shieldcortex 3.4.13 → 3.4.15

package/dist/api/routes/memories.js

@@ -343,29 +343,34 @@ export function registerMemoryRoutes(app, deps) {
             const params = project ? [project] : [];
             const stale = db.prepare(`
         SELECT * FROM memories
-        WHERE decayed_score < 0.3 ${projectFilter}
+        WHERE COALESCE(status, 'active') NOT IN ('archived', 'suppressed')
+        AND decayed_score < 0.3 ${projectFilter}
         AND last_accessed < datetime('now', '-30 days')
         ORDER BY decayed_score ASC LIMIT ?
       `).all(...params, limit);
             const neverUsed = db.prepare(`
         SELECT * FROM memories
-        WHERE access_count = 0 ${projectFilter}
+        WHERE COALESCE(status, 'active') NOT IN ('archived', 'suppressed')
+        AND access_count = 0 ${projectFilter}
         AND created_at < datetime('now', '-1 day')
         ORDER BY created_at DESC LIMIT ?
       `).all(...params, limit);
             const lowTrust = db.prepare(`
         SELECT * FROM memories
-        WHERE trust_score < 0.7 ${projectFilter}
+        WHERE COALESCE(status, 'active') NOT IN ('archived', 'suppressed')
+        AND trust_score < 0.7 ${projectFilter}
         ORDER BY trust_score ASC, updated_at DESC LIMIT ?
       `).all(...params, limit);
             const noisyAutoExtracted = db.prepare(`
         SELECT * FROM memories
-        WHERE (capture_method = 'auto' OR tags LIKE '%auto-extracted%') ${projectFilter}
+        WHERE COALESCE(status, 'active') NOT IN ('archived', 'suppressed')
+        AND (capture_method = 'auto' OR tags LIKE '%auto-extracted%') ${projectFilter}
         ORDER BY updated_at DESC LIMIT ?
       `).all(...params, limit);
             const projectless = db.prepare(`
         SELECT * FROM memories
-        WHERE (project IS NULL OR project = '') AND scope != 'global'
+        WHERE COALESCE(status, 'active') NOT IN ('archived', 'suppressed')
+        AND (project IS NULL OR project = '') AND scope != 'global'
         ORDER BY updated_at DESC LIMIT ?
       `).all(limit);
             const openClawSummary = db.prepare(`

package/dist/database/init.d.ts

@@ -2,6 +2,24 @@
  * Database initialization and connection management
  */
 import Database from 'better-sqlite3';
+type RuntimeKind = 'installed' | 'npx-cache' | 'project-checkout' | 'unknown';
+interface RuntimeInfo {
+    kind: RuntimeKind;
+    entryPath: string;
+}
+interface DatabaseInspection {
+    integrity: string;
+    count: number | null;
+}
+interface BackupCandidate {
+    path: string;
+    count: number;
+    mtimeMs: number;
+}
+declare function resolveRuntimeInfo(): RuntimeInfo;
+declare function enforceSafeRuntimePath(expandedPath: string, explicitDbPath: boolean): void;
+declare function inspectDatabaseFile(dbPath: string): DatabaseInspection;
+declare function listHealthyBackups(dbPath: string): BackupCandidate[];
 declare function isLikelyFtsIntegrityIssue(integrityResult: string): boolean;
 declare function attemptFtsRecovery(database: Database.Database): boolean;
 declare function verifyOnDiskIntegrity(dbPath: string): string;
@@ -9,6 +27,10 @@ export declare const __databaseTestUtils: {
     isLikelyFtsIntegrityIssue: typeof isLikelyFtsIntegrityIssue;
     attemptFtsRecovery: typeof attemptFtsRecovery;
     verifyOnDiskIntegrity: typeof verifyOnDiskIntegrity;
+    inspectDatabaseFile: typeof inspectDatabaseFile;
+    listHealthyBackups: typeof listHealthyBackups;
+    resolveRuntimeInfo: typeof resolveRuntimeInfo;
+    enforceSafeRuntimePath: typeof enforceSafeRuntimePath;
 };
 /**
  * Initialize the database connection

package/dist/database/init.js

@@ -2,8 +2,8 @@
  * Database initialization and connection management
  */
 import Database from 'better-sqlite3';
-import { existsSync, mkdirSync, readFileSync, statSync, writeFileSync, unlinkSync, renameSync, copyFileSync } from 'fs';
-import { dirname, join } from 'path';
+import { existsSync, mkdirSync, readFileSync, statSync, writeFileSync, unlinkSync, renameSync, copyFileSync, readdirSync, openSync, closeSync, realpathSync } from 'fs';
+import { basename, dirname, join } from 'path';
 import { homedir } from 'os';
 import { fileURLToPath } from 'url';
 import { execSync } from 'child_process';
@@ -13,6 +13,7 @@ const _currentDir = dirname(_currentFile);
 let db = null;
 let currentDbPath = null;
 let lockFilePath = null;
+let lockFileFd = null;
 // Anti-bloat: Database size limits
 const MAX_DB_SIZE = 100 * 1024 * 1024; // 100MB hard limit
 const WARN_DB_SIZE = 50 * 1024 * 1024; // 50MB warning threshold
@@ -40,6 +41,177 @@ function getDefaultDbPath() {
     // Fall back to legacy path for existing users
     return legacyPath;
 }
+function resolveRuntimeInfo() {
+    let entryPath = process.argv[1] ?? '';
+    try {
+        if (entryPath) {
+            entryPath = realpathSync(entryPath);
+        }
+    }
+    catch {
+        // Fall back to the raw argv path.
+    }
+    if (entryPath.includes('/.npm/_npx/')) {
+        return { kind: 'npx-cache', entryPath };
+    }
+    if (entryPath.includes('/node_modules/shieldcortex/')) {
+        return { kind: 'installed', entryPath };
+    }
+    if (entryPath.includes('/ShieldCortex/') || entryPath.includes('\\ShieldCortex\\')) {
+        return { kind: 'project-checkout', entryPath };
+    }
+    return { kind: 'unknown', entryPath };
+}
+function enforceSafeRuntimePath(expandedPath, explicitDbPath) {
+    if (explicitDbPath || process.env.SHIELDCORTEX_ALLOW_UNSAFE_RUNTIME === '1') {
+        return;
+    }
+    const defaultPath = expandPath(getDefaultDbPath());
+    if (expandedPath !== defaultPath) {
+        return;
+    }
+    const runtime = resolveRuntimeInfo();
+    if (runtime.kind === 'npx-cache' || runtime.kind === 'project-checkout') {
+        throw new Error(`[database] Refusing to open ${defaultPath} from ${runtime.kind === 'npx-cache' ? 'an npx cache' : 'a project checkout'}.\n` +
+            `Use the installed CLI (\`shieldcortex\`), pass \`--db\` to use a separate database, or set SHIELDCORTEX_ALLOW_UNSAFE_RUNTIME=1 if you really mean to do this.\n` +
+            `Runtime path: ${runtime.entryPath}`);
+    }
+}
+function inspectDatabaseFile(dbPath) {
+    let inspectionDb = null;
+    try {
+        inspectionDb = new Database(dbPath, {
+            readonly: true,
+            fileMustExist: true,
+        });
+        const integrity = runIntegrityCheck(inspectionDb);
+        let count = null;
+        try {
+            count = inspectionDb.prepare('SELECT COUNT(*) AS count FROM memories').get().count;
+        }
+        catch {
+            count = null;
+        }
+        return { integrity, count };
+    }
+    catch (error) {
+        return { integrity: `inspect threw: ${error}`, count: null };
+    }
+    finally {
+        try {
+            inspectionDb?.close();
+        }
+        catch {
+            // Best-effort close.
+        }
+    }
+}
+function listHealthyBackups(dbPath) {
+    const dir = dirname(dbPath);
+    const prefix = `${basename(dbPath)}.corrupt.`;
+    return readdirSync(dir)
+        .filter((name) => name.startsWith(prefix) && !name.endsWith('-wal') && !name.endsWith('-shm'))
+        .map((name) => join(dir, name))
+        .map((backupPath) => {
+        const inspection = inspectDatabaseFile(backupPath);
+        const stats = statSync(backupPath);
+        return {
+            path: backupPath,
+            integrity: inspection.integrity,
+            count: inspection.count,
+            mtimeMs: stats.mtimeMs,
+        };
+    })
+        .filter((candidate) => candidate.integrity === 'ok' && typeof candidate.count === 'number' && candidate.count > 0)
+        .sort((a, b) => b.mtimeMs - a.mtimeMs)
+        .map(({ path, count, mtimeMs }) => ({ path, count, mtimeMs }));
+}
+function stashLiveDatabase(dbPath, suffix) {
+    const timestamp = new Date().toISOString().replace(/[:.]/g, '-');
+    const stashPath = `${dbPath}.${suffix}.${timestamp}`;
+    if (existsSync(dbPath)) {
+        try {
+            renameSync(dbPath, stashPath);
+        }
+        catch {
+            try {
+                copyFileSync(dbPath, stashPath);
+                unlinkSync(dbPath);
+            }
+            catch {
+                // Last resort: leave the original in place.
+            }
+        }
+    }
+    for (const ext of ['-wal', '-shm']) {
+        const liveSidecar = dbPath + ext;
+        if (existsSync(liveSidecar)) {
+            try {
+                renameSync(liveSidecar, stashPath + ext);
+            }
+            catch {
+                try {
+                    unlinkSync(liveSidecar);
+                }
+                catch {
+                    // Best-effort cleanup.
+                }
+            }
+        }
+    }
+}
+function restoreBackupAsLive(dbPath, backupPath, reason) {
+    stashLiveDatabase(dbPath, reason);
+    copyFileSync(backupPath, dbPath);
+}
+function acquireStartupLock(dbPath) {
+    lockFilePath = `${dbPath}.lock`;
+    const runtime = resolveRuntimeInfo();
+    const payload = JSON.stringify({
+        pid: process.pid,
+        startedAt: new Date().toISOString(),
+        entryPath: runtime.entryPath,
+    }, null, 2);
+    const tryOpen = () => {
+        lockFileFd = openSync(lockFilePath, 'wx');
+        writeFileSync(lockFileFd, payload, 'utf-8');
+    };
+    try {
+        tryOpen();
+        return;
+    }
+    catch {
+        let activeProcessError = null;
+        try {
+            const existing = JSON.parse(readFileSync(lockFilePath, 'utf-8'));
+            if (typeof existing.pid === 'number') {
+                try {
+                    process.kill(existing.pid, 0);
+                    activeProcessError = new Error(`[database] Refusing startup because ShieldCortex PID ${existing.pid} is already using ${dbPath}` +
+                        (existing.entryPath ? ` (${existing.entryPath})` : ''));
+                }
+                catch (error) {
+                    if (error.code !== 'ESRCH') {
+                        activeProcessError = error;
+                    }
+                }
+            }
+        }
+        catch {
+            // Stale or unreadable lock file — remove and retry.
+        }
+        if (activeProcessError) {
+            throw activeProcessError;
+        }
+        try {
+            unlinkSync(lockFilePath);
+        }
+        catch {
+            // Best-effort stale lock cleanup.
+        }
+        tryOpen();
+    }
+}
 /**
  * Back up a corrupt database file with a timestamped name.
  * Returns the backup path.
@@ -164,30 +336,16 @@ function attemptFtsRecovery(database) {
     }
 }
 function verifyOnDiskIntegrity(dbPath) {
-    let verificationDb = null;
-    try {
-        verificationDb = new Database(dbPath, {
-            readonly: true,
-            fileMustExist: true,
-        });
-        return runIntegrityCheck(verificationDb);
-    }
-    catch (error) {
-        return `fresh integrity check threw: ${error}`;
-    }
-    finally {
-        try {
-            verificationDb?.close();
-        }
-        catch {
-            // Best-effort close for verification handles.
-        }
-    }
+    return inspectDatabaseFile(dbPath).integrity;
 }
 export const __databaseTestUtils = {
     isLikelyFtsIntegrityIssue,
     attemptFtsRecovery,
     verifyOnDiskIntegrity,
+    inspectDatabaseFile,
+    listHealthyBackups,
+    resolveRuntimeInfo,
+    enforceSafeRuntimePath,
 };
 /**
  * Initialize the database connection
@@ -195,10 +353,12 @@ export const __databaseTestUtils = {
 export function initDatabase(dbPath) {
     // Use auto-detected path if not specified
     const resolvedPath = dbPath || getDefaultDbPath();
+    const explicitDbPath = Boolean(dbPath);
     if (db) {
         return db;
     }
     const expandedPath = expandPath(resolvedPath);
+    enforceSafeRuntimePath(expandedPath, explicitDbPath);
     const dir = dirname(expandedPath);
     // Create directory if it doesn't exist
     if (!existsSync(dir)) {
@@ -206,6 +366,9 @@ export function initDatabase(dbPath) {
     }
     // Store path for size monitoring
     currentDbPath = expandedPath;
+    acquireStartupLock(expandedPath);
+    console.log(`[database] Startup runtime=${resolveRuntimeInfo().kind} db=${expandedPath} wal=${existsSync(expandedPath + '-wal')} shm=${existsSync(expandedPath + '-shm')}`);
+    const healthyBackups = listHealthyBackups(expandedPath);
     // Wrap the initial open in try/catch to handle corrupt files gracefully
     let database;
     try {
@@ -213,11 +376,19 @@ export function initDatabase(dbPath) {
     }
     catch (openError) {
         // Database file is corrupt or not a valid SQLite database
-        console.error('❌ Database file is corrupt or not a valid SQLite database.');
-        const backupPath = backupCorruptDatabase(expandedPath);
-        console.error(`   Backed up to ${backupPath}`);
-        console.error('   Creating fresh database...');
-        database = new Database(expandedPath);
+        console.error(`❌ Database open failed for ${expandedPath}: ${openError}`);
+        const latestHealthyBackup = healthyBackups[0];
+        if (latestHealthyBackup) {
+            console.error(`[database] Restoring latest healthy backup with ${latestHealthyBackup.count} memories: ${latestHealthyBackup.path}`);
+            restoreBackupAsLive(expandedPath, latestHealthyBackup.path, 'failed-open');
+            database = new Database(expandedPath);
+        }
+        else {
+            const backupPath = backupCorruptDatabase(expandedPath);
+            console.error(`   Backed up to ${backupPath}`);
+            console.error('   Creating fresh database...');
+            database = new Database(expandedPath);
+        }
     }
     // Integrity check on existing databases (skip for newly created files)
     if (existsSync(expandedPath) && statSync(expandedPath).size > 0) {
@@ -244,18 +415,40 @@ export function initDatabase(dbPath) {
                         database = recovered;
                     }
                     else {
-                        // Recovery failed — backup and create fresh
-                        if (existsSync(expandedPath)) {
-                            const backupPath = backupCorruptDatabase(expandedPath);
-                            console.error(`[database] Recovery failed. Backed up corrupt file to: ${backupPath}`);
+                        const latestHealthyBackup = healthyBackups[0];
+                        if (latestHealthyBackup) {
+                            console.error(`[database] Recovery failed. Restoring latest healthy backup with ${latestHealthyBackup.count} memories: ${latestHealthyBackup.path}`);
+                            restoreBackupAsLive(expandedPath, latestHealthyBackup.path, 'recovery-failed');
+                            database = new Database(expandedPath);
+                        }
+                        else {
+                            // Recovery failed — backup and create fresh
+                            if (existsSync(expandedPath)) {
+                                const backupPath = backupCorruptDatabase(expandedPath);
+                                console.error(`[database] Recovery failed. Backed up corrupt file to: ${backupPath}`);
+                            }
+                            console.error('[database] Creating fresh database...');
+                            database = new Database(expandedPath);
                         }
-                        console.error('[database] Creating fresh database...');
-                        database = new Database(expandedPath);
                     }
                 }
             }
         }
     }
+    const currentInspection = inspectDatabaseFile(expandedPath);
+    const latestHealthyBackup = healthyBackups[0];
+    const liveStats = existsSync(expandedPath) ? statSync(expandedPath) : null;
+    if (currentInspection.integrity === 'ok'
+        && currentInspection.count === 0
+        && latestHealthyBackup
+        && latestHealthyBackup.count >= 100
+        && liveStats
+        && (liveStats.mtimeMs - latestHealthyBackup.mtimeMs) < (24 * 60 * 60 * 1000)) {
+        console.error(`[database] Empty live database detected alongside a recent healthy backup (${latestHealthyBackup.count} memories). Restoring ${latestHealthyBackup.path}`);
+        database.close();
+        restoreBackupAsLive(expandedPath, latestHealthyBackup.path, 'empty-live');
+        database = new Database(expandedPath);
+    }
     db = database;
     // Enable WAL mode for better concurrency
     db.pragma('journal_mode = WAL');
@@ -265,15 +458,6 @@ export function initDatabase(dbPath) {
     db.pragma('busy_timeout = 10000');
     // Auto-checkpoint every 100 pages (~400KB) to prevent WAL bloat
     db.pragma('wal_autocheckpoint = 100');
-    // Create lock file to help detect concurrent instances
-    lockFilePath = expandedPath + '.lock';
-    const pid = process.pid;
-    try {
-        writeFileSync(lockFilePath, `${pid}\n${new Date().toISOString()}`);
-    }
-    catch {
-        // Non-fatal - lock file is advisory
-    }
     // Register cleanup handlers for graceful shutdown
     registerShutdownHandlers();
     // Run migrations FIRST for existing databases
@@ -633,16 +817,24 @@ export function closeDatabase() {
         db.close();
         db = null;
         currentDbPath = null;
-        // Remove lock file
-        if (lockFilePath && existsSync(lockFilePath)) {
-            try {
-                unlinkSync(lockFilePath);
-            }
-            catch {
-                // Non-fatal
-            }
-            lockFilePath = null;
+    }
+    if (lockFileFd !== null) {
+        try {
+            closeSync(lockFileFd);
+        }
+        catch {
+            // Best-effort close.
+        }
+        lockFileFd = null;
+    }
+    if (lockFilePath && existsSync(lockFilePath)) {
+        try {
+            unlinkSync(lockFilePath);
+        }
+        catch {
+            // Non-fatal
         }
+        lockFilePath = null;
     }
 }
 /**

package/dist/memory/consolidate.js

@@ -195,8 +195,8 @@ export function findDuplicateMemoryPairs(options) {
     const db = getDatabase();
     const limit = options?.limit ?? 20;
     const rows = options?.project
-        ? db.prepare("SELECT * FROM memories WHERE type = 'long_term' AND project = ? ORDER BY created_at ASC").all(options.project)
-        : db.prepare("SELECT * FROM memories WHERE type = 'long_term' ORDER BY created_at ASC").all();
+        ? db.prepare("SELECT * FROM memories WHERE type = 'long_term' AND project = ? AND COALESCE(status, 'active') NOT IN ('archived', 'suppressed') ORDER BY created_at ASC").all(options.project)
+        : db.prepare("SELECT * FROM memories WHERE type = 'long_term' AND COALESCE(status, 'active') NOT IN ('archived', 'suppressed') ORDER BY created_at ASC").all();
     const groups = new Map();
     for (const mem of rows) {
         const cat = mem.category || 'note';

package/dist/memory/contradiction.js

@@ -204,7 +204,9 @@ export function detectContradictions(options = {}) {
     SUBSTR(content, 1, 500) as content,
     project, tags, salience, access_count, last_accessed,
     created_at, decayed_score, metadata, scope, transferable
-    FROM memories WHERE 1=1`;
+    FROM memories
+    WHERE 1=1
+      AND COALESCE(status, 'active') NOT IN ('archived', 'suppressed')`;
     const params = [];
     if (project) {
         sql += ' AND project = ?';

package/dist/memory/store.js

@@ -578,6 +578,14 @@ export function updateMemory(id, updates) {
         fields.push('project = ?');
         values.push(updates.project);
     }
+    if (updates.scope !== undefined) {
+        fields.push('scope = ?');
+        values.push(updates.scope);
+    }
+    if (updates.transferable !== undefined) {
+        fields.push('transferable = ?');
+        values.push(updates.transferable ? 1 : 0);
+    }
     if (updates.tags !== undefined) {
         fields.push('tags = ?');
         values.push(JSON.stringify(updates.tags));

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "shieldcortex",
-  "version": "3.4.13",
+  "version": "3.4.15",
   "description": "Trustworthy memory and security for AI agents. Recall debugging, review queue, OpenClaw session capture, and memory poisoning defence for Claude Code, Codex, OpenClaw, LangChain, and MCP agents.",
   "main": "dist/index.js",
   "types": "dist/index.d.ts",