codedev-mcp 3.2.2 → 3.2.5

package/dist/analyzers/dep-vuln.js

@@ -3,9 +3,13 @@
  * Cross-references package lock files (package-lock.json, yarn.lock, pnpm-lock.yaml,
  * Cargo.lock, Pipfile.lock, go.sum) against known vulnerability patterns.
  * Checks for outdated packages, known-vulnerable version ranges, and security advisories.
+ * Integrates with npm audit for real-time vulnerability detection.
  */
 import { readFile } from 'node:fs/promises';
 import path from 'node:path';
+import { execFile } from 'node:child_process';
+import { promisify } from 'node:util';
+const execFileAsync = promisify(execFile);
 // Known patterns for vulnerable packages / versions (static heuristic-based)
 const KNOWN_VULN_PATTERNS = [
     // npm ecosystem
@@ -187,6 +191,116 @@ function parseGoSum(content) {
     }
     return deps;
 }
+/**
+ * Run npm audit and parse results.
+ * @param cwd - The working directory
+ * @returns Parsed npm audit vulnerabilities or null if audit fails
+ */
+async function runNpmAudit(cwd) {
+    try {
+        // Check if package.json exists
+        const packageJsonPath = path.join(cwd, 'package.json');
+        await readFile(packageJsonPath, 'utf-8');
+        // Run npm audit --json
+        // Note: npm audit exits with code 1 when vulnerabilities are found, which is normal
+        let stdout = '';
+        try {
+            const result = await execFileAsync('npm', ['audit', '--json'], {
+                cwd,
+                timeout: 30000, // 30 second timeout
+                maxBuffer: 10 * 1024 * 1024, // 10MB buffer
+            });
+            stdout = result.stdout;
+        }
+        catch (error) {
+            // npm audit exits with code 1 when vulnerabilities are found - this is expected
+            // Check if stderr contains the JSON output (npm writes to stderr on error)
+            const execError = error;
+            if (execError.code === 1 && execError.stderr) {
+                // Try to parse stderr as JSON (npm audit sometimes writes JSON to stderr)
+                try {
+                    const stderrJson = JSON.parse(execError.stderr);
+                    if (stderrJson.vulnerabilities) {
+                        stdout = execError.stderr;
+                    }
+                }
+                catch {
+                    // If stderr isn't JSON, try stdout
+                    if (execError.stdout) {
+                        stdout = execError.stdout;
+                    }
+                }
+            }
+            else if (execError.stdout) {
+                stdout = execError.stdout;
+            }
+            else {
+                // Real error (npm not found, network issue, etc.)
+                return null;
+            }
+        }
+        if (!stdout)
+            return null;
+        const auditData = JSON.parse(stdout);
+        const vulns = [];
+        // Parse npm audit v7+ format
+        if (auditData.vulnerabilities) {
+            for (const [pkgName, vulnInfo] of Object.entries(auditData.vulnerabilities)) {
+                const info = vulnInfo;
+                // Get severity (npm audit uses: critical, high, moderate, low, info)
+                const severity = (info.severity || 'info').toLowerCase();
+                const mappedSeverity = severity === 'critical'
+                    ? 'critical'
+                    : severity === 'high'
+                        ? 'high'
+                        : severity === 'moderate'
+                            ? 'medium'
+                            : severity === 'low'
+                                ? 'low'
+                                : 'info';
+                // Get CVE or advisory info
+                const via = info.via || [];
+                const cveInfo = via.find((v) => typeof v === 'object' && v.title);
+                const reason = cveInfo?.title || via.find((v) => typeof v === 'string') || 'Known vulnerability';
+                // Get fix recommendation
+                let recommendation;
+                if (info.fixAvailable) {
+                    if (typeof info.fixAvailable === 'object' && info.fixAvailable.name && info.fixAvailable.version) {
+                        recommendation = `Upgrade ${info.fixAvailable.name} to ${info.fixAvailable.version}`;
+                    }
+                    else if (info.fixAvailable === true) {
+                        recommendation = 'Run npm audit fix';
+                    }
+                }
+                // Extract version from package name (format: package@version or package@version@version)
+                // npm audit can return nested dependencies like: package@1.0.0@2.0.0
+                const parts = pkgName.split('@');
+                const pkgNameOnly = parts[0];
+                // Get the actual installed version (usually the last part)
+                const version = parts.length > 1 ? parts[parts.length - 1] : 'unknown';
+                vulns.push({
+                    name: pkgNameOnly,
+                    version,
+                    severity: mappedSeverity,
+                    reason: String(reason),
+                    file: 'package-lock.json',
+                    ecosystem: 'npm',
+                    recommendation,
+                });
+            }
+        }
+        return vulns;
+    }
+    catch {
+        // npm audit might fail if:
+        // - npm is not installed
+        // - package.json doesn't exist
+        // - network issues
+        // - audit database unavailable
+        // Return null to fall back to static patterns
+        return null;
+    }
+}
 /**
  * Main vulnerability scan function.
  * @param cwd - The working directory to scan
@@ -198,37 +312,61 @@ export async function scanDependencyVulns(cwd) {
     const ecosystems = new Set();
     let totalDeps = 0;
     let outdatedCount = 0;
-    // Scan npm lock files
-    for (const lockFile of ['package-lock.json', 'yarn.lock', 'pnpm-lock.yaml']) {
-        try {
-            const content = await readFile(path.join(cwd, lockFile), 'utf-8');
-            lockFiles.push(lockFile);
-            ecosystems.add('npm');
-            // Only parse JSON lock files for now
-            if (lockFile === 'package-lock.json') {
-                const deps = parseNpmLock(content);
-                totalDeps += deps.length;
-                for (const dep of deps) {
-                    for (const pattern of KNOWN_VULN_PATTERNS) {
-                        if (pattern.name.test(dep.name) && pattern.maxSafe && semverLessThan(dep.version, pattern.maxSafe)) {
-                            vulnerabilities.push({
-                                name: dep.name,
-                                version: dep.version,
-                                severity: pattern.severity,
-                                reason: pattern.reason,
-                                file: lockFile,
-                                ecosystem: 'npm',
-                                recommendation: `Upgrade to >= ${pattern.maxSafe}`,
-                            });
-                            if (pattern.severity !== 'info')
-                                outdatedCount++;
+    // Try npm audit first for accurate vulnerability detection
+    const npmAuditVulns = await runNpmAudit(cwd);
+    const hasNpmAuditResults = npmAuditVulns && npmAuditVulns.length > 0;
+    if (hasNpmAuditResults) {
+        vulnerabilities.push(...npmAuditVulns);
+        ecosystems.add('npm');
+        if (!lockFiles.includes('package-lock.json')) {
+            lockFiles.push('package-lock.json');
+        }
+    }
+    // Scan npm lock files (only if npm audit didn't run or failed)
+    if (!hasNpmAuditResults) {
+        for (const lockFile of ['package-lock.json', 'yarn.lock', 'pnpm-lock.yaml']) {
+            try {
+                const content = await readFile(path.join(cwd, lockFile), 'utf-8');
+                if (!lockFiles.includes(lockFile))
+                    lockFiles.push(lockFile);
+                ecosystems.add('npm');
+                // Only parse JSON lock files for now
+                if (lockFile === 'package-lock.json') {
+                    const deps = parseNpmLock(content);
+                    totalDeps += deps.length;
+                    for (const dep of deps) {
+                        for (const pattern of KNOWN_VULN_PATTERNS) {
+                            if (pattern.name.test(dep.name) && pattern.maxSafe && semverLessThan(dep.version, pattern.maxSafe)) {
+                                vulnerabilities.push({
+                                    name: dep.name,
+                                    version: dep.version,
+                                    severity: pattern.severity,
+                                    reason: pattern.reason,
+                                    file: lockFile,
+                                    ecosystem: 'npm',
+                                    recommendation: `Upgrade to >= ${pattern.maxSafe}`,
+                                });
+                                if (pattern.severity !== 'info')
+                                    outdatedCount++;
+                            }
                         }
                     }
                 }
             }
+            catch {
+                /* file doesn't exist */
+            }
+        }
+    }
+    // Always count total deps from lock file if it exists
+    if (hasNpmAuditResults) {
+        try {
+            const content = await readFile(path.join(cwd, 'package-lock.json'), 'utf-8');
+            const deps = parseNpmLock(content);
+            totalDeps += deps.length;
         }
         catch {
-            /* file doesn't exist */
+            /* skip */
         }
     }
     // Scan package.json if no lock file found

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package/dist/db/connection.js

@@ -27,7 +27,7 @@ export async function getDb() {
  */
 export async function closeDb() {
     if (dbInstance) {
-        dbInstance.close();
+        await dbInstance.close();
         dbInstance = null;
     }
 }

package/dist/db/connection.js.map

@@ -1 +1 @@
-{"version":3,"file":"connection.js","sourceRoot":"","sources":["../../src/db/connection.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,MAAM,mBAAmB,CAAC;AAChD,OAAO,EAAE,GAAG,EAAE,MAAM,cAAc,CAAC;AAEnC,IAAI,UAAU,GAAuB,IAAI,CAAC;AAC1C,IAAI,WAAW,GAAgC,IAAI,CAAC;AAEpD;;;;GAIG;AACH,MAAM,CAAC,KAAK,UAAU,KAAK;IACzB,IAAI,UAAU;QAAE,OAAO,UAAU,CAAC;IAElC,IAAI,CAAC,WAAW,EAAE,CAAC;QACjB,WAAW,GAAG,CAAC,KAAK,IAAI,EAAE;YACxB,MAAM,KAAK,GAAG,IAAI,WAAW,CAAC,GAAG,CAAC,CAAC;YACnC,MAAM,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;YACtB,uBAAuB;YACvB,MAAM,KAAK,CAAC,IAAI,EAAE,CAAC;YACnB,UAAU,GAAG,KAAK,CAAC;YACnB,OAAO,KAAK,CAAC;QACf,CAAC,CAAC,EAAE,CAAC;IACP,CAAC;IAED,OAAO,WAAW,CAAC;AACrB,CAAC;AAED;;GAEG;AACH,MAAM,CAAC,KAAK,UAAU,OAAO;IAC3B,IAAI,UAAU,EAAE,CAAC;QACf,UAAU,CAAC,KAAK,EAAE,CAAC;QACnB,UAAU,GAAG,IAAI,CAAC;IACpB,CAAC;AACH,CAAC"}
+{"version":3,"file":"connection.js","sourceRoot":"","sources":["../../src/db/connection.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,MAAM,mBAAmB,CAAC;AAChD,OAAO,EAAE,GAAG,EAAE,MAAM,cAAc,CAAC;AAEnC,IAAI,UAAU,GAAuB,IAAI,CAAC;AAC1C,IAAI,WAAW,GAAgC,IAAI,CAAC;AAEpD;;;;GAIG;AACH,MAAM,CAAC,KAAK,UAAU,KAAK;IACzB,IAAI,UAAU;QAAE,OAAO,UAAU,CAAC;IAElC,IAAI,CAAC,WAAW,EAAE,CAAC;QACjB,WAAW,GAAG,CAAC,KAAK,IAAI,EAAE;YACxB,MAAM,KAAK,GAAG,IAAI,WAAW,CAAC,GAAG,CAAC,CAAC;YACnC,MAAM,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;YACtB,uBAAuB;YACvB,MAAM,KAAK,CAAC,IAAI,EAAE,CAAC;YACnB,UAAU,GAAG,KAAK,CAAC;YACnB,OAAO,KAAK,CAAC;QACf,CAAC,CAAC,EAAE,CAAC;IACP,CAAC;IAED,OAAO,WAAW,CAAC;AACrB,CAAC;AAED;;GAEG;AACH,MAAM,CAAC,KAAK,UAAU,OAAO;IAC3B,IAAI,UAAU,EAAE,CAAC;QACf,MAAM,UAAU,CAAC,KAAK,EAAE,CAAC;QACzB,UAAU,GAAG,IAAI,CAAC;IACpB,CAAC;AACH,CAAC"}

package/dist/db/sqlite-store.d.ts

@@ -27,6 +27,8 @@ export declare class SqliteStore {
     private db;
     private dirty;
     private SQL;
+    private saveTimeout;
+    private readonly AUTO_SAVE_DELAY;
     /**
      * Create a new SqliteStore instance.
      * @param cwd - The working directory for the database file.
@@ -45,6 +47,13 @@ export declare class SqliteStore {
      * @returns An array of result rows.
      */
     private query;
+    /**
+     * Execute a statement with bind parameters (INSERT, UPDATE, DELETE).
+     * Uses prepared statements to properly handle parameters.
+     * @param sql - The SQL statement string.
+     * @param params - Bind parameters for the statement.
+     */
+    private execute;
     /**
      * Create tables if they don't exist.
      */
@@ -58,6 +67,11 @@ export declare class SqliteStore {
      * Save database to disk.
      */
     save(): Promise<void>;
+    /**
+     * Schedule an automatic save after a delay.
+     * Debounces multiple rapid updates into a single save operation.
+     */
+    private scheduleAutoSave;
     /**
      * Initialize a new empty database.
      * @param _ - The working directory (unused, kept for interface compatibility).
@@ -128,8 +142,9 @@ export declare class SqliteStore {
     } | null;
     /**
      * Close the database.
+     * Saves any pending changes before closing.
      */
-    close(): void;
+    close(): Promise<void>;
     /**
      * Log tool usage to DB.
      * @param tool - Tool name.

package/dist/db/sqlite-store.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"sqlite-store.d.ts","sourceRoot":"","sources":["../../src/db/sqlite-store.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAQH,UAAU,WAAW;IACnB,IAAI,EAAE,MAAM,CAAC;IACb,KAAK,EAAE,MAAM,CAAC;IACd,KAAK,EAAE,MAAM,CAAC;IACd,QAAQ,EAAE,MAAM,CAAC;IACjB,IAAI,EAAE,MAAM,CAAC;CACd;AAED,UAAU,aAAa;IACrB,IAAI,EAAE,MAAM,CAAC;IACb,IAAI,EAAE,MAAM,CAAC;IACb,IAAI,EAAE,MAAM,CAAC;IACb,IAAI,EAAE,MAAM,CAAC;IACb,QAAQ,EAAE,OAAO,CAAC;CACnB;AAMD;;GAEG;AACH,qBAAa,WAAW;IACtB,OAAO,CAAC,MAAM,CAAS;IACvB,OAAO,CAAC,EAAE,CAA8B;IACxC,OAAO,CAAC,KAAK,CAAS;IACtB,OAAO,CAAC,GAAG,CAA4B;IACvC,OAAO,CAAC,WAAW,CAA+B;IAClD,OAAO,CAAC,QAAQ,CAAC,eAAe,CAAQ;IAExC;;;OAGG;gBACS,GAAG,EAAE,MAAM;IAIvB;;;OAGG;YACW,SAAS;IAQvB;;;;;;OAMG;IACH,OAAO,CAAC,KAAK;IAmBb;;;;;OAKG;IACH,OAAO,CAAC,OAAO;IAgBf;;OAEG;IACH,OAAO,CAAC,YAAY;IA4DpB;;;OAGG;IACG,IAAI,IAAI,OAAO,CAAC,OAAO,CAAC;IAyB9B;;OAEG;IACG,IAAI,IAAI,OAAO,CAAC,IAAI,CAAC;IAU3B;;;OAGG;IACH,OAAO,CAAC,gBAAgB;IAkBxB;;;OAGG;IACG,IAAI,CAAC,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC;IAQpC;;;;OAIG;IACG,YAAY,CAAC,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,OAAO,CAAC;IAatD;;;OAGG;IACH,UAAU,CAAC,IAAI,EAAE,WAAW,GAAG,IAAI;IAanC;;;;OAIG;IACH,aAAa,CAAC,QAAQ,EAAE,MAAM,EAAE,OAAO,EAAE,aAAa,EAAE,GAAG,IAAI;IAgB/D;;;;OAIG;IACH,aAAa,CAAC,QAAQ,EAAE,MAAM,EAAE,OAAO,EAAE,MAAM,EAAE,GAAG,IAAI;IAUxD;;;;;OAKG;IACH,WAAW,CAAC,OAAO,EAAE,MAAM,EAAE,IAAI,CAAC,EAAE,MAAM,GAAG,aAAa,EAAE;IAoB5D;;;OAGG;IACH,QAAQ,IAAI,WAAW,EAAE;IAWzB;;;;OAIG;IACH,UAAU,CAAC,QAAQ,EAAE,MAAM,GAAG,MAAM,EAAE;IAKtC;;;;OAIG;IACH,YAAY,CAAC,QAAQ,EAAE,MAAM,GAAG,MAAM,EAAE;IAMxC;;;OAGG;IACH,UAAU,CAAC,QAAQ,EAAE,MAAM,GAAG,IAAI;IASlC;;;OAGG;IACH,KAAK,IAAI;QAAE,KAAK,EAAE,MAAM,CAAC;QAAC,OAAO,EAAE,MAAM,CAAC;QAAC,OAAO,EAAE,MAAM,CAAC;QAAC,OAAO,EAAE,MAAM,CAAC;QAAC,MAAM,EAAE,MAAM,CAAA;KAAE,GAAG,IAAI;IAepG;;;OAGG;IACG,KAAK,IAAI,OAAO,CAAC,IAAI,CAAC;IAuB5B;;;;;;OAMG;IACH,QAAQ,CAAC,IAAI,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,EAAE,OAAO,EAAE,OAAO,EAAE,MAAM,EAAE,OAAO,GAAG,IAAI;IAajF;;;OAGG;IACH,aAAa,IAAI;QAAE,IAAI,EAAE,MAAM,CAAC;QAAC,KAAK,EAAE,MAAM,CAAC;QAAC,UAAU,EAAE,MAAM,CAAC;QAAC,WAAW,EAAE,MAAM,CAAA;KAAE,EAAE;CAmB5F"}

package/dist/db/sqlite-store.js

@@ -8,6 +8,7 @@
 import { readFile, writeFile, mkdir } from 'node:fs/promises';
 import path from 'node:path';
 import { stat as fsStat } from 'node:fs/promises';
+import { logger } from '../utils/logger.js';
 const INDEX_DIR = '.codedev-mcp';
 const INDEX_FILE = 'index.sqlite';
 const SCHEMA_VERSION = 2;
@@ -19,6 +20,8 @@ export class SqliteStore {
     db = null;
     dirty = false;
     SQL = null;
+    saveTimeout = null;
+    AUTO_SAVE_DELAY = 2000; // Save 2 seconds after last update
     /**
      * Create a new SqliteStore instance.
      * @param cwd - The working directory for the database file.
@@ -63,6 +66,27 @@ export class SqliteStore {
             return [];
         }
     }
+    /**
+     * Execute a statement with bind parameters (INSERT, UPDATE, DELETE).
+     * Uses prepared statements to properly handle parameters.
+     * @param sql - The SQL statement string.
+     * @param params - Bind parameters for the statement.
+     */
+    execute(sql, params = []) {
+        if (!this.db)
+            return;
+        try {
+            const db = this.db;
+            const stmt = db.prepare(sql);
+            stmt.bind(params);
+            stmt.step(); // Execute the statement
+            stmt.free();
+        }
+        catch (error) {
+            // Log error but don't throw - allows graceful degradation
+            logger.error('SQL execution error', error instanceof Error ? error : String(error), { sql, params });
+        }
+    }
     /**
      * Create tables if they don't exist.
      */
@@ -121,8 +145,8 @@ export class SqliteStore {
         this.db.run(`CREATE INDEX IF NOT EXISTS idx_usage_tool ON usage_stats(tool)`);
         this.db.run(`CREATE INDEX IF NOT EXISTS idx_usage_ts ON usage_stats(timestamp)`);
         // Set schema version
-        this.db.run(`INSERT OR REPLACE INTO meta (key, value) VALUES ('version', ?)`, [String(SCHEMA_VERSION)]);
-        this.db.run(`INSERT OR REPLACE INTO meta (key, value) VALUES ('updated', ?)`, [new Date().toISOString()]);
+        this.execute(`INSERT OR REPLACE INTO meta (key, value) VALUES ('version', ?)`, [String(SCHEMA_VERSION)]);
+        this.execute(`INSERT OR REPLACE INTO meta (key, value) VALUES ('updated', ?)`, [new Date().toISOString()]);
     }
     /**
      * Load existing database from disk. Returns false if none exists or version mismatch.
@@ -158,13 +182,34 @@ export class SqliteStore {
     async save() {
         if (!this.db || !this.dirty)
             return;
-        this.db.run(`INSERT OR REPLACE INTO meta (key, value) VALUES ('updated', ?)`, [new Date().toISOString()]);
+        this.execute(`INSERT OR REPLACE INTO meta (key, value) VALUES ('updated', ?)`, [new Date().toISOString()]);
         const data = this.db.export();
         const dir = path.dirname(this.dbPath);
         await mkdir(dir, { recursive: true });
         await writeFile(this.dbPath, Buffer.from(data));
         this.dirty = false;
     }
+    /**
+     * Schedule an automatic save after a delay.
+     * Debounces multiple rapid updates into a single save operation.
+     */
+    scheduleAutoSave() {
+        // Clear existing timeout
+        if (this.saveTimeout) {
+            clearTimeout(this.saveTimeout);
+        }
+        // Schedule save after delay
+        this.saveTimeout = setTimeout(async () => {
+            try {
+                await this.save();
+            }
+            catch (error) {
+                // Silently ignore save errors to avoid breaking tool execution
+                logger.error('Auto-save failed', error instanceof Error ? error : String(error));
+            }
+            this.saveTimeout = null;
+        }, this.AUTO_SAVE_DELAY);
+    }
     /**
      * Initialize a new empty database.
      * @param _ - The working directory (unused, kept for interface compatibility).
@@ -173,7 +218,7 @@ export class SqliteStore {
         const SQL = await this.initSqlJs();
         this.db = new SQL.Database();
         this.createSchema();
-        this.db.run(`INSERT OR REPLACE INTO meta (key, value) VALUES ('created', ?)`, [new Date().toISOString()]);
+        this.execute(`INSERT OR REPLACE INTO meta (key, value) VALUES ('created', ?)`, [new Date().toISOString()]);
         this.dirty = true;
     }
     /**
@@ -203,7 +248,7 @@ export class SqliteStore {
     updateFile(file) {
         if (!this.db)
             return;
-        this.db.run(`INSERT OR REPLACE INTO files (path, mtime, lines, language, size) VALUES (?, ?, ?, ?, ?)`, [
+        this.execute(`INSERT OR REPLACE INTO files (path, mtime, lines, language, size) VALUES (?, ?, ?, ?, ?)`, [
             file.path,
             file.mtime,
             file.lines,
@@ -211,6 +256,7 @@ export class SqliteStore {
             file.size,
         ]);
         this.dirty = true;
+        this.scheduleAutoSave();
     }
     /**
      * Update symbols for a file (replaces all).
@@ -220,9 +266,9 @@ export class SqliteStore {
     updateSymbols(filePath, symbols) {
         if (!this.db)
             return;
-        this.db.run(`DELETE FROM symbols WHERE file = ?`, [filePath]);
+        this.execute(`DELETE FROM symbols WHERE file = ?`, [filePath]);
         for (const s of symbols) {
-            this.db.run(`INSERT INTO symbols (name, type, file, line, exported) VALUES (?, ?, ?, ?, ?)`, [
+            this.execute(`INSERT INTO symbols (name, type, file, line, exported) VALUES (?, ?, ?, ?, ?)`, [
                 s.name,
                 s.type,
                 s.file,
@@ -231,6 +277,7 @@ export class SqliteStore {
             ]);
         }
         this.dirty = true;
+        this.scheduleAutoSave();
     }
     /**
      * Update imports for a file.
@@ -240,11 +287,12 @@ export class SqliteStore {
     updateImports(filePath, imports) {
         if (!this.db)
             return;
-        this.db.run(`DELETE FROM imports WHERE file = ?`, [filePath]);
+        this.execute(`DELETE FROM imports WHERE file = ?`, [filePath]);
         for (const imp of imports) {
-            this.db.run(`INSERT INTO imports (file, import_path) VALUES (?, ?)`, [filePath, imp]);
+            this.execute(`INSERT INTO imports (file, import_path) VALUES (?, ?)`, [filePath, imp]);
         }
         this.dirty = true;
+        this.scheduleAutoSave();
     }
     /**
      * Query symbols by name pattern.
@@ -310,10 +358,11 @@ export class SqliteStore {
     removeFile(filePath) {
         if (!this.db)
             return;
-        this.db.run(`DELETE FROM files WHERE path = ?`, [filePath]);
-        this.db.run(`DELETE FROM symbols WHERE file = ?`, [filePath]);
-        this.db.run(`DELETE FROM imports WHERE file = ?`, [filePath]);
+        this.execute(`DELETE FROM files WHERE path = ?`, [filePath]);
+        this.execute(`DELETE FROM symbols WHERE file = ?`, [filePath]);
+        this.execute(`DELETE FROM imports WHERE file = ?`, [filePath]);
         this.dirty = true;
+        this.scheduleAutoSave();
     }
     /**
      * Get index stats.
@@ -336,8 +385,24 @@ export class SqliteStore {
     }
     /**
      * Close the database.
+     * Saves any pending changes before closing.
      */
-    close() {
+    async close() {
+        // Clear any pending auto-save
+        if (this.saveTimeout) {
+            clearTimeout(this.saveTimeout);
+            this.saveTimeout = null;
+        }
+        // Save any pending changes
+        if (this.dirty) {
+            try {
+                await this.save();
+            }
+            catch (error) {
+                // Log but don't throw - we're closing anyway
+                logger.error('Error saving database on close', error instanceof Error ? error : String(error));
+            }
+        }
         if (this.db) {
             this.db.close();
             this.db = null;
@@ -353,7 +418,7 @@ export class SqliteStore {
     logUsage(tool, duration, success, cached) {
         if (!this.db)
             return;
-        this.db.run(`INSERT INTO usage_stats (tool, timestamp, duration, success, cached) VALUES (?, ?, ?, ?, ?)`, [
+        this.execute(`INSERT INTO usage_stats (tool, timestamp, duration, success, cached) VALUES (?, ?, ?, ?, ?)`, [
             tool,
             Date.now(),
             duration,
@@ -361,6 +426,7 @@ export class SqliteStore {
             cached ? 1 : 0,
         ]);
         this.dirty = true;
+        this.scheduleAutoSave();
     }
     /**
      * Get usage stats.

package/dist/db/sqlite-store.js.map

@@ -1 +1 @@
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package/dist/tools/quality.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"quality.d.ts","sourceRoot":"","sources":["../../src/tools/quality.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,MAAM,yCAAyC,CAAC;AAWpE;;;GAGG;AACH,wBAAgB,oBAAoB,CAAC,MAAM,EAAE,SAAS,QAytBrD"}