@coreyuan/vector-mind 1.0.53 → 1.1.0

package/dist/database-runtime.js

@@ -2,20 +2,26 @@ import fs from "node:fs";
 import path from "node:path";
 import Database from "better-sqlite3";
 import { MEMORY_ITEMS_FTS_TABLE } from "./memory-recall.js";
+import { shouldIgnoreDbFilePath } from "./path-rules.js";
 export const FTS_TABLE_NAME = MEMORY_ITEMS_FTS_TABLE;
 let db;
 let dbPath = "";
 let ftsAvailable = false;
 let insertRequirementStmt;
 let getActiveRequirementStmt;
+let getActiveRequirementByIdStmt;
+let getActiveRequirementByGoalKeyStmt;
 let listActiveRequirementsStmt;
 let listRecentRequirementsStmt;
 let completeAllActiveRequirementsStmt;
 let completeRequirementByIdStmt;
-let completeAllActiveRequirementMemoryItemsStmt;
 let completeRequirementMemoryItemByReqIdStmt;
 let listChangeLogsForRequirementStmt;
 let insertChangeLogStmt;
+let upsertSyncedFileStateStmt;
+let getSyncedFileStateStmt;
+let insertMcpGuardEventStmt;
+let insertMcpToolMetricStmt;
 let insertMemoryItemStmt;
 let getMemoryItemByIdStmt;
 let getRequirementMemoryItemIdStmt;
@@ -50,66 +56,69 @@ let indexFileSymbolsTx = null;
 function initMemoryItemsFts() {
     ftsAvailable = false;
     try {
-        const existed = db
-            .prepare(`SELECT 1 FROM sqlite_master WHERE type='table' AND name=?`)
-            .get(FTS_TABLE_NAME);
-        const alreadyExists = !!existed;
-        if (!alreadyExists) {
-            try {
-                db.exec(`
-          CREATE VIRTUAL TABLE ${FTS_TABLE_NAME} USING fts5(
-            kind,
-            title,
-            content,
-            file_path,
-            metadata_json,
-            content='memory_items',
-            content_rowid='id',
-            tokenize='trigram'
-          );
-        `);
+        const initializeFts = db.transaction(() => {
+            const existed = db
+                .prepare(`SELECT 1 FROM sqlite_master WHERE type='table' AND name=?`)
+                .get(FTS_TABLE_NAME);
+            const alreadyExists = !!existed;
+            if (!alreadyExists) {
+                try {
+                    db.exec(`
+            CREATE VIRTUAL TABLE ${FTS_TABLE_NAME} USING fts5(
+              kind,
+              title,
+              content,
+              file_path,
+              metadata_json,
+              content='memory_items',
+              content_rowid='id',
+              tokenize='trigram'
+            );
+          `);
+                }
+                catch {
+                    db.exec(`
+            CREATE VIRTUAL TABLE ${FTS_TABLE_NAME} USING fts5(
+              kind,
+              title,
+              content,
+              file_path,
+              metadata_json,
+              content='memory_items',
+              content_rowid='id'
+            );
+          `);
+                }
+                try {
+                    db.exec(`INSERT INTO ${FTS_TABLE_NAME}(${FTS_TABLE_NAME}) VALUES('rebuild');`);
+                }
+                catch (err) {
+                    console.error("[vectormind] fts rebuild failed:", err);
+                }
             }
-            catch {
-                db.exec(`
-          CREATE VIRTUAL TABLE ${FTS_TABLE_NAME} USING fts5(
-            kind,
-            title,
-            content,
-            file_path,
-            metadata_json,
-            content='memory_items',
-            content_rowid='id'
-          );
-        `);
-            }
-            try {
-                db.exec(`INSERT INTO ${FTS_TABLE_NAME}(${FTS_TABLE_NAME}) VALUES('rebuild');`);
-            }
-            catch (err) {
-                console.error("[vectormind] fts rebuild failed:", err);
-            }
-        }
-        db.exec(`
-      CREATE TRIGGER IF NOT EXISTS vectormind_memory_items_fts_ai
-      AFTER INSERT ON memory_items BEGIN
-        INSERT INTO ${FTS_TABLE_NAME}(rowid, kind, title, content, file_path, metadata_json)
-        VALUES (new.id, new.kind, new.title, new.content, new.file_path, new.metadata_json);
-      END;
-
-      CREATE TRIGGER IF NOT EXISTS vectormind_memory_items_fts_ad
-      AFTER DELETE ON memory_items BEGIN
-        INSERT INTO ${FTS_TABLE_NAME}(${FTS_TABLE_NAME}, rowid, kind, title, content, file_path, metadata_json)
-        VALUES ('delete', old.id, old.kind, old.title, old.content, old.file_path, old.metadata_json);
-      END;
-
-      CREATE TRIGGER IF NOT EXISTS vectormind_memory_items_fts_au
-      AFTER UPDATE ON memory_items BEGIN
-        INSERT INTO ${FTS_TABLE_NAME}(${FTS_TABLE_NAME}, rowid, kind, title, content, file_path, metadata_json)
-        VALUES ('delete', old.id, old.kind, old.title, old.content, old.file_path, old.metadata_json);
-        INSERT INTO ${FTS_TABLE_NAME}(rowid, kind, title, content, file_path, metadata_json)
-        VALUES (new.id, new.kind, new.title, new.content, new.file_path, new.metadata_json);
-      END;
-    `);
+            db.exec(`
+        CREATE TRIGGER IF NOT EXISTS vectormind_memory_items_fts_ai
+        AFTER INSERT ON memory_items BEGIN
+          INSERT INTO ${FTS_TABLE_NAME}(rowid, kind, title, content, file_path, metadata_json)
+          VALUES (new.id, new.kind, new.title, new.content, new.file_path, new.metadata_json);
+        END;
+
+        CREATE TRIGGER IF NOT EXISTS vectormind_memory_items_fts_ad
+        AFTER DELETE ON memory_items BEGIN
+          INSERT INTO ${FTS_TABLE_NAME}(${FTS_TABLE_NAME}, rowid, kind, title, content, file_path, metadata_json)
+          VALUES ('delete', old.id, old.kind, old.title, old.content, old.file_path, old.metadata_json);
+        END;
+
+        CREATE TRIGGER IF NOT EXISTS vectormind_memory_items_fts_au
+        AFTER UPDATE ON memory_items BEGIN
+          INSERT INTO ${FTS_TABLE_NAME}(${FTS_TABLE_NAME}, rowid, kind, title, content, file_path, metadata_json)
+          VALUES ('delete', old.id, old.kind, old.title, old.content, old.file_path, old.metadata_json);
+          INSERT INTO ${FTS_TABLE_NAME}(rowid, kind, title, content, file_path, metadata_json)
+          VALUES (new.id, new.kind, new.title, new.content, new.file_path, new.metadata_json);
+        END;
+      `);
+        });
+        initializeFts.immediate();
         db.prepare(`SELECT rowid FROM ${FTS_TABLE_NAME} LIMIT 1`).get();
         ftsAvailable = true;
     }
@@ -126,6 +135,295 @@ function columnExists(table, column) {
         return false;
     }
 }
+function safeParseObject(value) {
+    if (!value)
+        return {};
+    try {
+        const parsed = JSON.parse(value);
+        return parsed && typeof parsed === "object" && !Array.isArray(parsed) ? parsed : {};
+    }
+    catch {
+        return {};
+    }
+}
+function stringValue(value) {
+    return typeof value === "string" && value.length > 0 ? value : undefined;
+}
+function nullableStringValue(value) {
+    if (value === null)
+        return null;
+    return stringValue(value);
+}
+function mergeStringArrays(values) {
+    const merged = [];
+    for (const value of values) {
+        if (!Array.isArray(value))
+            continue;
+        for (const item of value) {
+            if (typeof item === "string" && item.length > 0 && !merged.includes(item))
+                merged.push(item);
+        }
+    }
+    return merged;
+}
+function migrationFileKey(filePath) {
+    const normalized = filePath.replace(/\\/g, "/");
+    return process.platform === "win32" ? normalized.toLowerCase() : normalized;
+}
+function addMigrationFileEntry(filesByPath, filePath, metadata = {}) {
+    const normalizedFilePath = stringValue(filePath)?.replace(/\\/g, "/");
+    if (!normalizedFilePath || normalizedFilePath === "(multiple)" || normalizedFilePath === "(unspecified)")
+        return;
+    if (shouldIgnoreDbFilePath(normalizedFilePath))
+        return;
+    const key = migrationFileKey(normalizedFilePath);
+    const existing = filesByPath.get(key) ?? { file_path: normalizedFilePath };
+    const event = stringValue(metadata.event);
+    const source = stringValue(metadata.source);
+    const fileStateHash = nullableStringValue(metadata.file_state_hash);
+    if (event && !existing.event)
+        existing.event = event;
+    if (source && !existing.source)
+        existing.source = source;
+    if (fileStateHash !== undefined && existing.file_state_hash === undefined)
+        existing.file_state_hash = fileStateHash;
+    filesByPath.set(key, existing);
+}
+function addMigrationFilesFromMetadata(filesByPath, metadata) {
+    const files = metadata.files;
+    if (!Array.isArray(files))
+        return;
+    for (const item of files) {
+        if (!item || typeof item !== "object" || Array.isArray(item))
+            continue;
+        const entry = item;
+        addMigrationFileEntry(filesByPath, entry.file_path, entry);
+    }
+}
+function migrationFilesJson(filesByPath) {
+    return JSON.stringify([...filesByPath.values()].map((file) => ({
+        file_path: file.file_path,
+        event: file.event,
+        source: file.source,
+        file_state_hash: file.file_state_hash ?? null,
+    })));
+}
+function repairDuplicateChangeLogs() {
+    const groups = db
+        .prepare(`SELECT req_id, timestamp, intent_summary, MIN(id) AS keep_id, COUNT(*) AS row_count
+       FROM change_logs
+       GROUP BY req_id, timestamp, intent_summary
+       HAVING COUNT(*) > 1`)
+        .all();
+    if (!groups.length)
+        return 0;
+    const selectGroupRows = db.prepare(`SELECT id, req_id, file_path, intent_summary, files_json, file_count, timestamp
+     FROM change_logs
+     WHERE req_id IS ? AND timestamp IS ? AND intent_summary IS ?
+     ORDER BY id ASC`);
+    const updateKeepRow = db.prepare(`UPDATE change_logs
+     SET file_path = ?, files_json = ?, file_count = ?
+     WHERE id = ?`);
+    const deleteRow = db.prepare(`DELETE FROM change_logs WHERE id = ?`);
+    let removedRows = 0;
+    const tx = db.transaction(() => {
+        for (const group of groups) {
+            const rows = selectGroupRows.all(group.req_id, group.timestamp, group.intent_summary);
+            if (rows.length <= 1)
+                continue;
+            const distinctLegacyFiles = new Set(rows.map((row) => row.file_path).filter((value) => !!value));
+            const hasAggregateRows = rows.some((row) => {
+                try {
+                    const parsed = row.files_json ? JSON.parse(row.files_json) : null;
+                    return Array.isArray(parsed) && parsed.length > 0;
+                }
+                catch {
+                    return false;
+                }
+            });
+            if (hasAggregateRows || distinctLegacyFiles.size < 2)
+                continue;
+            const filesByPath = new Map();
+            for (const row of rows) {
+                addMigrationFilesFromMetadata(filesByPath, safeParseObject(row.files_json));
+                addMigrationFileEntry(filesByPath, row.file_path);
+            }
+            const files = [...filesByPath.values()];
+            const primaryFilePath = files.length === 1 ? files[0].file_path : files.length > 1 ? "(multiple)" : null;
+            const keepId = Number(group.keep_id);
+            updateKeepRow.run(primaryFilePath, migrationFilesJson(filesByPath), files.length, keepId);
+            for (const row of rows) {
+                if (row.id === keepId)
+                    continue;
+                deleteRow.run(row.id);
+                removedRows += 1;
+            }
+        }
+    });
+    tx();
+    return removedRows;
+}
+function repairDuplicateChangeIntentMemoryItems() {
+    const groups = db
+        .prepare(`SELECT req_id, content, MIN(id) AS keep_id, COUNT(*) AS row_count
+       FROM memory_items
+       WHERE kind = 'change_intent'
+       GROUP BY req_id, content
+       HAVING COUNT(*) > 1`)
+        .all();
+    if (!groups.length)
+        return 0;
+    const selectGroupRows = db.prepare(`SELECT id, title, content, file_path, req_id, metadata_json, updated_at
+     FROM memory_items
+     WHERE kind = 'change_intent'
+       AND req_id IS ?
+       AND content IS ?
+     ORDER BY id ASC`);
+    const updateKeepRow = db.prepare(`UPDATE memory_items
+     SET file_path = ?, metadata_json = ?
+     WHERE id = ?`);
+    const deleteRow = db.prepare(`DELETE FROM memory_items WHERE id = ?`);
+    let removedRows = 0;
+    const tx = db.transaction(() => {
+        for (const group of groups) {
+            const rows = selectGroupRows.all(group.req_id, group.content);
+            if (rows.length <= 1)
+                continue;
+            const filesByPath = new Map();
+            const metadataList = rows.map((row) => safeParseObject(row.metadata_json));
+            const distinctLegacyFiles = new Set(rows.map((row) => row.file_path).filter((value) => !!value));
+            if (metadataList.some((metadata) => Array.isArray(metadata.files)) || distinctLegacyFiles.size < 2)
+                continue;
+            for (let i = 0; i < rows.length; i += 1) {
+                const row = rows[i];
+                const metadata = metadataList[i] ?? {};
+                addMigrationFilesFromMetadata(filesByPath, metadata);
+                addMigrationFileEntry(filesByPath, row.file_path, metadata);
+            }
+            const files = [...filesByPath.values()];
+            const keepId = Number(group.keep_id);
+            const keepRow = rows.find((row) => row.id === keepId) ?? rows[0];
+            const keepMetadata = safeParseObject(keepRow.metadata_json);
+            const sourceChangeIds = new Set();
+            for (const metadata of metadataList) {
+                if (typeof metadata.change_log_id === "number")
+                    sourceChangeIds.add(metadata.change_log_id);
+                if (Array.isArray(metadata.source_change_ids)) {
+                    for (const id of metadata.source_change_ids) {
+                        if (typeof id === "number")
+                            sourceChangeIds.add(id);
+                    }
+                }
+            }
+            const nextMetadata = {
+                ...keepMetadata,
+                files: files.map((file) => ({
+                    file_path: file.file_path,
+                    event: file.event,
+                    source: file.source,
+                    file_state_hash: file.file_state_hash ?? null,
+                })),
+                file_count: files.length,
+            };
+            const verification = mergeStringArrays(metadataList.map((metadata) => metadata.verification));
+            const verificationGaps = mergeStringArrays(metadataList.map((metadata) => metadata.verification_gaps));
+            if (verification.length)
+                nextMetadata.verification = verification;
+            if (verificationGaps.length)
+                nextMetadata.verification_gaps = verificationGaps;
+            if (sourceChangeIds.size)
+                nextMetadata.source_change_ids = [...sourceChangeIds];
+            if (files.length === 1) {
+                const onlyFile = files[0];
+                nextMetadata.event = onlyFile.event;
+                nextMetadata.source = onlyFile.source;
+                nextMetadata.file_state_hash = onlyFile.file_state_hash ?? null;
+            }
+            else {
+                delete nextMetadata.event;
+                delete nextMetadata.source;
+                delete nextMetadata.file_state_hash;
+            }
+            updateKeepRow.run(files.length === 1 ? files[0].file_path : null, JSON.stringify(nextMetadata), keepId);
+            for (const row of rows) {
+                if (row.id === keepId)
+                    continue;
+                deleteRow.run(row.id);
+                removedRows += 1;
+            }
+        }
+    });
+    tx();
+    return removedRows;
+}
+function backfillSyncedFileStatesFromChangeIntentMemory() {
+    const rows = db
+        .prepare(`SELECT id, file_path, metadata_json, updated_at
+       FROM memory_items
+       WHERE kind = 'change_intent'
+       ORDER BY updated_at ASC, id ASC`)
+        .all();
+    if (!rows.length)
+        return 0;
+    const upsert = db.prepare(`INSERT INTO synced_file_states (file_path, file_state_hash, source_change_id, updated_at)
+     VALUES (?, ?, ?, COALESCE(?, CURRENT_TIMESTAMP))
+     ON CONFLICT(file_path) DO UPDATE SET
+       file_state_hash = excluded.file_state_hash,
+       source_change_id = excluded.source_change_id,
+       updated_at = CASE
+         WHEN synced_file_states.updated_at IS NULL OR synced_file_states.updated_at <= excluded.updated_at
+           THEN excluded.updated_at
+         ELSE synced_file_states.updated_at
+       END`);
+    let written = 0;
+    const tx = db.transaction(() => {
+        for (const row of rows) {
+            const metadata = safeParseObject(row.metadata_json);
+            const sourceChangeId = typeof metadata.change_log_id === "number"
+                ? metadata.change_log_id
+                : Array.isArray(metadata.source_change_ids) && typeof metadata.source_change_ids[0] === "number"
+                    ? metadata.source_change_ids[0]
+                    : null;
+            const filesByPath = new Map();
+            addMigrationFilesFromMetadata(filesByPath, metadata);
+            addMigrationFileEntry(filesByPath, row.file_path, metadata);
+            for (const file of filesByPath.values()) {
+                if (typeof file.file_state_hash !== "string")
+                    continue;
+                upsert.run(file.file_path, file.file_state_hash, sourceChangeId, row.updated_at);
+                written += 1;
+            }
+        }
+    });
+    tx();
+    return written;
+}
+function repairHistoricalDuplicateChangeRecords() {
+    const migrationKey = "migration:aggregate_change_records:v1";
+    try {
+        if (db.prepare(`SELECT 1 FROM meta_kv WHERE key = ? LIMIT 1`).get(migrationKey))
+            return;
+        const removedChangeLogs = repairDuplicateChangeLogs();
+        const removedChangeIntentMemory = repairDuplicateChangeIntentMemoryItems();
+        const syncedFileStates = backfillSyncedFileStatesFromChangeIntentMemory();
+        const result = JSON.stringify({
+            removed_change_logs: removedChangeLogs,
+            removed_change_intent_memory: removedChangeIntentMemory,
+            synced_file_states: syncedFileStates,
+            ran_at: new Date().toISOString(),
+        });
+        db.transaction(() => {
+            db.prepare(`INSERT INTO meta_kv (key, value, updated_at)
+         VALUES (?, ?, CURRENT_TIMESTAMP)`).run(migrationKey, result);
+            db.prepare(`INSERT INTO meta_kv (key, value, updated_at)
+         VALUES ('maintenance:dedupe_change_records:last_run', ?, CURRENT_TIMESTAMP)
+         ON CONFLICT(key) DO UPDATE SET value = excluded.value, updated_at = CURRENT_TIMESTAMP`).run(result);
+        })();
+    }
+    catch (err) {
+        console.error("[vectormind] historical duplicate change-record repair failed:", err);
+    }
+}
 export function openDatabaseRuntime(projectRoot) {
     const vmDir = path.join(projectRoot, ".vectormind");
     try {
@@ -139,23 +437,26 @@ export function openDatabaseRuntime(projectRoot) {
     db.pragma("journal_mode = WAL");
     db.pragma("foreign_keys = ON");
     db.exec(`
-    CREATE TABLE IF NOT EXISTS requirements (
-      id INTEGER PRIMARY KEY AUTOINCREMENT,
-      title TEXT NOT NULL,
-      status TEXT DEFAULT 'active',
-      context_data TEXT,
-      created_at DATETIME DEFAULT CURRENT_TIMESTAMP,
-      updated_at DATETIME DEFAULT CURRENT_TIMESTAMP
+    CREATE TABLE IF NOT EXISTS requirements (
+      id INTEGER PRIMARY KEY AUTOINCREMENT,
+      title TEXT NOT NULL,
+      status TEXT DEFAULT 'active',
+      context_data TEXT,
+      goal_key TEXT,
+      created_at DATETIME DEFAULT CURRENT_TIMESTAMP,
+      updated_at DATETIME DEFAULT CURRENT_TIMESTAMP
     );
 
-    CREATE TABLE IF NOT EXISTS change_logs (
-      id INTEGER PRIMARY KEY AUTOINCREMENT,
-      req_id INTEGER,
-      file_path TEXT,
-      intent_summary TEXT,
-      timestamp DATETIME DEFAULT CURRENT_TIMESTAMP,
-      FOREIGN KEY(req_id) REFERENCES requirements(id)
-    );
+    CREATE TABLE IF NOT EXISTS change_logs (
+      id INTEGER PRIMARY KEY AUTOINCREMENT,
+      req_id INTEGER,
+      file_path TEXT,
+      intent_summary TEXT,
+      files_json TEXT,
+      file_count INTEGER DEFAULT 1,
+      timestamp DATETIME DEFAULT CURRENT_TIMESTAMP,
+      FOREIGN KEY(req_id) REFERENCES requirements(id)
+    );
 
     CREATE TABLE IF NOT EXISTS symbols (
       name TEXT,
@@ -165,11 +466,55 @@ export function openDatabaseRuntime(projectRoot) {
       PRIMARY KEY(name, file_path)
     );
 
-    CREATE INDEX IF NOT EXISTS idx_change_logs_req_id_timestamp
-      ON change_logs(req_id, timestamp DESC);
-
-    CREATE INDEX IF NOT EXISTS idx_symbols_name
-      ON symbols(name);
+    CREATE INDEX IF NOT EXISTS idx_change_logs_req_id_timestamp
+      ON change_logs(req_id, timestamp DESC);
+
+    CREATE TABLE IF NOT EXISTS synced_file_states (
+      file_path TEXT PRIMARY KEY,
+      file_state_hash TEXT,
+      source_change_id INTEGER,
+      updated_at DATETIME DEFAULT CURRENT_TIMESTAMP
+    );
+
+    CREATE INDEX IF NOT EXISTS idx_synced_file_states_updated_at
+      ON synced_file_states(updated_at DESC);
+
+    CREATE TABLE IF NOT EXISTS mcp_guard_events (
+      id INTEGER PRIMARY KEY AUTOINCREMENT,
+      tool_name TEXT NOT NULL,
+      event_type TEXT NOT NULL,
+      severity TEXT DEFAULT 'info',
+      title TEXT NOT NULL,
+      detail TEXT,
+      metadata_json TEXT,
+      created_at DATETIME DEFAULT CURRENT_TIMESTAMP
+    );
+
+    CREATE INDEX IF NOT EXISTS idx_mcp_guard_events_created_at
+      ON mcp_guard_events(created_at DESC, id DESC);
+
+    CREATE INDEX IF NOT EXISTS idx_mcp_guard_events_type_created_at
+      ON mcp_guard_events(event_type, created_at DESC);
+
+    CREATE TABLE IF NOT EXISTS mcp_tool_metrics (
+      id INTEGER PRIMARY KEY AUTOINCREMENT,
+      tool_name TEXT NOT NULL,
+      duration_ms REAL NOT NULL,
+      raw_output_chars INTEGER NOT NULL,
+      output_chars INTEGER NOT NULL,
+      is_error INTEGER NOT NULL DEFAULT 0,
+      root_source TEXT,
+      created_at DATETIME DEFAULT CURRENT_TIMESTAMP
+    );
+
+    CREATE INDEX IF NOT EXISTS idx_mcp_tool_metrics_created_at
+      ON mcp_tool_metrics(created_at DESC, id DESC);
+
+    CREATE INDEX IF NOT EXISTS idx_mcp_tool_metrics_tool_created_at
+      ON mcp_tool_metrics(tool_name, created_at DESC);
+
+    CREATE INDEX IF NOT EXISTS idx_symbols_name
+      ON symbols(name);
 
     CREATE TABLE IF NOT EXISTS memory_items (
       id INTEGER PRIMARY KEY AUTOINCREMENT,
@@ -259,58 +604,118 @@ export function openDatabaseRuntime(projectRoot) {
       updated_at DATETIME DEFAULT CURRENT_TIMESTAMP
     );
   `);
-    if (!columnExists("requirements", "updated_at")) {
-        db.exec(`ALTER TABLE requirements ADD COLUMN updated_at DATETIME`);
-        db.exec(`UPDATE requirements SET updated_at = COALESCE(created_at, CURRENT_TIMESTAMP) WHERE updated_at IS NULL`);
-    }
-    db.exec(`
-    UPDATE requirements SET updated_at = COALESCE(updated_at, created_at, CURRENT_TIMESTAMP) WHERE updated_at IS NULL;
-    CREATE INDEX IF NOT EXISTS idx_requirements_status_updated_at
-      ON requirements(status, updated_at DESC, id DESC);
-    CREATE TRIGGER IF NOT EXISTS vectormind_requirements_touch_updated_at
-    AFTER UPDATE ON requirements
-    FOR EACH ROW
-    WHEN NEW.updated_at = OLD.updated_at
-    BEGIN
-      UPDATE requirements SET updated_at = CURRENT_TIMESTAMP WHERE id = NEW.id;
-    END;
-  `);
+    const migrateLegacyColumns = db.transaction(() => {
+        if (!columnExists("requirements", "updated_at")) {
+            db.exec(`ALTER TABLE requirements ADD COLUMN updated_at DATETIME`);
+            db.exec(`UPDATE requirements SET updated_at = COALESCE(created_at, CURRENT_TIMESTAMP) WHERE updated_at IS NULL`);
+        }
+        if (!columnExists("requirements", "goal_key")) {
+            db.exec(`ALTER TABLE requirements ADD COLUMN goal_key TEXT`);
+        }
+        if (!columnExists("change_logs", "files_json")) {
+            db.exec(`ALTER TABLE change_logs ADD COLUMN files_json TEXT`);
+        }
+        if (!columnExists("change_logs", "file_count")) {
+            db.exec(`ALTER TABLE change_logs ADD COLUMN file_count INTEGER DEFAULT 1`);
+            db.exec(`UPDATE change_logs SET file_count = 1 WHERE file_count IS NULL`);
+        }
+    });
+    migrateLegacyColumns.immediate();
+    db.transaction(() => {
+        db.exec(`
+      UPDATE requirements SET updated_at = COALESCE(updated_at, created_at, CURRENT_TIMESTAMP) WHERE updated_at IS NULL;
+      UPDATE requirements
+         SET updated_at = (
+           SELECT MAX(mi.updated_at)
+             FROM memory_items mi
+            WHERE mi.kind = 'requirement' AND mi.req_id = requirements.id
+         )
+       WHERE (
+           SELECT MAX(mi.updated_at)
+             FROM memory_items mi
+            WHERE mi.kind = 'requirement' AND mi.req_id = requirements.id
+         ) IS NOT NULL
+         AND datetime((
+           SELECT MAX(mi.updated_at)
+             FROM memory_items mi
+            WHERE mi.kind = 'requirement' AND mi.req_id = requirements.id
+         )) > datetime(COALESCE(requirements.updated_at, requirements.created_at, '1970-01-01 00:00:00'));
+      UPDATE requirements
+         SET status = 'superseded', updated_at = CURRENT_TIMESTAMP
+       WHERE status = 'active'
+         AND goal_key IS NOT NULL
+         AND EXISTS (
+           SELECT 1 FROM requirements newer
+            WHERE newer.status = 'active'
+              AND newer.goal_key = requirements.goal_key
+              AND newer.id > requirements.id
+         );
+      UPDATE memory_items
+         SET metadata_json = json_set(
+             CASE
+               WHEN json_valid(COALESCE(metadata_json, '{}')) THEN COALESCE(metadata_json, '{}')
+               ELSE '{}'
+             END,
+             '$.status',
+             'superseded',
+             '$.superseded',
+             json('true')
+           ),
+           updated_at = CURRENT_TIMESTAMP
+       WHERE kind = 'requirement'
+         AND req_id IN (
+           SELECT id FROM requirements WHERE status = 'superseded'
+         )
+         AND COALESCE(json_extract(
+           CASE
+             WHEN json_valid(COALESCE(metadata_json, '{}')) THEN COALESCE(metadata_json, '{}')
+             ELSE '{}'
+           END,
+           '$.status'
+         ), 'active') <> 'superseded';
+      CREATE INDEX IF NOT EXISTS idx_requirements_status_updated_at
+        ON requirements(status, updated_at DESC, id DESC);
+      CREATE INDEX IF NOT EXISTS idx_requirements_goal_key_status
+        ON requirements(goal_key, status, updated_at DESC, id DESC);
+      CREATE UNIQUE INDEX IF NOT EXISTS idx_requirements_active_goal_key_unique
+        ON requirements(goal_key) WHERE status = 'active' AND goal_key IS NOT NULL;
+      CREATE TRIGGER IF NOT EXISTS vectormind_requirements_touch_updated_at
+      AFTER UPDATE ON requirements
+      FOR EACH ROW
+      WHEN NEW.updated_at = OLD.updated_at
+      BEGIN
+        UPDATE requirements SET updated_at = CURRENT_TIMESTAMP WHERE id = NEW.id;
+      END;
+    `);
+    })();
     initMemoryItemsFts();
-    insertRequirementStmt = db.prepare(`INSERT INTO requirements (title, context_data, status) VALUES (?, ?, 'active')`);
-    completeAllActiveRequirementsStmt = db.prepare(`UPDATE requirements SET status = 'completed' WHERE status = 'active'`);
-    completeRequirementByIdStmt = db.prepare(`UPDATE requirements SET status = 'completed' WHERE id = ?`);
-    getActiveRequirementStmt = db.prepare(`SELECT id, title, status, context_data, created_at
-     FROM requirements
+    repairHistoricalDuplicateChangeRecords();
+    insertRequirementStmt = db.prepare(`INSERT INTO requirements (title, context_data, goal_key, status) VALUES (?, ?, ?, 'active')`);
+    completeAllActiveRequirementsStmt = db.prepare(`UPDATE requirements SET status = 'completed', updated_at = CURRENT_TIMESTAMP WHERE status = 'active'`);
+    completeRequirementByIdStmt = db.prepare(`UPDATE requirements SET status = 'completed', updated_at = CURRENT_TIMESTAMP WHERE id = ?`);
+    getActiveRequirementStmt = db.prepare(`SELECT id, title, status, context_data, goal_key, created_at
+     FROM requirements
      WHERE status = 'active'
      ORDER BY updated_at DESC, created_at DESC, id DESC
      LIMIT 1`);
-    listActiveRequirementsStmt = db.prepare(`SELECT id, title, status, context_data, created_at
+    getActiveRequirementByIdStmt = db.prepare(`SELECT id, title, status, context_data, goal_key, created_at
+     FROM requirements
+     WHERE status = 'active' AND id = ?
+     LIMIT 1`);
+    getActiveRequirementByGoalKeyStmt = db.prepare(`SELECT id, title, status, context_data, goal_key, created_at
+     FROM requirements
+     WHERE status = 'active' AND goal_key = ?
+     ORDER BY updated_at DESC, created_at DESC, id DESC
+     LIMIT 1`);
+    listActiveRequirementsStmt = db.prepare(`SELECT id, title, status, context_data, goal_key, created_at
      FROM requirements
      WHERE status = 'active'
      ORDER BY updated_at DESC, created_at DESC, id DESC
      LIMIT ?`);
-    listRecentRequirementsStmt = db.prepare(`SELECT id, title, status, context_data, created_at
+    listRecentRequirementsStmt = db.prepare(`SELECT id, title, status, context_data, goal_key, created_at
      FROM requirements
      ORDER BY updated_at DESC, created_at DESC, id DESC
      LIMIT ?`);
-    completeAllActiveRequirementMemoryItemsStmt = db.prepare(`UPDATE memory_items
-     SET metadata_json = json_set(
-         CASE
-           WHEN json_valid(COALESCE(metadata_json, '{}')) THEN COALESCE(metadata_json, '{}')
-           ELSE '{}'
-         END,
-         '$.status',
-         ?
-       ),
-       updated_at = CURRENT_TIMESTAMP
-     WHERE kind = 'requirement'
-       AND json_extract(
-         CASE
-           WHEN json_valid(COALESCE(metadata_json, '{}')) THEN COALESCE(metadata_json, '{}')
-           ELSE '{}'
-         END,
-         '$.status'
-       ) = ?`);
     completeRequirementMemoryItemByReqIdStmt = db.prepare(`UPDATE memory_items
      SET metadata_json = json_set(
          CASE
@@ -323,12 +728,30 @@ export function openDatabaseRuntime(projectRoot) {
        updated_at = CURRENT_TIMESTAMP
      WHERE kind = 'requirement'
        AND req_id = ?`);
-    listChangeLogsForRequirementStmt = db.prepare(`SELECT id, req_id, file_path, intent_summary, timestamp
-     FROM change_logs
-     WHERE req_id = ?
-     ORDER BY timestamp DESC, id DESC
+    listChangeLogsForRequirementStmt = db.prepare(`SELECT id, req_id, file_path, intent_summary, files_json, file_count, timestamp
+     FROM change_logs
+     WHERE req_id = ?
+     ORDER BY timestamp DESC, id DESC
      LIMIT ?`);
-    insertChangeLogStmt = db.prepare(`INSERT INTO change_logs (req_id, file_path, intent_summary) VALUES (?, ?, ?)`);
+    insertChangeLogStmt = db.prepare(`INSERT INTO change_logs (req_id, file_path, intent_summary, files_json, file_count)
+     VALUES (?, ?, ?, ?, ?)`);
+    upsertSyncedFileStateStmt = db.prepare(`INSERT INTO synced_file_states (file_path, file_state_hash, source_change_id, updated_at)
+     VALUES (?, ?, ?, CURRENT_TIMESTAMP)
+     ON CONFLICT(file_path) DO UPDATE SET
+       file_state_hash = excluded.file_state_hash,
+       source_change_id = excluded.source_change_id,
+       updated_at = CURRENT_TIMESTAMP`);
+    getSyncedFileStateStmt = db.prepare(`SELECT file_path, file_state_hash, source_change_id, updated_at
+     FROM synced_file_states
+     WHERE file_path = ?
+     LIMIT 1`);
+    insertMcpGuardEventStmt = db.prepare(`INSERT INTO mcp_guard_events
+       (tool_name, event_type, severity, title, detail, metadata_json)
+     VALUES
+       (?, ?, ?, ?, ?, ?)`);
+    insertMcpToolMetricStmt = db.prepare(`INSERT INTO mcp_tool_metrics
+      (tool_name, duration_ms, raw_output_chars, output_chars, is_error, root_source)
+     VALUES (?, ?, ?, ?, ?, ?)`);
     insertMemoryItemStmt = db.prepare(`INSERT INTO memory_items
        (kind, title, content, file_path, start_line, end_line, req_id, metadata_json, content_hash)
      VALUES
@@ -468,14 +891,19 @@ export function openDatabaseRuntime(projectRoot) {
         statements: {
             insertRequirementStmt,
             getActiveRequirementStmt,
+            getActiveRequirementByIdStmt,
+            getActiveRequirementByGoalKeyStmt,
             listActiveRequirementsStmt,
             listRecentRequirementsStmt,
             completeAllActiveRequirementsStmt,
             completeRequirementByIdStmt,
-            completeAllActiveRequirementMemoryItemsStmt,
             completeRequirementMemoryItemByReqIdStmt,
             listChangeLogsForRequirementStmt,
             insertChangeLogStmt,
+            upsertSyncedFileStateStmt,
+            getSyncedFileStateStmt,
+            insertMcpGuardEventStmt,
+            insertMcpToolMetricStmt,
             insertMemoryItemStmt,
             getMemoryItemByIdStmt,
             getRequirementMemoryItemIdStmt,