDATE observations\n    SET deleted_at = datetime('now'), updated_at = datetime('now')\n    WHERE id = ? AND project_hash = ? AND deleted_at IS NULL\n  `);\n\n  const purgeTransaction = db.transaction(() => {\n    for (const id of candidateIds) {\n      const result = softDeleteStmt.run(id, projectHash);\n      observationsPurged += result.changes;\n    }\n\n    // Remove dead orphan graph nodes\n    let orphanNodesRemoved = 0;\n    const deleteNodeStmt = db.prepare('DELETE FROM graph_nodes WHERE id = ?');\n    for (const node of report.orphanNodes) {\n      const result = deleteNodeStmt.run(node.id);\n      orphanNodesRemoved += result.changes;\n    }\n\n    return { observationsPurged, orphanNodesRemoved };\n  });\n\n  return purgeTransaction();\n}\n","import type { ToolType, ToolScope } from '../shared/tool-types.js';\n\n/**\n * Infers the tool type from a tool name seen in PostToolUse.\n *\n * - MCP tools have the `mcp__` prefix\n * - Built-in tools are PascalCase single words (Write, Edit, Bash, Read, etc.)\n * - Anything else is unknown\n */\nexport function inferToolType(toolName: string): ToolType {\n  if (toolName.startsWith('mcp__')) {\n    return 'mcp_tool';\n  }\n  if (/^[A-Z][a-zA-Z]+$/.test(toolName)) {\n    return 'builtin';\n  }\n  return 'unknown';\n}\n\n/**\n * Infers the scope of a tool from its name.\n *\n * - Plugin MCP tools (mcp__plugin_*) are plugin-scoped\n * - Other MCP tools default to project-scoped (conservative; may be global but unknown from name alone)\n * - Non-MCP tools (builtins) are always global\n */\nexport function inferScope(toolName: string): ToolScope {\n  if (toolName.startsWith('mcp__plugin_')) {\n    return 'plugin';\n  }\n  if (toolName.startsWith('mcp__')) {\n    return 'project';\n  }\n  return 'global';\n}\n\n/**\n * Extracts the MCP server name from a tool name.\n *\n * Plugin MCP tools: `mcp__plugin_<pluginName>_<serverName>__<tool>`\n *   Example: `mcp__plugin_laminark_laminark__recall` -> server is `laminark`\n *\n * Project MCP tools: `mcp__<serverName>__<tool>`\n *   Example: `mcp__playwright__browser_screenshot` -> server is `playwright`\n *\n * Returns null for non-MCP tools.\n */\nexport function extractServerName(toolName: string): string | null {\n  // Plugin MCP tools: mcp__plugin_<pluginName>_<serverName>__<tool>\n  const pluginMatch = toolName.match(\n    /^mcp__plugin_([^_]+(?:_[^_]+)*)_([^_]+(?:_[^_]+)*)__/,\n  );\n  if (pluginMatch) {\n    return pluginMatch[2];\n  }\n\n  // Project MCP tools: mcp__<serverName>__<tool>\n  const projectMatch = toolName.match(/^mcp__([^_]+(?:_[^_]+)*)__/);\n  if (projectMatch) {\n    return projectMatch[1];\n  }\n\n  return null;\n}\n","/**\n * Repository for thought branch CRUD operations.\n *\n * Every query is scoped to the projectHash provided at construction time.\n * All SQL statements are prepared once in the constructor and reused for\n * every call (same pattern as PathRepository).\n */\n\nimport type BetterSqlite3 from 'better-sqlite3';\nimport { randomBytes } from 'node:crypto';\n\nimport type {\n  ThoughtBranch,\n  BranchObservation,\n  BranchStatus,\n  BranchType,\n  ArcStage,\n  TriggerSource,\n} from './types.js';\n\nexport class BranchRepository {\n  private readonly db: BetterSqlite3.Database;\n  private readonly projectHash: string;\n\n  // Prepared statements — branch lifecycle\n  private readonly stmtCreate: BetterSqlite3.Statement;\n  private readonly stmtComplete: BetterSqlite3.Statement;\n  private readonly stmtAbandon: BetterSqlite3.Statement;\n  private readonly stmtGetActive: BetterSqlite3.Statement;\n  private readonly stmtGetById: BetterSqlite3.Statement;\n  private readonly stmtList: BetterSqlite3.Statement;\n  private readonly stmtListByStatus: BetterSqlite3.Statement;\n  private readonly stmtListByType: BetterSqlite3.Statement;\n\n  // Prepared statements — branch updates\n  private readonly stmtUpdateArcStage: BetterSqlite3.Statement;\n  private readonly stmtUpdateToolPattern: BetterSqlite3.Statement;\n  private readonly stmtUpdateClassification: BetterSqlite3.Statement;\n  private readonly stmtUpdateSummary: BetterSqlite3.Statement;\n  private readonly stmtIncrementObsCount: BetterSqlite3.Statement;\n  private readonly stmtLinkDebugPath: BetterSqlite3.Statement;\n\n  // Prepared statements — observations\n  private readonly stmtAddObservation: BetterSqlite3.Statement;\n  private readonly stmtGetObservations: BetterSqlite3.Statement;\n  private readonly stmtMaxSequence: BetterSqlite3.Statement;\n\n  // Prepared statements — maintenance\n  private readonly stmtFindStale: BetterSqlite3.Statement;\n  private readonly stmtFindUnclassified: BetterSqlite3.Statement;\n  private readonly stmtFindRecentCompleted: BetterSqlite3.Statement;\n  private readonly stmtFindRecentActive: BetterSqlite3.Statement;\n  private readonly stmtListRecent: BetterSqlite3.Statement;\n\n  constructor(db: BetterSqlite3.Database, projectHash: string) {\n    this.db = db;\n    this.projectHash = projectHash;\n\n    // --- Branch lifecycle ---\n\n    this.stmtCreate = db.prepare(`\n      INSERT INTO thought_branches\n        (id, project_hash, session_id, status, trigger_source, trigger_observation_id, started_at)\n      VALUES (?, ?, ?, 'active', ?, ?, datetime('now'))\n    `);\n\n    this.stmtComplete = db.prepare(`\n      UPDATE thought_branches\n      SET status = 'completed', arc_stage = 'completed', ended_at = datetime('now')\n      WHERE id = ? AND project_hash = ?\n    `);\n\n    this.stmtAbandon = db.prepare(`\n      UPDATE thought_branches\n      SET status = 'abandoned', ended_at = datetime('now')\n      WHERE id = ? AND project_hash = ?\n    `);\n\n    this.stmtGetActive = db.prepare(`\n      SELECT * FROM thought_branches\n      WHERE project_hash = ? AND status = 'active'\n      ORDER BY started_at DESC\n      LIMIT 1\n    `);\n\n    this.stmtGetById = db.prepare(`\n      SELECT * FROM thought_branches\n      WHERE id = ? AND project_hash = ?\n    `);\n\n    this.stmtList = db.prepare(`\n      SELECT * FROM thought_branches\n      WHERE project_hash = ?\n      ORDER BY started_at DESC\n      LIMIT ?\n    `);\n\n    this.stmtListByStatus = db.prepare(`\n      SELECT * FROM thought_branches\n      WHERE project_hash = ? AND status = ?\n      ORDER BY started_at DESC\n      LIMIT ?\n    `);\n\n    this.stmtListByType = db.prepare(`\n      SELECT * FROM thought_branches\n      WHERE project_hash = ? AND branch_type = ?\n      ORDER BY started_at DESC\n      LIMIT ?\n    `);\n\n    // --- Branch updates ---\n\n    this.stmtUpdateArcStage = db.prepare(`\n      UPDATE thought_branches SET arc_stage = ? WHERE id = ? AND project_hash = ?\n    `);\n\n    this.stmtUpdateToolPattern = db.prepare(`\n      UPDATE thought_branches SET tool_pattern = ? WHERE id = ? AND project_hash = ?\n    `);\n\n    this.stmtUpdateClassification = db.prepare(`\n      UPDATE thought_branches SET branch_type = ?, title = ? WHERE id = ? AND project_hash = ?\n    `);\n\n    this.stmtUpdateSummary = db.prepare(`\n      UPDATE thought_branches SET summary = ? WHERE id = ? AND project_hash = ?\n    `);\n\n    this.stmtIncrementObsCount = db.prepare(`\n      UPDATE thought_branches SET observation_count = observation_count + 1 WHERE id = ? AND project_hash = ?\n    `);\n\n    this.stmtLinkDebugPath = db.prepare(`\n      UPDATE thought_branches SET linked_debug_path_id = ? WHERE id = ? AND project_hash = ?\n    `);\n\n    // --- Observations ---\n\n    this.stmtAddObservation = db.prepare(`\n      INSERT OR IGNORE INTO branch_observations\n        (branch_id, observation_id, sequence_order, tool_name, arc_stage_at_add)\n      VALUES (?, ?, ?, ?, ?)\n    `);\n\n    this.stmtGetObservations = db.prepare(`\n      SELECT * FROM branch_observations\n      WHERE branch_id = ?\n      ORDER BY sequence_order ASC\n    `);\n\n    this.stmtMaxSequence = db.prepare(`\n      SELECT COALESCE(MAX(sequence_order), 0) AS max_seq FROM branch_observations\n      WHERE branch_id = ?\n    `);\n\n    // --- Maintenance ---\n\n    this.stmtFindStale = db.prepare(`\n      SELECT * FROM thought_branches\n      WHERE project_hash = ? AND status = 'active'\n        AND started_at < datetime('now', '-24 hours')\n    `);\n\n    this.stmtFindUnclassified = db.prepare(`\n      SELECT * FROM thought_branches\n      WHERE project_hash = ? AND branch_type = 'unknown'\n        AND observation_count >= 3\n      ORDER BY started_at DESC\n      LIMIT ?\n    `);\n\n    this.stmtFindRecentCompleted = db.prepare(`\n      SELECT * FROM thought_branches\n      WHERE project_hash = ? AND status = 'completed' AND summary IS NULL\n        AND ended_at > datetime('now', '-1 hour')\n      ORDER BY ended_at DESC\n      LIMIT ?\n    `);\n\n    this.stmtFindRecentActive = db.prepare(`\n      SELECT * FROM thought_branches\n      WHERE project_hash = ? AND status = 'active'\n        AND started_at > datetime('now', '-24 hours')\n      ORDER BY started_at DESC\n      LIMIT 1\n    `);\n\n    this.stmtListRecent = db.prepare(`\n      SELECT * FROM thought_branches\n      WHERE project_hash = ?\n        AND started_at > datetime('now', ? || ' hours')\n      ORDER BY started_at DESC\n    `);\n  }\n\n  // ===========================================================================\n  // Branch Lifecycle\n  // ===========================================================================\n\n  createBranch(\n    sessionId: string | null,\n    triggerSource: TriggerSource,\n    triggerObservationId?: string,\n  ): ThoughtBranch {\n    const id = randomBytes(16).toString('hex');\n    this.stmtCreate.run(\n      id,\n      this.projectHash,\n      sessionId,\n      triggerSource,\n      triggerObservationId ?? null,\n    );\n    return this.getBranch(id)!;\n  }\n\n  completeBranch(branchId: string): void {\n    this.stmtComplete.run(branchId, this.projectHash);\n  }\n\n  abandonBranch(branchId: string): void {\n    this.stmtAbandon.run(branchId, this.projectHash);\n  }\n\n  getActiveBranch(): ThoughtBranch | null {\n    const row = this.stmtGetActive.get(this.projectHash) as BranchRow | undefined;\n    return row ? rowToBranch(row) : null;\n  }\n\n  getBranch(branchId: string): ThoughtBranch | null {\n    const row = this.stmtGetById.get(branchId, this.projectHash) as BranchRow | undefined;\n    return row ? rowToBranch(row) : null;\n  }\n\n  listBranches(limit: number = 20): ThoughtBranch[] {\n    const rows = this.stmtList.all(this.projectHash, limit) as BranchRow[];\n    return rows.map(rowToBranch);\n  }\n\n  listByStatus(status: BranchStatus, limit: number = 20): ThoughtBranch[] {\n    const rows = this.stmtListByStatus.all(this.projectHash, status, limit) as BranchRow[];\n    return rows.map(rowToBranch);\n  }\n\n  listByType(branchType: BranchType, limit: number = 20): ThoughtBranch[] {\n    const rows = this.stmtListByType.all(this.projectHash, branchType, limit) as BranchRow[];\n    return rows.map(rowToBranch);\n  }\n\n  // ===========================================================================\n  // Branch Updates\n  // ===========================================================================\n\n  updateArcStage(branchId: string, stage: ArcStage): void {\n    this.stmtUpdateArcStage.run(stage, branchId, this.projectHash);\n  }\n\n  updateToolPattern(branchId: string, pattern: Record<string, number>): void {\n    this.stmtUpdateToolPattern.run(JSON.stringify(pattern), branchId, this.projectHash);\n  }\n\n  updateClassification(branchId: string, branchType: BranchType, title: string): void {\n    this.stmtUpdateClassification.run(branchType, title, branchId, this.projectHash);\n  }\n\n  updateSummary(branchId: string, summary: string): void {\n    this.stmtUpdateSummary.run(summary, branchId, this.projectHash);\n  }\n\n  linkDebugPath(branchId: string, debugPathId: string): void {\n    this.stmtLinkDebugPath.run(debugPathId, branchId, this.projectHash);\n  }\n\n  // ===========================================================================\n  // Observation Management\n  // ===========================================================================\n\n  addObservation(\n    branchId: string,\n    observationId: string,\n    toolName: string | null,\n    arcStage: ArcStage | null,\n  ): void {\n    const { max_seq } = this.stmtMaxSequence.get(branchId) as { max_seq: number };\n    this.stmtAddObservation.run(\n      branchId,\n      observationId,\n      max_seq + 1,\n      toolName,\n      arcStage,\n    );\n    this.stmtIncrementObsCount.run(branchId, this.projectHash);\n  }\n\n  getObservations(branchId: string): BranchObservation[] {\n    const rows = this.stmtGetObservations.all(branchId) as BranchObservationRow[];\n    return rows.map(rowToBranchObservation);\n  }\n\n  // ===========================================================================\n  // Maintenance Queries\n  // ===========================================================================\n\n  findStaleBranches(): ThoughtBranch[] {\n    const rows = this.stmtFindStale.all(this.projectHash) as BranchRow[];\n    return rows.map(rowToBranch);\n  }\n\n  findUnclassifiedBranches(limit: number = 5): ThoughtBranch[] {\n    const rows = this.stmtFindUnclassified.all(this.projectHash, limit) as BranchRow[];\n    return rows.map(rowToBranch);\n  }\n\n  findRecentCompletedUnsummarized(limit: number = 3): ThoughtBranch[] {\n    const rows = this.stmtFindRecentCompleted.all(this.projectHash, limit) as BranchRow[];\n    return rows.map(rowToBranch);\n  }\n\n  findRecentActiveBranch(): ThoughtBranch | null {\n    const row = this.stmtFindRecentActive.get(this.projectHash) as BranchRow | undefined;\n    return row ? rowToBranch(row) : null;\n  }\n\n  listRecentBranches(hours: number): ThoughtBranch[] {\n    const rows = this.stmtListRecent.all(this.projectHash, `-${hours}`) as BranchRow[];\n    return rows.map(rowToBranch);\n  }\n}\n\n// =============================================================================\n// Raw Row Types\n// =============================================================================\n\ninterface BranchRow {\n  id: string;\n  project_hash: string;\n  session_id: string | null;\n  status: string;\n  branch_type: string;\n  arc_stage: string;\n  title: string | null;\n  summary: string | null;\n  parent_branch_id: string | null;\n  linked_debug_path_id: string | null;\n  trigger_source: string | null;\n  trigger_observation_id: string | null;\n  observation_count: number;\n  tool_pattern: string;\n  started_at: string;\n  ended_at: string | null;\n  created_at: string;\n}\n\ninterface BranchObservationRow {\n  branch_id: string;\n  observation_id: string;\n  sequence_order: number;\n  tool_name: string | null;\n  arc_stage_at_add: string | null;\n  created_at: string;\n}\n\n// =============================================================================\n// Row Mapping\n// =============================================================================\n\nfunction rowToBranch(row: BranchRow): ThoughtBranch {\n  let toolPattern: Record<string, number> = {};\n  try {\n    toolPattern = JSON.parse(row.tool_pattern);\n  } catch {\n    // Default to empty\n  }\n\n  return {\n    id: row.id,\n    project_hash: row.project_hash,\n    session_id: row.session_id,\n    status: row.status as BranchStatus,\n    branch_type: row.branch_type as BranchType,\n    arc_stage: row.arc_stage as ArcStage,\n    title: row.title,\n    summary: row.summary,\n    parent_branch_id: row.parent_branch_id,\n    linked_debug_path_id: row.linked_debug_path_id,\n    trigger_source: row.trigger_source as TriggerSource | null,\n    trigger_observation_id: row.trigger_observation_id,\n    observation_count: row.observation_count,\n    tool_pattern: toolPattern,\n    started_at: row.started_at,\n    ended_at: row.ended_at,\n    created_at: row.created_at,\n  };\n}\n\nfunction rowToBranchObservation(row: BranchObservationRow): BranchObservation {\n  return {\n    branch_id: row.branch_id,\n    observation_id: row.observation_id,\n    sequence_order: row.sequence_order,\n    tool_name: row.tool_name,\n    arc_stage_at_add: row.arc_stage_at_add as ArcStage | null,\n    created_at: row.created_at,\n  };\n}\n","import type BetterSqlite3 from 'better-sqlite3';\n\nimport { debug } from '../shared/debug.js';\n\n/**\n * Lightweight buffer for exploration tool events (Read, Glob, Grep).\n *\n * Instead of creating full observations for these low-signal tools,\n * they are stored in a temporary buffer. When a Write/Edit observation\n * is created, the recent buffer entries are attached as research context,\n * creating provenance links between exploration and changes.\n *\n * Buffer entries are flushed after 30 minutes.\n */\nexport class ResearchBufferRepository {\n  private readonly db: BetterSqlite3.Database;\n  private readonly projectHash: string;\n\n  private readonly stmtInsert: BetterSqlite3.Statement;\n  private readonly stmtGetRecent: BetterSqlite3.Statement;\n  private readonly stmtFlush: BetterSqlite3.Statement;\n\n  constructor(db: BetterSqlite3.Database, projectHash: string) {\n    this.db = db;\n    this.projectHash = projectHash;\n\n    this.stmtInsert = db.prepare(`\n      INSERT INTO research_buffer (project_hash, session_id, tool_name, target)\n      VALUES (?, ?, ?, ?)\n    `);\n\n    this.stmtGetRecent = db.prepare(`\n      SELECT tool_name, target, created_at FROM research_buffer\n      WHERE session_id = ? AND project_hash = ?\n        AND created_at >= datetime('now', '-' || ? || ' minutes')\n      ORDER BY created_at DESC\n    `);\n\n    this.stmtFlush = db.prepare(`\n      DELETE FROM research_buffer\n      WHERE created_at < datetime('now', '-' || ? || ' minutes')\n    `);\n\n    debug('research-buffer', 'ResearchBufferRepository initialized', { projectHash });\n  }\n\n  /**\n   * Records a research tool event in the buffer.\n   */\n  add(entry: {\n    sessionId: string | null;\n    toolName: string;\n    target: string;\n  }): void {\n    this.stmtInsert.run(\n      this.projectHash,\n      entry.sessionId,\n      entry.toolName,\n      entry.target,\n    );\n    debug('research-buffer', 'Buffered research event', {\n      tool: entry.toolName,\n      target: entry.target,\n    });\n  }\n\n  /**\n   * Returns recent buffer entries for a session within a time window.\n   */\n  getRecent(\n    sessionId: string,\n    windowMinutes: number = 5,\n  ): Array<{ toolName: string; target: string; createdAt: string }> {\n    const rows = this.stmtGetRecent.all(\n      sessionId,\n      this.projectHash,\n      windowMinutes,\n    ) as Array<{ tool_name: string; target: string; created_at: string }>;\n\n    return rows.map(r => ({\n      toolName: r.tool_name,\n      target: r.target,\n      createdAt: r.created_at,\n    }));\n  }\n\n  /**\n   * Deletes buffer entries older than the specified number of minutes.\n   */\n  flush(olderThanMinutes: number = 30): number {\n    const result = this.stmtFlush.run(olderThanMinutes);\n    if (result.changes > 0) {\n      debug('research-buffer', 'Flushed old entries', { deleted: result.changes });\n    }\n    return result.changes;\n  }\n}\n","import type BetterSqlite3 from 'better-sqlite3';\nimport { randomBytes } from 'node:crypto';\nimport { debug } from '../shared/debug.js';\n\nexport interface PendingNotification {\n  id: string;\n  projectId: string;\n  message: string;\n  createdAt: string;\n}\n\nexport class NotificationStore {\n  private readonly stmtInsert: BetterSqlite3.Statement;\n  private readonly stmtConsume: BetterSqlite3.Statement;\n  private readonly stmtSelect: BetterSqlite3.Statement;\n\n  constructor(db: BetterSqlite3.Database) {\n    // Create table inline (no migration needed -- simple transient store)\n    db.exec(`\n      CREATE TABLE IF NOT EXISTS pending_notifications (\n        id TEXT PRIMARY KEY,\n        project_id TEXT NOT NULL,\n        message TEXT NOT NULL,\n        created_at TEXT NOT NULL DEFAULT (datetime('now'))\n      )\n    `);\n\n    this.stmtInsert = db.prepare(\n      'INSERT INTO pending_notifications (id, project_id, message) VALUES (?, ?, ?)'\n    );\n    this.stmtSelect = db.prepare(\n      'SELECT * FROM pending_notifications WHERE project_id = ? ORDER BY created_at ASC LIMIT 10'\n    );\n    this.stmtConsume = db.prepare(\n      'DELETE FROM pending_notifications WHERE project_id = ?'\n    );\n    debug('db', 'NotificationStore initialized');\n  }\n\n  add(projectId: string, message: string): void {\n    const id = randomBytes(16).toString('hex');\n    this.stmtInsert.run(id, projectId, message);\n    debug('db', 'Notification added', { projectId });\n  }\n\n  /** Fetch and delete all pending notifications for a project (consume pattern). */\n  consumePending(projectId: string): PendingNotification[] {\n    const rows = this.stmtSelect.all(projectId) as Array<{\n      id: string; project_id: string; message: string; created_at: string;\n    }>;\n    if (rows.length > 0) {\n      this.stmtConsume.run(projectId);\n    }\n    return rows.map(r => ({\n      id: r.id,\n      projectId: r.project_id,\n      message: r.message,\n      createdAt: r.created_at,\n    }));\n  }\n}\n","/**\n * Debug path schema initialization.\n *\n * Creates debug_paths and path_waypoints tables with indexes.\n * Uses CREATE TABLE IF NOT EXISTS for idempotent initialization\n * (same pattern as graph/schema.ts initGraphSchema).\n */\n\nimport type BetterSqlite3 from 'better-sqlite3';\n\nconst PATH_SCHEMA_DDL = `\n  CREATE TABLE IF NOT EXISTS debug_paths (\n    id TEXT PRIMARY KEY,\n    status TEXT NOT NULL DEFAULT 'active' CHECK(status IN ('active', 'resolved', 'abandoned')),\n    trigger_summary TEXT NOT NULL,\n    resolution_summary TEXT,\n    kiss_summary TEXT,\n    started_at TEXT NOT NULL DEFAULT (datetime('now')),\n    resolved_at TEXT,\n    project_hash TEXT NOT NULL\n  );\n\n  CREATE TABLE IF NOT EXISTS path_waypoints (\n    id TEXT PRIMARY KEY,\n    path_id TEXT NOT NULL REFERENCES debug_paths(id) ON DELETE CASCADE,\n    observation_id TEXT,\n    waypoint_type TEXT NOT NULL CHECK(waypoint_type IN ('error', 'attempt', 'failure', 'success', 'pivot', 'revert', 'discovery', 'resolution')),\n    sequence_order INTEGER NOT NULL,\n    summary TEXT NOT NULL,\n    created_at TEXT NOT NULL DEFAULT (datetime('now'))\n  );\n\n  CREATE INDEX IF NOT EXISTS idx_debug_paths_project_status\n    ON debug_paths(project_hash, status);\n\n  CREATE INDEX IF NOT EXISTS idx_debug_paths_started\n    ON debug_paths(started_at DESC);\n\n  CREATE INDEX IF NOT EXISTS idx_path_waypoints_path_order\n    ON path_waypoints(path_id, sequence_order);\n`;\n\n/**\n * Initializes debug path tables if they do not exist.\n * Safe to call multiple times (all statements use IF NOT EXISTS).\n */\nexport function initPathSchema(db: BetterSqlite3.Database): void {\n  db.exec(PATH_SCHEMA_DDL);\n}\n","/**\n * Repository for debug path CRUD operations.\n *\n * Every query is scoped to the projectHash provided at construction time.\n * All SQL statements are prepared once in the constructor and reused for\n * every call (same pattern as ObservationRepository).\n */\n\nimport type BetterSqlite3 from 'better-sqlite3';\nimport { randomBytes } from 'node:crypto';\n\nimport type { DebugPath, PathStatus, PathWaypoint, WaypointType } from './types.js';\n\nexport class PathRepository {\n  private readonly db: BetterSqlite3.Database;\n  private readonly projectHash: string;\n\n  // Prepared statements — path lifecycle\n  private readonly stmtCreatePath: BetterSqlite3.Statement;\n  private readonly stmtResolvePath: BetterSqlite3.Statement;\n  private readonly stmtAbandonPath: BetterSqlite3.Statement;\n  private readonly stmtGetActivePath: BetterSqlite3.Statement;\n  private readonly stmtGetPath: BetterSqlite3.Statement;\n  private readonly stmtListPaths: BetterSqlite3.Statement;\n\n  // Prepared statements — KISS summary\n  private readonly stmtUpdateKiss: BetterSqlite3.Statement;\n\n  // Prepared statements — cross-session linking\n  private readonly stmtFindRecentActive: BetterSqlite3.Statement;\n  private readonly stmtListByStatus: BetterSqlite3.Statement;\n\n  // Prepared statements — waypoint management\n  private readonly stmtAddWaypoint: BetterSqlite3.Statement;\n  private readonly stmtGetWaypoints: BetterSqlite3.Statement;\n  private readonly stmtCountWaypoints: BetterSqlite3.Statement;\n  private readonly stmtMaxSequence: BetterSqlite3.Statement;\n\n  constructor(db: BetterSqlite3.Database, projectHash: string) {\n    this.db = db;\n    this.projectHash = projectHash;\n\n    // --- Path lifecycle statements ---\n\n    this.stmtCreatePath = db.prepare(`\n      INSERT INTO debug_paths (id, status, trigger_summary, started_at, project_hash)\n      VALUES (?, 'active', ?, datetime('now'), ?)\n    `);\n\n    this.stmtResolvePath = db.prepare(`\n      UPDATE debug_paths\n      SET status = 'resolved', resolution_summary = ?, resolved_at = datetime('now')\n      WHERE id = ? AND project_hash = ?\n    `);\n\n    this.stmtAbandonPath = db.prepare(`\n      UPDATE debug_paths\n      SET status = 'abandoned', resolved_at = datetime('now')\n      WHERE id = ? AND project_hash = ?\n    `);\n\n    this.stmtGetActivePath = db.prepare(`\n      SELECT * FROM debug_paths\n      WHERE project_hash = ? AND status = 'active'\n      ORDER BY started_at DESC\n      LIMIT 1\n    `);\n\n    this.stmtGetPath = db.prepare(`\n      SELECT * FROM debug_paths\n      WHERE id = ? AND project_hash = ?\n    `);\n\n    this.stmtListPaths = db.prepare(`\n      SELECT * FROM debug_paths\n      WHERE project_hash = ?\n      ORDER BY started_at DESC\n      LIMIT ?\n    `);\n\n    // --- Cross-session linking statements ---\n\n    this.stmtFindRecentActive = db.prepare(`\n      SELECT * FROM debug_paths\n      WHERE project_hash = ? AND status = 'active'\n        AND started_at > datetime('now', '-24 hours')\n      ORDER BY started_at DESC\n      LIMIT 1\n    `);\n\n    this.stmtListByStatus = db.prepare(`\n      SELECT * FROM debug_paths\n      WHERE project_hash = ? AND status = ?\n      ORDER BY started_at DESC\n      LIMIT ?\n    `);\n\n    // --- KISS summary statement ---\n\n    this.stmtUpdateKiss = db.prepare(`\n      UPDATE debug_paths SET kiss_summary = ? WHERE id = ? AND project_hash = ?\n    `);\n\n    // --- Waypoint statements ---\n\n    this.stmtAddWaypoint = db.prepare(`\n      INSERT INTO path_waypoints (id, path_id, observation_id, waypoint_type, sequence_order, summary, created_at)\n      VALUES (?, ?, ?, ?, ?, ?, datetime('now'))\n    `);\n\n    this.stmtGetWaypoints = db.prepare(`\n      SELECT * FROM path_waypoints\n      WHERE path_id = ?\n      ORDER BY sequence_order ASC\n    `);\n\n    this.stmtCountWaypoints = db.prepare(`\n      SELECT COUNT(*) AS count FROM path_waypoints\n      WHERE path_id = ?\n    `);\n\n    this.stmtMaxSequence = db.prepare(`\n      SELECT COALESCE(MAX(sequence_order), 0) AS max_seq FROM path_waypoints\n      WHERE path_id = ?\n    `);\n  }\n\n  // ===========================================================================\n  // Path Lifecycle\n  // ===========================================================================\n\n  /**\n   * Creates a new active debug path.\n   * Generates a UUID id, sets status='active' and started_at=now.\n   */\n  createPath(triggerSummary: string): DebugPath {\n    const id = randomBytes(16).toString('hex');\n    this.stmtCreatePath.run(id, triggerSummary, this.projectHash);\n    return this.getPath(id)!;\n  }\n\n  /**\n   * Resolves a debug path with a resolution summary.\n   * Sets status='resolved', resolved_at=now.\n   */\n  resolvePath(pathId: string, resolutionSummary: string): void {\n    this.stmtResolvePath.run(resolutionSummary, pathId, this.projectHash);\n  }\n\n  /**\n   * Abandons a debug path.\n   * Sets status='abandoned', resolved_at=now.\n   */\n  abandonPath(pathId: string): void {\n    this.stmtAbandonPath.run(pathId, this.projectHash);\n  }\n\n  /**\n   * Returns the active path for this project (at most one active at a time).\n   * Returns null if no active path exists.\n   */\n  getActivePath(): DebugPath | null {\n    const row = this.stmtGetActivePath.get(this.projectHash) as DebugPathRow | undefined;\n    return row ? rowToDebugPath(row) : null;\n  }\n\n  /**\n   * Gets a debug path by ID, scoped to this project.\n   * Returns null if not found.\n   */\n  getPath(pathId: string): DebugPath | null {\n    const row = this.stmtGetPath.get(pathId, this.projectHash) as DebugPathRow | undefined;\n    return row ? rowToDebugPath(row) : null;\n  }\n\n  /**\n   * Lists recent paths for this project, ordered by started_at DESC.\n   * Default limit is 20.\n   */\n  listPaths(limit: number = 20): DebugPath[] {\n    const rows = this.stmtListPaths.all(this.projectHash, limit) as DebugPathRow[];\n    return rows.map(rowToDebugPath);\n  }\n\n  /**\n   * Finds a recently active path (started within the last 24 hours).\n   * Used for cross-session path linking — detects paths that may need\n   * continuation from a prior session.\n   */\n  findRecentActivePath(): DebugPath | null {\n    const row = this.stmtFindRecentActive.get(this.projectHash) as DebugPathRow | undefined;\n    return row ? rowToDebugPath(row) : null;\n  }\n\n  /**\n   * Lists paths filtered by status, ordered by started_at DESC.\n   * Useful for filtering to resolved/active/abandoned paths specifically.\n   */\n  listPathsByStatus(status: PathStatus, limit: number = 20): DebugPath[] {\n    const rows = this.stmtListByStatus.all(this.projectHash, status, limit) as DebugPathRow[];\n    return rows.map(rowToDebugPath);\n  }\n\n  // ===========================================================================\n  // KISS Summary\n  // ===========================================================================\n\n  /**\n   * Updates the kiss_summary column for a resolved debug path.\n   * Stores the full KissSummary JSON string.\n   */\n  updateKissSummary(pathId: string, kissSummary: string): void {\n    this.stmtUpdateKiss.run(kissSummary, pathId, this.projectHash);\n  }\n\n  // ===========================================================================\n  // Waypoint Management\n  // ===========================================================================\n\n  /**\n   * Adds a waypoint to a debug path.\n   * Auto-increments sequence_order based on existing waypoints.\n   */\n  addWaypoint(\n    pathId: string,\n    type: WaypointType,\n    summary: string,\n    observationId?: string,\n  ): PathWaypoint {\n    const id = randomBytes(16).toString('hex');\n    const { max_seq } = this.stmtMaxSequence.get(pathId) as { max_seq: number };\n    const sequenceOrder = max_seq + 1;\n\n    this.stmtAddWaypoint.run(\n      id,\n      pathId,\n      observationId ?? null,\n      type,\n      sequenceOrder,\n      summary,\n    );\n\n    return this.getWaypoints(pathId).find(w => w.id === id)!;\n  }\n\n  /**\n   * Returns all waypoints for a path, ordered by sequence_order ASC.\n   */\n  getWaypoints(pathId: string): PathWaypoint[] {\n    const rows = this.stmtGetWaypoints.all(pathId) as PathWaypointRow[];\n    return rows.map(rowToPathWaypoint);\n  }\n\n  /**\n   * Counts waypoints for a path. Used for cap enforcement (max 30 per path).\n   */\n  countWaypoints(pathId: string): number {\n    const row = this.stmtCountWaypoints.get(pathId) as { count: number };\n    return row.count;\n  }\n}\n\n// =============================================================================\n// Raw Row Types (snake_case, matches SQL columns)\n// =============================================================================\n\ninterface DebugPathRow {\n  id: string;\n  status: string;\n  trigger_summary: string;\n  resolution_summary: string | null;\n  kiss_summary: string | null;\n  started_at: string;\n  resolved_at: string | null;\n  project_hash: string;\n}\n\ninterface PathWaypointRow {\n  id: string;\n  path_id: string;\n  observation_id: string | null;\n  waypoint_type: string;\n  sequence_order: number;\n  summary: string;\n  created_at: string;\n}\n\n// =============================================================================\n// Row Mapping\n// =============================================================================\n\nfunction rowToDebugPath(row: DebugPathRow): DebugPath {\n  return {\n    id: row.id,\n    status: row.status as DebugPath['status'],\n    trigger_summary: row.trigger_summary,\n    resolution_summary: row.resolution_summary,\n    kiss_summary: row.kiss_summary,\n    started_at: row.started_at,\n    resolved_at: row.resolved_at,\n    project_hash: row.project_hash,\n  };\n}\n\nfunction rowToPathWaypoint(row: PathWaypointRow): PathWaypoint {\n  return {\n    id: row.id,\n    path_id: row.path_id,\n    observation_id: row.observation_id,\n    waypoint_type: row.waypoint_type as PathWaypoint['waypoint_type'],\n    sequence_order: row.sequence_order,\n    summary: row.summary,\n    created_at: row.created_at,\n  };\n}\n","import type BetterSqlite3 from 'better-sqlite3';\n\nimport { debug } from '../shared/debug.js';\nimport type { DiscoveredTool, ToolRegistryRow, ToolSearchResult, ToolUsageStats } from '../shared/tool-types.js';\nimport { reciprocalRankFusion } from '../search/hybrid.js';\n\n/**\n * Repository for tool registry CRUD operations.\n *\n * Unlike ObservationRepository, this is NOT scoped to a single project --\n * the tool registry spans all scopes (global, project, plugin) and is\n * queried cross-project for tool discovery and routing.\n *\n * All SQL statements are prepared once in the constructor and reused for\n * every call (better-sqlite3 performance best practice).\n */\nexport class ToolRegistryRepository {\n  private readonly db: BetterSqlite3.Database;\n\n  // Prepared statements (prepared once, reused for every call)\n  private readonly stmtUpsert: BetterSqlite3.Statement;\n  private readonly stmtRecordUsage: BetterSqlite3.Statement;\n  private readonly stmtGetByScope: BetterSqlite3.Statement;\n  private readonly stmtGetByName: BetterSqlite3.Statement;\n  private readonly stmtGetAll: BetterSqlite3.Statement;\n  private readonly stmtCount: BetterSqlite3.Statement;\n  private readonly stmtGetAvailableForSession: BetterSqlite3.Statement;\n  private readonly stmtInsertEvent: BetterSqlite3.Statement;\n  private readonly stmtGetUsageForTool: BetterSqlite3.Statement;\n  private readonly stmtGetUsageForSession: BetterSqlite3.Statement;\n  private readonly stmtGetUsageSince: BetterSqlite3.Statement;\n  private readonly stmtGetRecentUsage: BetterSqlite3.Statement;\n  private readonly stmtMarkStale: BetterSqlite3.Statement;\n  private readonly stmtMarkDemoted: BetterSqlite3.Statement;\n  private readonly stmtMarkActive: BetterSqlite3.Statement;\n  private readonly stmtGetConfigSourced: BetterSqlite3.Statement;\n  private readonly stmtGetRecentEventsForTool: BetterSqlite3.Statement;\n\n  constructor(db: BetterSqlite3.Database) {\n    this.db = db;\n\n    try {\n      this.stmtUpsert = db.prepare(`\n        INSERT INTO tool_registry (name, tool_type, scope, source, project_hash, description, server_name, trigger_hints, discovered_at)\n        VALUES (?, ?, ?, ?, ?, ?, ?, ?, datetime('now'))\n        ON CONFLICT (name, COALESCE(project_hash, ''))\n        DO UPDATE SET\n          description = COALESCE(excluded.description, tool_registry.description),\n          trigger_hints = COALESCE(excluded.trigger_hints, tool_registry.trigger_hints),\n          source = excluded.source,\n          status = 'active',\n          updated_at = datetime('now')\n      `);\n\n      this.stmtRecordUsage = db.prepare(`\n        UPDATE tool_registry\n        SET usage_count = usage_count + 1,\n            last_used_at = datetime('now'),\n            updated_at = datetime('now')\n        WHERE name = ? AND COALESCE(project_hash, '') = COALESCE(?, '')\n      `);\n\n      this.stmtGetByScope = db.prepare(`\n        SELECT * FROM tool_registry\n        WHERE scope = 'global' OR project_hash = ?\n        ORDER BY usage_count DESC, discovered_at DESC\n      `);\n\n      this.stmtGetByName = db.prepare(`\n        SELECT * FROM tool_registry\n        WHERE name = ?\n        ORDER BY usage_count DESC\n        LIMIT 1\n      `);\n\n      this.stmtGetAll = db.prepare(`\n        SELECT * FROM tool_registry\n        ORDER BY usage_count DESC, discovered_at DESC\n      `);\n\n      this.stmtCount = db.prepare(`\n        SELECT COUNT(*) AS count FROM tool_registry\n      `);\n\n      this.stmtGetAvailableForSession = db.prepare(`\n        SELECT * FROM tool_registry\n        WHERE\n          scope = 'global'\n          OR (scope = 'project' AND project_hash = ?)\n          OR (scope = 'plugin' AND (project_hash IS NULL OR project_hash = ?))\n        ORDER BY\n          CASE status\n            WHEN 'active' THEN 0\n            WHEN 'stale' THEN 1\n            WHEN 'demoted' THEN 2\n            ELSE 3\n          END,\n          CASE tool_type\n            WHEN 'mcp_server' THEN 0\n            WHEN 'slash_command' THEN 1\n            WHEN 'skill' THEN 2\n            WHEN 'plugin' THEN 3\n            ELSE 4\n          END,\n          usage_count DESC,\n          discovered_at DESC\n      `);\n\n      this.stmtInsertEvent = db.prepare(`\n        INSERT INTO tool_usage_events (tool_name, session_id, project_hash, success)\n        VALUES (?, ?, ?, ?)\n      `);\n\n      this.stmtGetUsageForTool = db.prepare(`\n        SELECT tool_name, COUNT(*) as usage_count, MAX(created_at) as last_used\n        FROM tool_usage_events\n        WHERE tool_name = ? AND project_hash = ?\n          AND created_at >= datetime('now', ?)\n        GROUP BY tool_name\n      `);\n\n      this.stmtGetUsageForSession = db.prepare(`\n        SELECT tool_name, COUNT(*) as usage_count, MAX(created_at) as last_used\n        FROM tool_usage_events\n        WHERE session_id = ?\n        GROUP BY tool_name\n        ORDER BY usage_count DESC\n      `);\n\n      this.stmtGetUsageSince = db.prepare(`\n        SELECT tool_name, COUNT(*) as usage_count, MAX(created_at) as last_used\n        FROM tool_usage_events\n        WHERE project_hash = ?\n          AND created_at >= datetime('now', ?)\n        GROUP BY tool_name\n        ORDER BY usage_count DESC\n      `);\n\n      this.stmtGetRecentUsage = db.prepare(`\n        SELECT tool_name, COUNT(*) as usage_count, MAX(created_at) as last_used\n        FROM (\n          SELECT tool_name, created_at\n          FROM tool_usage_events\n          WHERE project_hash = ?\n          ORDER BY created_at DESC\n          LIMIT ?\n        )\n        GROUP BY tool_name\n        ORDER BY usage_count DESC\n      `);\n\n      this.stmtMarkStale = db.prepare(`\n        UPDATE tool_registry\n        SET status = 'stale', updated_at = datetime('now')\n        WHERE name = ? AND COALESCE(project_hash, '') = COALESCE(?, '')\n          AND status != 'stale'\n      `);\n\n      this.stmtMarkDemoted = db.prepare(`\n        UPDATE tool_registry\n        SET status = 'demoted', updated_at = datetime('now')\n        WHERE name = ? AND COALESCE(project_hash, '') = COALESCE(?, '')\n      `);\n\n      this.stmtMarkActive = db.prepare(`\n        UPDATE tool_registry\n        SET status = 'active', updated_at = datetime('now')\n        WHERE name = ? AND COALESCE(project_hash, '') = COALESCE(?, '')\n          AND status != 'active'\n      `);\n\n      this.stmtGetConfigSourced = db.prepare(`\n        SELECT * FROM tool_registry\n        WHERE source LIKE 'config:%'\n          AND status = 'active'\n          AND (project_hash = ? OR project_hash IS NULL)\n      `);\n\n      this.stmtGetRecentEventsForTool = db.prepare(`\n        SELECT success FROM tool_usage_events\n        WHERE tool_name = ? AND project_hash = ?\n        ORDER BY created_at DESC\n        LIMIT ?\n      `);\n\n      debug('tool-registry', 'ToolRegistryRepository initialized');\n    } catch (err) {\n      // Table may not exist if database is pre-migration-16.\n      // Callers should catch this gracefully.\n      throw err;\n    }\n  }\n\n  /**\n   * Inserts or updates a discovered tool in the registry.\n   * On conflict (same name + project_hash), updates description and source.\n   */\n  upsert(tool: DiscoveredTool): void {\n    try {\n      this.stmtUpsert.run(\n        tool.name,\n        tool.toolType,\n        tool.scope,\n        tool.source,\n        tool.projectHash,\n        tool.description,\n        tool.serverName,\n        tool.triggerHints,\n      );\n      debug('tool-registry', 'Upserted tool', { name: tool.name, scope: tool.scope });\n    } catch (err) {\n      debug('tool-registry', 'Failed to upsert tool', { name: tool.name, error: String(err) });\n    }\n  }\n\n  /**\n   * Increments usage_count and updates last_used_at for a tool.\n   * Called from organic PostToolUse discovery to track usage.\n   */\n  recordUsage(name: string, projectHash: string | null): void {\n    try {\n      this.stmtRecordUsage.run(name, projectHash);\n      debug('tool-registry', 'Recorded usage', { name });\n    } catch (err) {\n      debug('tool-registry', 'Failed to record usage', { name, error: String(err) });\n    }\n  }\n\n  /**\n   * Records usage for an existing tool, or creates it if not yet in the registry.\n   * This is the entry point for organic discovery -- an upsert-and-increment-if-exists pattern.\n   *\n   * First tries recordUsage. If the tool is not in the registry (changes === 0),\n   * calls upsert with the full tool info, which initializes it with usage_count = 0.\n   */\n  recordOrCreate(\n    name: string,\n    defaults: Omit<DiscoveredTool, 'name'>,\n    sessionId?: string | null,\n    success?: boolean,\n  ): void {\n    try {\n      const result = this.stmtRecordUsage.run(name, defaults.projectHash);\n      if (result.changes === 0) {\n        // Tool not yet in registry -- create it\n        this.upsert({ name, ...defaults });\n      }\n      // Insert usage event with session context (UTRK-02)\n      if (sessionId !== undefined) {\n        this.stmtInsertEvent.run(name, sessionId, defaults.projectHash, success === false ? 0 : 1);\n      }\n      debug('tool-registry', 'recordOrCreate completed', { name, created: result.changes === 0 });\n    } catch (err) {\n      debug('tool-registry', 'Failed recordOrCreate', { name, error: String(err) });\n    }\n  }\n\n  /**\n   * Returns global tools plus project-specific tools for the given project.\n   */\n  getForProject(projectHash: string): ToolRegistryRow[] {\n    return this.stmtGetByScope.all(projectHash) as ToolRegistryRow[];\n  }\n\n  /**\n   * Returns tools available in the resolved scope for a given project.\n   * Implements SCOP-01/SCOP-02/SCOP-03 scope resolution rules.\n   */\n  getAvailableForSession(projectHash: string): ToolRegistryRow[] {\n    return this.stmtGetAvailableForSession.all(projectHash, projectHash) as ToolRegistryRow[];\n  }\n\n  /**\n   * Returns the top-usage entry for a given tool name.\n   */\n  getByName(name: string): ToolRegistryRow | null {\n    const row = this.stmtGetByName.get(name) as ToolRegistryRow | undefined;\n    return row ?? null;\n  }\n\n  /**\n   * Returns all tools in the registry (for debugging/admin).\n   */\n  getAll(): ToolRegistryRow[] {\n    return this.stmtGetAll.all() as ToolRegistryRow[];\n  }\n\n  /**\n   * Returns total number of tools in the registry.\n   */\n  count(): number {\n    const row = this.stmtCount.get() as { count: number };\n    return row.count;\n  }\n\n  /**\n   * Returns usage stats for a specific tool within a time window.\n   * @param timeModifier - SQLite datetime modifier, e.g., '-7 days', '-30 days'\n   */\n  getUsageForTool(toolName: string, projectHash: string, timeModifier: string = '-7 days'): ToolUsageStats | null {\n    const row = this.stmtGetUsageForTool.get(toolName, projectHash, timeModifier) as ToolUsageStats | undefined;\n    return row ?? null;\n  }\n\n  /**\n   * Returns per-tool usage stats for a specific session.\n   */\n  getUsageForSession(sessionId: string): ToolUsageStats[] {\n    return this.stmtGetUsageForSession.all(sessionId) as ToolUsageStats[];\n  }\n\n  /**\n   * Returns per-tool usage stats since a time offset for a project.\n   * @param timeModifier - SQLite datetime modifier, e.g., '-7 days', '-30 days'\n   */\n  getUsageSince(projectHash: string, timeModifier: string = '-7 days'): ToolUsageStats[] {\n    return this.stmtGetUsageSince.all(projectHash, timeModifier) as ToolUsageStats[];\n  }\n\n  /**\n   * Returns per-tool usage stats from the last N events for a project.\n   * Event-count-based window instead of time-based — immune to usage gaps.\n   * @param limit - Number of recent events to consider (default 200)\n   */\n  getRecentUsage(projectHash: string, limit: number = 200): ToolUsageStats[] {\n    return this.stmtGetRecentUsage.all(projectHash, limit) as ToolUsageStats[];\n  }\n\n  // ---------------------------------------------------------------------------\n  // Staleness management methods\n  // ---------------------------------------------------------------------------\n\n  /**\n   * Marks a tool as stale (no longer in config but still in registry).\n   * Idempotent -- no-op if already stale.\n   */\n  markStale(name: string, projectHash: string | null): void {\n    try {\n      this.stmtMarkStale.run(name, projectHash);\n      debug('tool-registry', 'Marked tool stale', { name });\n    } catch (err) {\n      debug('tool-registry', 'Failed to mark tool stale', { name, error: String(err) });\n    }\n  }\n\n  /**\n   * Marks a tool as demoted (high failure rate detected).\n   */\n  markDemoted(name: string, projectHash: string | null): void {\n    try {\n      this.stmtMarkDemoted.run(name, projectHash);\n      debug('tool-registry', 'Marked tool demoted', { name });\n    } catch (err) {\n      debug('tool-registry', 'Failed to mark tool demoted', { name, error: String(err) });\n    }\n  }\n\n  /**\n   * Marks a tool as active (restored from stale/demoted).\n   * Idempotent -- no-op if already active.\n   */\n  markActive(name: string, projectHash: string | null): void {\n    try {\n      this.stmtMarkActive.run(name, projectHash);\n      debug('tool-registry', 'Marked tool active', { name });\n    } catch (err) {\n      debug('tool-registry', 'Failed to mark tool active', { name, error: String(err) });\n    }\n  }\n\n  /**\n   * Returns all config-sourced active tools for a given project (or global).\n   * Used by staleness detection to compare against current config state.\n   */\n  getConfigSourcedTools(projectHash: string): ToolRegistryRow[] {\n    try {\n      return this.stmtGetConfigSourced.all(projectHash) as ToolRegistryRow[];\n    } catch (err) {\n      debug('tool-registry', 'Failed to get config-sourced tools', { error: String(err) });\n      return [];\n    }\n  }\n\n  /**\n   * Returns recent success/failure events for a specific tool.\n   * Used by failure-driven demotion to check failure rate.\n   * @param limit - Number of recent events to check (default 5)\n   */\n  getRecentEventsForTool(toolName: string, projectHash: string, limit: number = 5): Array<{ success: number }> {\n    try {\n      return this.stmtGetRecentEventsForTool.all(toolName, projectHash, limit) as Array<{ success: number }>;\n    } catch (err) {\n      debug('tool-registry', 'Failed to get recent events for tool', { toolName, error: String(err) });\n      return [];\n    }\n  }\n\n  // ---------------------------------------------------------------------------\n  // Search methods (FTS5 + vector + hybrid)\n  // ---------------------------------------------------------------------------\n\n  /**\n   * Sanitizes a user query for safe FTS5 MATCH usage.\n   * Removes FTS5 operators and special characters to prevent syntax errors.\n   * Returns null if the query is empty after sanitization.\n   */\n  private sanitizeQuery(query: string): string | null {\n    const words = query.trim().split(/\\s+/).filter(Boolean);\n    if (words.length === 0) return null;\n    const sanitized = words\n      .map(w => {\n        let cleaned = w.replace(/[\"*()^{}[\\]]/g, '');\n        if (/^(NEAR|OR|AND|NOT)$/i.test(cleaned)) return '';\n        cleaned = cleaned.replace(/[^\\w\\-]/g, '');\n        return cleaned;\n      })\n      .filter(Boolean);\n    if (sanitized.length === 0) return null;\n    return sanitized.join(' ');\n  }\n\n  /**\n   * FTS5 keyword search on tool_registry_fts (name + description).\n   * Returns ranked results using BM25 with name weighted 2x over description.\n   */\n  searchByKeyword(query: string, options?: { scope?: string; limit?: number }): ToolSearchResult[] {\n    const sanitized = this.sanitizeQuery(query);\n    if (!sanitized) return [];\n    const limit = options?.limit ?? 20;\n\n    let sql = `\n      SELECT tr.*, bm25(tool_registry_fts, 2.0, 1.0) AS rank\n      FROM tool_registry_fts\n      JOIN tool_registry tr ON tr.id = tool_registry_fts.rowid\n      WHERE tool_registry_fts MATCH ?\n    `;\n    const params: unknown[] = [sanitized];\n\n    if (options?.scope) {\n      sql += ' AND tr.scope = ?';\n      params.push(options.scope);\n    }\n\n    sql += ' ORDER BY rank LIMIT ?';\n    params.push(limit);\n\n    try {\n      const rows = this.db.prepare(sql).all(...params) as (ToolRegistryRow & { rank: number })[];\n      return rows.map(({ rank, ...toolFields }) => ({\n        tool: toolFields as ToolRegistryRow,\n        score: Math.abs(rank),\n        matchType: 'fts' as const,\n      }));\n    } catch (err) {\n      debug('tool-registry', 'FTS5 search failed', { error: String(err) });\n      return [];\n    }\n  }\n\n  /**\n   * Vector similarity search on tool_registry_embeddings using vec0 KNN.\n   * Returns tool IDs and distances sorted by cosine similarity.\n   */\n  searchByVector(queryEmbedding: Float32Array, options?: { scope?: string; limit?: number }): Array<{ tool_id: number; distance: number }> {\n    const limit = options?.limit ?? 40;\n    try {\n      let sql: string;\n      const params: unknown[] = [queryEmbedding];\n\n      if (options?.scope) {\n        sql = `\n          SELECT tre.tool_id, tre.distance\n          FROM tool_registry_embeddings tre\n          JOIN tool_registry tr ON tr.id = tre.tool_id\n          WHERE tre.embedding MATCH ? AND tr.scope = ?\n          ORDER BY tre.distance LIMIT ?\n        `;\n        params.push(options.scope);\n      } else {\n        sql = `\n          SELECT tre.tool_id, tre.distance\n          FROM tool_registry_embeddings tre\n          WHERE tre.embedding MATCH ?\n          ORDER BY tre.distance LIMIT ?\n        `;\n      }\n\n      params.push(limit);\n      return this.db.prepare(sql).all(...params) as Array<{ tool_id: number; distance: number }>;\n    } catch (err) {\n      debug('tool-registry', 'Vector search failed', { error: String(err) });\n      return [];\n    }\n  }\n\n  /**\n   * Hybrid search combining FTS5 keyword and vec0 vector results via\n   * reciprocal rank fusion (RRF). Falls back to FTS5-only when vector\n   * search is unavailable (no worker, no sqlite-vec, no embeddings).\n   */\n  async searchTools(\n    query: string,\n    options?: {\n      scope?: string;\n      limit?: number;\n      worker?: { isReady(): boolean; embed(text: string): Promise<Float32Array | null> } | null;\n      hasVectorSupport?: boolean;\n    },\n  ): Promise<ToolSearchResult[]> {\n    const limit = options?.limit ?? 20;\n\n    // Step 1: FTS5 keyword search\n    const ftsResults = this.searchByKeyword(query, { scope: options?.scope, limit });\n\n    // Step 2: Vector search (if available)\n    let vectorResults: Array<{ tool_id: number; distance: number }> = [];\n    if (options?.worker?.isReady() && options?.hasVectorSupport) {\n      const queryEmbedding = await options.worker.embed(query);\n      if (queryEmbedding) {\n        vectorResults = this.searchByVector(queryEmbedding, { scope: options?.scope, limit: limit * 2 });\n      }\n    }\n\n    // Step 3: FTS-only fallback\n    if (vectorResults.length === 0) {\n      return ftsResults.slice(0, limit);\n    }\n\n    // Step 4: Fuse with RRF\n    const ftsRanked = ftsResults.map(r => ({ id: String(r.tool.id) }));\n    const vecRanked = vectorResults.map(r => ({ id: String(r.tool_id) }));\n    const fused = reciprocalRankFusion([ftsRanked, vecRanked]);\n\n    // Build lookup maps\n    const ftsMap = new Map<string, ToolSearchResult>();\n    for (const r of ftsResults) {\n      ftsMap.set(String(r.tool.id), r);\n    }\n    const vecIds = new Set(vectorResults.map(r => String(r.tool_id)));\n\n    // Assemble results\n    const results: ToolSearchResult[] = [];\n    for (const item of fused) {\n      if (results.length >= limit) break;\n      const fromFts = ftsMap.get(item.id);\n      const fromVec = vecIds.has(item.id);\n\n      if (fromFts) {\n        results.push({\n          tool: fromFts.tool,\n          score: item.fusedScore,\n          matchType: fromFts && fromVec ? 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* Returns tools that have descriptions but no embedding yet.\n   * Used by the background embedding loop to find work.\n   */\n  findUnembeddedTools(limit: number = 5): Array<{ id: number; name: string; description: string }> {\n    try {\n      return this.db.prepare(`\n        SELECT id, name, description FROM tool_registry\n        WHERE description IS NOT NULL\n          AND id NOT IN (SELECT tool_id FROM tool_registry_embeddings)\n        LIMIT ?\n      `).all(limit) as Array<{ id: number; name: string; description: string }>;\n    } catch (err) {\n      debug('tool-registry', 'Failed to find unembedded tools', { error: String(err) });\n      return [];\n    }\n  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