code-auditor-mcp 2.0.2 → 2.2.0

package/dist/languages/UniversalAnalyzer.js

@@ -3,6 +3,7 @@
  */
 import { LanguageRegistry } from './LanguageRegistry.js';
 import { promises as fs } from 'fs';
+import { IS_DEV_MODE } from '../constants.js';
 export class UniversalAnalyzer {
     /**
      * Main entry point - processes files and returns violations
@@ -19,26 +20,40 @@ export class UniversalAnalyzer {
         const totalFiles = files.length;
         // Process each language group
         for (const [adapter, adapterFiles] of filesByAdapter) {
-            console.error(`[DEBUG] ${this.name}: Processing ${adapterFiles.length} files with adapter:`, adapter.constructor.name);
+            if (IS_DEV_MODE) {
+                console.error(`[DEBUG] ${this.name}: Processing ${adapterFiles.length} files with adapter:`, adapter.constructor.name);
+            }
             for (const file of adapterFiles) {
-                console.error(`[DEBUG] ${this.name}: Processing file:`, file);
+                if (IS_DEV_MODE) {
+                    console.error(`[DEBUG] ${this.name}: Processing file:`, file);
+                }
                 try {
                     const content = await fs.readFile(file, 'utf8');
-                    console.error(`[DEBUG] ${this.name}: Read file content, length:`, content.length);
+                    if (IS_DEV_MODE) {
+                        console.error(`[DEBUG] ${this.name}: Read file content, length:`, content.length);
+                    }
                     const ast = await adapter.parse(file, content);
-                    console.error(`[DEBUG] ${this.name}: Parsed AST, errors:`, ast.errors.length);
+                    if (IS_DEV_MODE) {
+                        console.error(`[DEBUG] ${this.name}: Parsed AST, errors:`, ast.errors.length);
+                    }
                     if (ast.errors.length > 0) {
                         // Record parse errors but continue
-                        console.error(`[DEBUG] ${this.name}: Parse errors:`, ast.errors);
+                        if (IS_DEV_MODE) {
+                            console.error(`[DEBUG] ${this.name}: Parse errors:`, ast.errors);
+                        }
                         errors.push(...ast.errors.map(e => ({
                             file,
                             error: `Parse error: ${e.message}`
                         })));
                     }
                     // Run language-agnostic analysis
-                    console.error(`[DEBUG] ${this.name}: About to call analyzeAST for:`, file);
+                    if (IS_DEV_MODE) {
+                        console.error(`[DEBUG] ${this.name}: About to call analyzeAST for:`, file);
+                    }
                     const fileViolations = await this.analyzeAST(ast, adapter, config, content);
-                    console.error(`[DEBUG] ${this.name}: analyzeAST returned ${fileViolations.length} violations for:`, file);
+                    if (IS_DEV_MODE) {
+                        console.error(`[DEBUG] ${this.name}: analyzeAST returned ${fileViolations.length} violations for:`, file);
+                    }
                     violations.push(...fileViolations);
                     filesProcessed++;
                     if (options.progressCallback) {
@@ -46,6 +61,7 @@ export class UniversalAnalyzer {
                     }
                 }
                 catch (error) {
+                    // Always log errors, not just in dev mode
                     console.error(`[DEBUG] ${this.name}: ERROR processing file ${file}:`, error);
                     errors.push({
                         file,

package/dist/languages/UniversalAnalyzer.js.map

@@ -1 +1 @@
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+{"version":3,"file":"UniversalAnalyzer.js","sourceRoot":"","sources":["../../src/languages/UniversalAnalyzer.ts"],"names":[],"mappings":"AAAA;;GAEG;AAIH,OAAO,EAAE,gBAAgB,EAAE,MAAM,uBAAuB,CAAC;AACzD,OAAO,EAAE,QAAQ,IAAI,EAAE,EAAE,MAAM,IAAI,CAAC;AACpC,OAAO,EAAE,WAAW,EAAE,MAAM,iBAAiB,CAAC;AAO9C,MAAM,OAAgB,iBAAiB;IAKrC;;OAEG;IACH,KAAK,CAAC,OAAO,CACX,KAAe,EACf,SAAc,EAAE,EAChB,UAAoC,EAAE;QAEtC,OAAO,CAAC,KAAK,CAAC,WAAW,IAAI,CAAC,IAAI,kDAAkD,EAAE,KAAK,CAAC,CAAC;QAC7F,MAAM,UAAU,GAAgB,EAAE,CAAC;QACnC,MAAM,MAAM,GAA2C,EAAE,CAAC;QAC1D,MAAM,SAAS,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC;QAE7B,0BAA0B;QAC1B,MAAM,cAAc,GAAG,IAAI,CAAC,mBAAmB,CAAC,KAAK,CAAC,CAAC;QACvD,OAAO,CAAC,KAAK,CAAC,WAAW,IAAI,CAAC,IAAI,6BAA6B,EAAE,CAAC,GAAG,cAAc,CAAC,IAAI,EAAE,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,WAAW,CAAC,IAAI,CAAC,CAAC,CAAC;QAE1H,IAAI,cAAc,GAAG,CAAC,CAAC;QACvB,MAAM,UAAU,GAAG,KAAK,CAAC,MAAM,CAAC;QAEhC,8BAA8B;QAC9B,KAAK,MAAM,CAAC,OAAO,EAAE,YAAY,CAAC,IAAI,cAAc,EAAE,CAAC;YACrD,IAAI,WAAW,EAAE,CAAC;gBAChB,OAAO,CAAC,KAAK,CAAC,WAAW,IAAI,CAAC,IAAI,gBAAgB,YAAY,CAAC,MAAM,sBAAsB,EAAE,OAAO,CAAC,WAAW,CAAC,IAAI,CAAC,CAAC;YACzH,CAAC;YACD,KAAK,MAAM,IAAI,IAAI,YAAY,EAAE,CAAC;gBAChC,IAAI,WAAW,EAAE,CAAC;oBAChB,OAAO,CAAC,KAAK,CAAC,WAAW,IAAI,CAAC,IAAI,oBAAoB,EAAE,IAAI,CAAC,CAAC;gBAChE,CAAC;gBACD,IAAI,CAAC;oBACH,MAAM,OAAO,GAAG,MAAM,EAAE,CAAC,QAAQ,CAAC,IAAI,EAAE,MAAM,CAAC,CAAC;oBAChD,IAAI,WAAW,EAAE,CAAC;wBAChB,OAAO,CAAC,KAAK,CAAC,WAAW,IAAI,CAAC,IAAI,8BAA8B,EAAE,OAAO,CAAC,MAAM,CAAC,CAAC;oBACpF,CAAC;oBACD,MAAM,GAAG,GAAG,MAAM,OAAO,CAAC,KAAK,CAAC,IAAI,EAAE,OAAO,CAAC,CAAC;oBAC/C,IAAI,WAAW,EAAE,CAAC;wBAChB,OAAO,CAAC,KAAK,CAAC,WAAW,IAAI,CAAC,IAAI,uBAAuB,EAAE,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC;oBAChF,CAAC;oBAED,IAAI,GAAG,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;wBAC1B,mCAAmC;wBACnC,IAAI,WAAW,EAAE,CAAC;4BAChB,OAAO,CAAC,KAAK,CAAC,WAAW,IAAI,CAAC,IAAI,iBAAiB,EAAE,GAAG,CAAC,MAAM,CAAC,CAAC;wBACnE,CAAC;wBACD,MAAM,CAAC,IAAI,CAAC,GAAG,GAAG,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC;4BAClC,IAAI;4BACJ,KAAK,EAAE,gBAAgB,CAAC,CAAC,OAAO,EAAE;yBACnC,CAAC,CAAC,CAAC,CAAC;oBACP,CAAC;oBAED,iCAAiC;oBACjC,IAAI,WAAW,EAAE,CAAC;wBAChB,OAAO,CAAC,KAAK,CAAC,WAAW,IAAI,CAAC,IAAI,iCAAiC,EAAE,IAAI,CAAC,CAAC;oBAC7E,CAAC;oBACD,MAAM,cAAc,GAAG,MAAM,IAAI,CAAC,UAAU,CAC1C,GAAG,EACH,OAAO,EACP,MAAM,EACN,OAAO,CACR,CAAC;oBACF,IAAI,WAAW,EAAE,CAAC;wBAChB,OAAO,CAAC,KAAK,CAAC,WAAW,IAAI,CAAC,IAAI,yBAAyB,cAAc,CAAC,MAAM,kBAAkB,EAAE,IAAI,CAAC,CAAC;oBAC5G,CAAC;oBAED,UAAU,CAAC,IAAI,CAAC,GAAG,cAAc,CAAC,CAAC;oBAEnC,cAAc,EAAE,CAAC;oBACjB,IAAI,OAAO,CAAC,gBAAgB,EAAE,CAAC;wBAC7B,OAAO,CAAC,gBAAgB,CAAC,cAAc,GAAG,UAAU,CAAC,CAAC;oBACxD,CAAC;gBACH,CAAC;gBAAC,OAAO,KAAK,EAAE,CAAC;oBACf,0CAA0C;oBAC1C,OAAO,CAAC,KAAK,CAAC,WAAW,IAAI,CAAC,IAAI,2BAA2B,IAAI,GAAG,EAAE,KAAK,CAAC,CAAC;oBAC7E,MAAM,CAAC,IAAI,CAAC;wBACV,IAAI;wBACJ,KAAK,EAAE,KAAK,YAAY,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC;qBAC9D,CAAC,CAAC;gBACL,CAAC;YACH,CAAC;QACH,CAAC;QAED,OAAO;YACL,UAAU;YACV,MAAM;YACN,cAAc;YACd,aAAa,EAAE,IAAI,CAAC,GAAG,EAAE,GAAG,SAAS;YACrC,OAAO,EAAE;gBACP,aAAa,EAAE,cAAc;gBAC7B,eAAe,EAAE,UAAU,CAAC,MAAM;gBAClC,aAAa,EAAE,IAAI,CAAC,GAAG,EAAE,GAAG,SAAS;aACtC;SACF,CAAC;IACJ,CAAC;IAYD;;OAEG;IACK,mBAAmB,CAAC,KAAe;QACzC,MAAM,QAAQ,GAAG,gBAAgB,CAAC,WAAW,EAAE,CAAC;QAChD,MAAM,MAAM,GAAG,IAAI,GAAG,EAA6B,CAAC;QAEpD,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE,CAAC;YACzB,MAAM,OAAO,GAAG,QAAQ,CAAC,iBAAiB,CAAC,IAAI,CAAC,CAAC;YACjD,IAAI,OAAO,EAAE,CAAC;gBACZ,MAAM,YAAY,GAAG,MAAM,CAAC,GAAG,CAAC,OAAO,CAAC,IAAI,EAAE,CAAC;gBAC/C,YAAY,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;gBACxB,MAAM,CAAC,GAAG,CAAC,OAAO,EAAE,YAAY,CAAC,CAAC;YACpC,CAAC;QACH,CAAC;QAED,OAAO,MAAM,CAAC;IAChB,CAAC;IAED;;OAEG;IACO,eAAe,CACvB,IAAY,EACZ,QAA0C,EAC1C,OAAe,EACf,QAA+C,EAC/C,IAAY,EACZ,GAA0C;QAE1C,OAAO;YACL,IAAI;YACJ,IAAI,EAAE,QAAQ,CAAC,IAAI;YACnB,MAAM,EAAE,QAAQ,CAAC,MAAM;YACvB,QAAQ;YACR,OAAO;YACP,IAAI;YACJ,QAAQ,EAAE,IAAI,CAAC,IAAI;YACnB,GAAG;SACJ,CAAC;IACJ,CAAC;CACF"}

package/dist/mcp-index.d.ts

@@ -6,6 +6,8 @@
  *   node mcp-index.js              # stdio mode (default)
  *   node mcp-index.js --ui         # HTTP/UI mode
  *   node mcp-index.js --stdio      # explicit stdio mode
+ *   node mcp-index.js --data-dir /abs/path   # persist index under that directory
+ *   node mcp-index.js --auto-index /project  # index-only harness (no MCP stdio); logs to stderr
  */
-export {};
+import './applyDataDirEnv.js';
 //# sourceMappingURL=mcp-index.d.ts.map

package/dist/mcp-index.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"mcp-index.d.ts","sourceRoot":"","sources":["../src/mcp-index.ts"],"names":[],"mappings":";AAEA;;;;;;;GAOG"}
+{"version":3,"file":"mcp-index.d.ts","sourceRoot":"","sources":["../src/mcp-index.ts"],"names":[],"mappings":";AAEA;;;;;;;;;GASG;AAEH,OAAO,sBAAsB,CAAC"}

package/dist/mcp-index.js

@@ -6,14 +6,12 @@
  *   node mcp-index.js              # stdio mode (default)
  *   node mcp-index.js --ui         # HTTP/UI mode
  *   node mcp-index.js --stdio      # explicit stdio mode
+ *   node mcp-index.js --data-dir /abs/path   # persist index under that directory
+ *   node mcp-index.js --auto-index /project  # index-only harness (no MCP stdio); logs to stderr
  */
+import './applyDataDirEnv.js';
 import chalk from 'chalk';
-// Parse command line arguments
-const args = process.argv.slice(2);
-const uiMode = args.includes('--ui');
-const stdioMode = args.includes('--stdio');
-const helpMode = args.includes('--help') || args.includes('-h');
-if (helpMode) {
+function printHelp() {
     console.log(`
 ${chalk.blue('MCP Code Auditor Server')}
 
@@ -21,6 +19,8 @@ Usage:
   ${chalk.cyan('node mcp-index.js')}              # stdio mode (default)
   ${chalk.cyan('node mcp-index.js --ui')}         # HTTP/UI mode
   ${chalk.cyan('node mcp-index.js --stdio')}      # explicit stdio mode
+  ${chalk.cyan('node mcp-index.js --data-dir /path')}  # index DB at /path/index.db
+  ${chalk.cyan('node mcp-index.js --auto-index /project')}  # discover + index only (testing)
 
 Modes:
   ${chalk.yellow('stdio')}   - Standard MCP protocol over stdin/stdout (for Claude Desktop, VS Code)
@@ -30,15 +30,37 @@ Examples:
   ${chalk.gray('# For Claude Desktop')}
   node mcp-index.js
 
-  ${chalk.gray('# For interactive web dashboards')}
-  node mcp-index.js --ui
+  ${chalk.gray('# Index a repo without MCP (stderr logs; use CODE_AUDITOR_DEBUG=1 for verbose)')}
+  CODE_AUDITOR_DEBUG=1 node mcp-index.js --auto-index /path/to/repo
 
 Environment Variables:
   ${chalk.cyan('MCP_UI_PORT')}=3001              # Port for UI mode (default: 3001)
   ${chalk.cyan('MCP_MODE')}=stdio|ui             # Override mode detection
+  ${chalk.cyan('CODE_AUDITOR_DATA_DIR')}=/path   # Storage directory; index file is /path/index.db
+  ${chalk.cyan('CODE_AUDITOR_DEBUG')}=1          # Verbose mcpDiagnostics traces
+  ${chalk.cyan('CODE_AUDITOR_LOG_FILE')}=/path   # Append diagnostics lines to this file
 `);
+}
+// Parse command line arguments
+const args = process.argv.slice(2);
+const helpMode = args.includes('--help') || args.includes('-h');
+if (helpMode) {
+    printHelp();
+    process.exit(0);
+}
+const autoIndexPos = args.findIndex((a) => a === '--auto-index');
+if (autoIndexPos >= 0) {
+    const projectPath = args[autoIndexPos + 1];
+    if (!projectPath || projectPath.startsWith('-')) {
+        console.error('Usage: node mcp-index.js --auto-index <project-root>');
+        process.exit(1);
+    }
+    const { runAutoIndex } = await import('./mcpAutoIndex.js');
+    await runAutoIndex(projectPath);
     process.exit(0);
 }
+const uiMode = args.includes('--ui');
+const stdioMode = args.includes('--stdio');
 // Determine mode
 let mode;
 if (process.env.MCP_MODE) {

package/dist/mcp-index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"mcp-index.js","sourceRoot":"","sources":["../src/mcp-index.ts"],"names":[],"mappings":";AAEA;;;;;;;;;GASG;AAEH,OAAO,sBAAsB,CAAC;AAC9B,OAAO,KAAK,MAAM,OAAO,CAAC;AAE1B,SAAS,SAAS;IAChB,OAAO,CAAC,GAAG,CAAC;EACZ,KAAK,CAAC,IAAI,CAAC,yBAAyB,CAAC;;;IAGnC,KAAK,CAAC,IAAI,CAAC,mBAAmB,CAAC;IAC/B,KAAK,CAAC,IAAI,CAAC,wBAAwB,CAAC;IACpC,KAAK,CAAC,IAAI,CAAC,2BAA2B,CAAC;IACvC,KAAK,CAAC,IAAI,CAAC,oCAAoC,CAAC;IAChD,KAAK,CAAC,IAAI,CAAC,yCAAyC,CAAC;;;IAGrD,KAAK,CAAC,MAAM,CAAC,OAAO,CAAC;IACrB,KAAK,CAAC,MAAM,CAAC,IAAI,CAAC;;;IAGlB,KAAK,CAAC,IAAI,CAAC,sBAAsB,CAAC;;;IAGlC,KAAK,CAAC,IAAI,CAAC,gFAAgF,CAAC;;;;IAI5F,KAAK,CAAC,IAAI,CAAC,aAAa,CAAC;IACzB,KAAK,CAAC,IAAI,CAAC,UAAU,CAAC;IACtB,KAAK,CAAC,IAAI,CAAC,uBAAuB,CAAC;IACnC,KAAK,CAAC,IAAI,CAAC,oBAAoB,CAAC;IAChC,KAAK,CAAC,IAAI,CAAC,uBAAuB,CAAC;CACtC,CAAC,CAAC;AACH,CAAC;AAED,+BAA+B;AAC/B,MAAM,IAAI,GAAG,OAAO,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC;AACnC,MAAM,QAAQ,GAAG,IAAI,CAAC,QAAQ,CAAC,QAAQ,CAAC,IAAI,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC;AAEhE,IAAI,QAAQ,EAAE,CAAC;IACb,SAAS,EAAE,CAAC;IACZ,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;AAClB,CAAC;AAED,MAAM,YAAY,GAAG,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,KAAK,cAAc,CAAC,CAAC;AACjE,IAAI,YAAY,IAAI,CAAC,EAAE,CAAC;IACtB,MAAM,WAAW,GAAG,IAAI,CAAC,YAAY,GAAG,CAAC,CAAC,CAAC;IAC3C,IAAI,CAAC,WAAW,IAAI,WAAW,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC;QAChD,OAAO,CAAC,KAAK,CAAC,sDAAsD,CAAC,CAAC;QACtE,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;IAClB,CAAC;IACD,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,MAAM,CAAC,mBAAmB,CAAC,CAAC;IAC3D,MAAM,YAAY,CAAC,WAAW,CAAC,CAAC;IAChC,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;AAClB,CAAC;AAED,MAAM,MAAM,GAAG,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAC;AACrC,MAAM,SAAS,GAAG,IAAI,CAAC,QAAQ,CAAC,SAAS,CAAC,CAAC;AAE3C,iBAAiB;AACjB,IAAI,IAAoB,CAAC;AAEzB,IAAI,OAAO,CAAC,GAAG,CAAC,QAAQ,EAAE,CAAC;IACzB,IAAI,GAAG,OAAO,CAAC,GAAG,CAAC,QAA0B,CAAC;IAC9C,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,IAAI,CAAC,OAAO,CAAC,EAAE,+CAA+C,IAAI,EAAE,CAAC,CAAC;AAC5F,CAAC;KAAM,IAAI,MAAM,EAAE,CAAC;IAClB,IAAI,GAAG,IAAI,CAAC;IACZ,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,IAAI,CAAC,OAAO,CAAC,EAAE,iCAAiC,CAAC,CAAC;AACxE,CAAC;KAAM,IAAI,SAAS,EAAE,CAAC;IACrB,IAAI,GAAG,OAAO,CAAC;IACf,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,IAAI,CAAC,OAAO,CAAC,EAAE,uCAAuC,CAAC,CAAC;AAC9E,CAAC;KAAM,CAAC;IACN,8CAA8C;IAC9C,IAAI,GAAG,OAAO,CAAC;IACf,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,IAAI,CAAC,OAAO,CAAC,EAAE,0DAA0D,CAAC,CAAC;AACjG,CAAC;AAED,gCAAgC;AAChC,KAAK,UAAU,WAAW;IACxB,IAAI,CAAC;QACH,IAAI,IAAI,KAAK,IAAI,EAAE,CAAC;YAClB,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,OAAO,CAAC,EAAE,4BAA4B,CAAC,CAAC;YAClE,MAAM,EAAE,gBAAgB,EAAE,GAAG,MAAM,MAAM,CAAC,oBAAoB,CAAC,CAAC;YAChE,MAAM,gBAAgB,EAAE,CAAC;QAC3B,CAAC;aAAM,CAAC;YACN,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,OAAO,CAAC,EAAE,0BAA0B,CAAC,CAAC;YAChE,MAAM,MAAM,CAAC,UAAU,CAAC,CAAC;QAC3B,CAAC;IACH,CAAC;IAAC,OAAO,KAAK,EAAE,CAAC;QACf,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,GAAG,CAAC,aAAa,CAAC,EAAE,yBAAyB,EAAE,KAAK,CAAC,CAAC;QAC1E,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,GAAG,CAAC,SAAS,CAAC,EAAE,QAAQ,EAAE,KAAK,YAAY,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC;QACjG,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;IAClB,CAAC;AACH,CAAC;AAED,6BAA6B;AAC7B,OAAO,CAAC,EAAE,CAAC,QAAQ,EAAE,GAAG,EAAE;IACxB,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC,OAAO,CAAC,EAAE,iBAAiB,IAAI,YAAY,CAAC,CAAC;IACxE,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;AAClB,CAAC,CAAC,CAAC;AAEH,OAAO,CAAC,EAAE,CAAC,SAAS,EAAE,GAAG,EAAE;IACzB,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC,OAAO,CAAC,EAAE,mCAAmC,IAAI,YAAY,CAAC,CAAC;IAC1F,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;AAClB,CAAC,CAAC,CAAC;AAEH,OAAO,CAAC,EAAE,CAAC,mBAAmB,EAAE,CAAC,KAAK,EAAE,EAAE;IACxC,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,GAAG,CAAC,aAAa,CAAC,EAAE,qBAAqB,EAAE,KAAK,CAAC,CAAC;IACtE,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,GAAG,CAAC,SAAS,CAAC,EAAE,QAAQ,EAAE,KAAK,CAAC,KAAK,CAAC,CAAC;IAC3D,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;AAClB,CAAC,CAAC,CAAC;AAEH,OAAO,CAAC,EAAE,CAAC,oBAAoB,EAAE,CAAC,MAAM,EAAE,OAAO,EAAE,EAAE;IACnD,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,GAAG,CAAC,aAAa,CAAC,EAAE,yBAAyB,EAAE,OAAO,CAAC,CAAC;IAC5E,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,GAAG,CAAC,SAAS,CAAC,EAAE,SAAS,EAAE,MAAM,CAAC,CAAC;IACvD,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;AAClB,CAAC,CAAC,CAAC;AAEH,mBAAmB;AACnB,WAAW,EAAE,CAAC"}

package/dist/mcp-standalone.d.ts

@@ -1,3 +1,3 @@
 #!/usr/bin/env node
-export {};
+import './applyDataDirEnv.js';
 //# sourceMappingURL=mcp-standalone.d.ts.map

package/dist/mcp-standalone.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"mcp-standalone.d.ts","sourceRoot":"","sources":["../src/mcp-standalone.ts"],"names":[],"mappings":""}
+{"version":3,"file":"mcp-standalone.d.ts","sourceRoot":"","sources":["../src/mcp-standalone.ts"],"names":[],"mappings":";AAEA,OAAO,sBAAsB,CAAC"}

package/dist/mcp-standalone.js

@@ -1,4 +1,5 @@
 #!/usr/bin/env node
+import './applyDataDirEnv.js';
 import { Server } from '@modelcontextprotocol/sdk/server/index.js';
 import { StdioServerTransport } from '@modelcontextprotocol/sdk/server/stdio.js';
 import { CallToolRequestSchema, ListToolsRequestSchema, InitializeRequestSchema } from '@modelcontextprotocol/sdk/types.js';
@@ -6,10 +7,12 @@ import { createAuditRunner } from './auditRunner.js';
 import { syncFileIndex, searchFunctions, findDefinition, clearIndex } from './codeIndexService.js';
 import { CodeIndexDB } from './codeIndexDB.js';
 import { ConfigGeneratorFactory } from './generators/ConfigGeneratorFactory.js';
-import { IS_DEV_MODE } from './constants.js';
+import { IS_DEV_MODE, PACKAGE_VERSION } from './constants.js';
 import { scanFunctionsInDirectory } from './functionScanner.js';
 import path from 'node:path';
 import chalk from 'chalk';
+import { assertAuditPathExists, formatMcpToolErrorPayload } from './mcpToolErrors.js';
+import { logMcpInfo, mcpDebugStderr } from './mcpDiagnostics.js';
 import { createWriteStream } from 'node:fs';
 // Set up file logging (only in development mode)
 let logStream = null;
@@ -181,13 +184,13 @@ const tools = [
     },
     {
         name: 'sync_index',
-        description: 'Synchronize, cleanup, or reset the code index',
+        description: 'Synchronize, cleanup, or reset analysis-derived data (indexed functions, cached audits, code maps, schema overlays). Project tasks, analyzer configs, and whitelist entries are preserved on reset.',
         parameters: [
             {
                 name: 'mode',
                 type: 'string',
                 required: false,
-                description: 'Operation mode: sync (update), cleanup (remove stale), or reset (clear all)',
+                description: 'sync: update index from files; cleanup: remove index rows for deleted files; reset: clear all analysis-derived data (not tasks/config/whitelist)',
                 default: 'sync',
                 enum: ['sync', 'cleanup', 'reset'],
             },
@@ -388,6 +391,124 @@ const tools = [
             },
         ],
     },
+    {
+        name: 'project_tasks',
+        description: 'Manage a persistent per-project task queue. Tasks and analyzer configs survive sync_index reset; reset clears function index, cached audits, code maps, and schema overlays. Use delete to remove a task.',
+        parameters: [
+            {
+                name: 'action',
+                type: 'string',
+                required: true,
+                description: 'list | create | get | update | delete. list/create use projectPath or default to process.cwd(); create also needs title; get/update/delete need taskId; update needs patch object.',
+                enum: ['list', 'create', 'get', 'update', 'delete'],
+            },
+            {
+                name: 'projectPath',
+                type: 'string',
+                required: false,
+                description: 'Project root (resolved). Omit to use the MCP server working directory; response includes projectPathDefaulted when omitted.',
+            },
+            {
+                name: 'taskId',
+                type: 'string',
+                required: false,
+                description: 'Stable task id (UUID). Required for get, update, delete.',
+            },
+            {
+                name: 'title',
+                type: 'string',
+                required: false,
+                description: 'Task title. Required for create.',
+            },
+            {
+                name: 'description',
+                type: 'string',
+                required: false,
+                description: 'Longer description / notes.',
+            },
+            {
+                name: 'status',
+                type: 'string',
+                required: false,
+                description: 'pending | in_progress | blocked | done | cancelled. Filter for list; initial status for create; can be set via update patch.',
+                enum: ['pending', 'in_progress', 'blocked', 'done', 'cancelled'],
+            },
+            {
+                name: 'priority',
+                type: 'string',
+                required: false,
+                description: 'Optional priority for create/update patch.',
+                enum: ['low', 'medium', 'high'],
+            },
+            {
+                name: 'labels',
+                type: 'array',
+                required: false,
+                description: 'String tags (e.g. ["audit","refactor"]).',
+            },
+            {
+                name: 'metadata',
+                type: 'object',
+                required: false,
+                description: 'Arbitrary JSON object: related file paths, links, audit IDs, etc.',
+            },
+            {
+                name: 'parentTaskId',
+                type: 'string',
+                required: false,
+                description: 'Optional parent task for subtasks.',
+            },
+            {
+                name: 'source',
+                type: 'string',
+                required: false,
+                description: 'manual | audit | mcp. Filter for list; provenance for create; can be set via update patch.',
+                enum: ['manual', 'audit', 'mcp'],
+            },
+            {
+                name: 'blockedBy',
+                type: 'array',
+                required: false,
+                description: 'Task IDs this item is blocked by (waiting-on).',
+            },
+            {
+                name: 'dueAt',
+                type: 'string',
+                required: false,
+                description: 'ISO 8601 due datetime for create; omit or null in patch to clear.',
+            },
+            {
+                name: 'sortOrder',
+                type: 'number',
+                required: false,
+                description: 'Lower numbers sort first within a project (default 0).',
+            },
+            {
+                name: 'relatedFiles',
+                type: 'array',
+                required: false,
+                description: 'Repo-relative or absolute file paths tied to the task.',
+            },
+            {
+                name: 'relatedSymbols',
+                type: 'array',
+                required: false,
+                description: 'Function, class, or component names for cross-linking.',
+            },
+            {
+                name: 'patch',
+                type: 'object',
+                required: false,
+                description: 'For update: partial fields (title, description, status, priority, labels, metadata, parentTaskId, source, blockedBy, dueAt, sortOrder, relatedFiles, relatedSymbols).',
+            },
+            {
+                name: 'limit',
+                type: 'number',
+                required: false,
+                description: 'Max tasks to return for list (default 500, max 1000).',
+            },
+        ],
+    },
 ];
 function getAllViolations(result) {
     const violations = [];
@@ -424,29 +545,27 @@ function calculateHealthScore(result) {
     return Math.max(0, Math.round(Math.min(100, score)));
 }
 async function startMcpServer() {
-    console.error(chalk.blue('[INFO]'), 'Starting Code Auditor MCP Server (standalone)...');
-    console.error(chalk.blue('[DEBUG]'), `Process PID: ${process.pid}`);
-    console.error(chalk.blue('[DEBUG]'), `Node version: ${process.version}`);
-    console.error(chalk.blue('[DEBUG]'), `Working directory: ${process.cwd()}`);
+    logMcpInfo('startup', `code-auditor-mcp ${PACKAGE_VERSION} (standalone stdio)`, {
+        pid: process.pid,
+        cwd: process.cwd(),
+        dataDir: process.env.CODE_AUDITOR_DATA_DIR ?? '(default)'
+    });
+    mcpDebugStderr(chalk.blue('[DEBUG]'), `Node ${process.version} · cwd ${process.cwd()}`);
     const server = new Server({
         name: 'code-auditor',
+        version: PACKAGE_VERSION,
     }, {
         capabilities: {
             tools: {},
         },
     });
-    console.error(chalk.blue('[INFO]'), 'Server instance created');
-    console.error(chalk.blue('[DEBUG]'), 'Server capabilities:', JSON.stringify({ tools: {} }));
     // Add error handler
     server.onerror = (error) => {
         console.error(chalk.red('[ERROR]'), 'Server error occurred:', error);
         console.error(chalk.red('[ERROR]'), 'Error stack:', error.stack);
     };
-    // Handle tool listing
-    console.error(chalk.blue('[INFO]'), 'Setting up request handlers...');
     server.setRequestHandler(ListToolsRequestSchema, async (request) => {
-        console.error(chalk.blue('[DEBUG]'), 'Received ListTools request');
-        console.error(chalk.blue('[DEBUG]'), 'Request:', JSON.stringify(request, null, 2));
+        mcpDebugStderr(chalk.blue('[DEBUG]'), 'ListTools', JSON.stringify(request, null, 2));
         const response = {
             tools: tools.map(tool => ({
                 name: tool.name,
@@ -466,15 +585,11 @@ async function startMcpServer() {
                 },
             })),
         };
-        console.error(chalk.blue('[DEBUG]'), `Returning ${response.tools.length} tools`);
-        console.error(chalk.blue('[DEBUG]'), 'ListTools response:', JSON.stringify(response, null, 2));
+        mcpDebugStderr(chalk.blue('[DEBUG]'), `ListTools → ${response.tools.length} tools`);
         return response;
     });
-    console.error(chalk.blue('[INFO]'), `Registered ${tools.length} tools`);
-    // Add handler for initialize request
     server.setRequestHandler(InitializeRequestSchema, async (request) => {
-        console.error(chalk.blue('[DEBUG]'), 'Received initialize request');
-        console.error(chalk.blue('[DEBUG]'), 'Request:', JSON.stringify(request, null, 2));
+        mcpDebugStderr(chalk.blue('[DEBUG]'), 'initialize', JSON.stringify(request, null, 2));
         const response = {
             protocolVersion: '2024-11-05',
             capabilities: {
@@ -482,21 +597,17 @@ async function startMcpServer() {
             },
             serverInfo: {
                 name: 'code-auditor',
-                version: '1.0.0',
+                version: PACKAGE_VERSION,
             },
         };
-        console.error(chalk.blue('[DEBUG]'), 'Initialize response:', JSON.stringify(response, null, 2));
+        mcpDebugStderr(chalk.blue('[DEBUG]'), 'initialize response', JSON.stringify(response, null, 2));
         return response;
     });
-    // Handle tool execution
     server.setRequestHandler(CallToolRequestSchema, async (request) => {
-        console.error(chalk.blue('[DEBUG]'), 'Received CallTool request');
-        console.error(chalk.blue('[DEBUG]'), 'Request:', JSON.stringify(request, null, 2));
+        mcpDebugStderr(chalk.blue('[DEBUG]'), 'CallTool raw', JSON.stringify(request, null, 2));
         const { name, arguments: args } = request.params;
-        console.error(chalk.blue('[DEBUG]'), `Tool name: ${name}`);
-        console.error(chalk.blue('[DEBUG]'), `Tool arguments:`, JSON.stringify(args, null, 2));
+        mcpDebugStderr(chalk.blue('[DEBUG]'), `CallTool ${name}`, JSON.stringify(args, null, 2));
         try {
-            console.error(chalk.blue('[DEBUG]'), `Starting tool execution for: ${name}`);
             let result;
             switch (name) {
                 case 'audit': {
@@ -504,19 +615,20 @@ async function startMcpServer() {
                     const indexFunctions = args.indexFunctions !== false; // Default true
                     const analyzers = args.analyzers || ['solid', 'dry'];
                     const minSeverity = args.minSeverity;
-                    const limit = Math.min(args.limit || 50, 100); // Max 100
-                    const offset = args.offset || 0;
+                    const limit = Math.min(Math.max(0, Number(args.limit)) || 50, 100); // Max 100
+                    const offset = Math.max(0, Number(args.offset) || 0);
                     const useCache = args.useCache !== false; // Default true
                     const providedAuditId = args.auditId;
                     let auditResult;
                     let auditId = providedAuditId;
+                    const db = CodeIndexDB.getInstance();
+                    await db.initialize();
                     // Check if we should use cached results
                     if (providedAuditId) {
-                        const db = CodeIndexDB.getInstance();
                         const cachedResult = await db.getAuditResults(providedAuditId);
                         if (cachedResult) {
                             auditResult = cachedResult;
-                            console.error(chalk.blue('[INFO]'), `Using cached audit results: ${providedAuditId}`);
+                            mcpDebugStderr(chalk.blue('[INFO]'), `Using cached audit results: ${providedAuditId}`);
                         }
                         else {
                             console.error(chalk.yellow('[WARN]'), `Cached audit not found: ${providedAuditId}, running new audit`);
@@ -524,9 +636,8 @@ async function startMcpServer() {
                     }
                     // Run new audit if no cached result
                     if (!auditResult) {
+                        await assertAuditPathExists(auditPath);
                         // Get stored analyzer configs from database
-                        const db = CodeIndexDB.getInstance();
-                        await db.initialize();
                         const storedConfigs = await db.getAllAnalyzerConfigs(auditPath);
                         // Merge stored configs with any provided configs
                         const analyzerConfigs = {
@@ -545,9 +656,8 @@ async function startMcpServer() {
                         const runResult = await runner.run();
                         // Store in cache if requested
                         if (useCache) {
-                            const db = CodeIndexDB.getInstance();
                             auditId = await db.storeAuditResults(runResult, auditPath);
-                            console.error(chalk.blue('[INFO]'), `Stored audit results with ID: ${auditId}`);
+                            mcpDebugStderr(chalk.blue('[INFO]'), `Stored audit results with ID: ${auditId}`);
                         }
                         auditResult = runResult;
                     }
@@ -569,14 +679,14 @@ async function startMcpServer() {
                                 failed: 0,
                                 syncStats
                             };
-                            console.error(chalk.blue('[INFO]'), `Synced functions: ${syncStats.added} added, ${syncStats.updated} updated, ${syncStats.removed} removed`);
+                            mcpDebugStderr(chalk.blue('[INFO]'), `Synced functions: ${syncStats.added} added, ${syncStats.updated} updated, ${syncStats.removed} removed`);
                             // Auto-detect and populate whitelist entries after indexing
                             try {
                                 const { WhitelistService } = await import('./services/whitelistService.js');
                                 const whitelistService = WhitelistService.getInstance();
                                 const whitelistResult = await whitelistService.whitelistAllDependencies(auditPath);
                                 if (whitelistResult.added > 0) {
-                                    console.error(chalk.blue('[INFO]'), `Auto-added ${whitelistResult.added} whitelist entries`);
+                                    mcpDebugStderr(chalk.blue('[INFO]'), `Auto-added ${whitelistResult.added} whitelist entries`);
                                 }
                             }
                             catch (error) {
@@ -618,6 +728,7 @@ async function startMcpServer() {
                 }
                 case 'audit_health': {
                     const auditPath = path.resolve(args.path || process.cwd());
+                    await assertAuditPathExists(auditPath);
                     const indexFunctions = args.indexFunctions !== false; // Default true
                     // Get stored analyzer configs from database
                     const db = CodeIndexDB.getInstance();
@@ -656,7 +767,7 @@ async function startMcpServer() {
                                 failed: 0,
                                 syncStats
                             };
-                            console.error(chalk.blue('[INFO]'), `Synced functions: ${syncStats.added} added, ${syncStats.updated} updated, ${syncStats.removed} removed`);
+                            mcpDebugStderr(chalk.blue('[INFO]'), `Synced functions: ${syncStats.added} added, ${syncStats.updated} updated, ${syncStats.removed} removed`);
                         }
                         catch (error) {
                             console.error(chalk.yellow('[WARN]'), 'Failed to index functions:', error);
@@ -767,7 +878,7 @@ async function startMcpServer() {
                             result = {
                                 success: true,
                                 mode: 'reset',
-                                message: 'Index cleared successfully'
+                                message: 'Analysis-derived data cleared (functions, search index, cached audits, code maps, schemas). Project tasks, whitelist, and analyzer configs were preserved.'
                             };
                             break;
                         }
@@ -961,6 +1072,11 @@ async function startMcpServer() {
                     result = await handleWhitelistDetect(args);
                     break;
                 }
+                case 'project_tasks': {
+                    const { handleProjectTasks } = await import('./mcp-tools/projectTasks.js');
+                    result = await handleProjectTasks((args || {}));
+                    break;
+                }
                 default:
                     throw new Error(`Unknown tool: ${name}`);
             }
@@ -972,8 +1088,7 @@ async function startMcpServer() {
                     },
                 ],
             };
-            console.error(chalk.blue('[DEBUG]'), `Tool ${name} executed successfully`);
-            console.error(chalk.blue('[DEBUG]'), 'CallTool response:', JSON.stringify(response, null, 2).substring(0, 500) + '...');
+            mcpDebugStderr(chalk.blue('[DEBUG]'), `Tool ${name} ok`, JSON.stringify(response, null, 2).substring(0, 500) + '...');
             return response;
         }
         catch (error) {
@@ -983,19 +1098,14 @@ async function startMcpServer() {
                 content: [
                     {
                         type: 'text',
-                        text: JSON.stringify({
-                            error: error instanceof Error ? error.message : 'Unknown error',
-                            tool: name,
-                        }),
+                        text: JSON.stringify(formatMcpToolErrorPayload(name, error), null, 2),
                     },
                 ],
                 isError: true,
             };
         }
     });
-    console.error(chalk.blue('[INFO]'), 'Request handlers configured');
     const transport = new StdioServerTransport();
-    console.error(chalk.blue('[INFO]'), 'Creating stdio transport...');
     // Add transport event handlers if available
     if (transport.onclose) {
         transport.onclose = () => {
@@ -1007,16 +1117,13 @@ async function startMcpServer() {
             console.error(chalk.red('[ERROR]'), 'Transport error:', error);
         };
     }
-    console.error(chalk.blue('[DEBUG]'), 'Connecting server to transport...');
     await server.connect(transport);
-    console.error(chalk.blue('[DEBUG]'), 'Server connected to transport');
     console.error(chalk.green('✓ Code Auditor MCP Server started (standalone mode)'));
-    console.error(chalk.gray('Listening on stdio...'));
-    console.error(chalk.blue('[DEBUG]'), 'Server state after initialization:', {
+    console.error(chalk.gray(`Listening on stdio · ${tools.length} tools · ${PACKAGE_VERSION}`));
+    mcpDebugStderr(chalk.blue('[DEBUG]'), 'Server ready', {
         name: 'code-auditor',
         transport: 'stdio',
-        handlers: ['ListTools', 'CallTool', 'initialize'],
-        toolCount: tools.length,
+        toolCount: tools.length
     });
 }
 // Error handlers
@@ -1048,8 +1155,6 @@ process.stdin.on('error', (error) => {
 process.stdout.on('error', (error) => {
     console.error(chalk.red('[ERROR]'), 'stdout error:', error);
 });
-// Start server
-console.error(chalk.blue('[INFO]'), 'Initializing server...');
 startMcpServer().catch(error => {
     console.error(chalk.red('[ERROR]'), 'Failed to start MCP server:', error);
     console.error(chalk.red('[ERROR]'), 'Stack:', error.stack);