code-auditor-mcp 2.0.3 → 2.2.1

package/README.md

@@ -57,6 +57,9 @@ You: "Set SOLID analyzer to allow 3 responsibilities for components"
 Claude: Configuration saved! All future audits will use this setting.
 ```
 
+### 📋 Project task queue (MCP)
+Use the **`project_tasks`** tool to keep a per-project task list in the local database (titles, status, priorities, due dates, blockers, related files/symbols, and more). **Tasks survive `sync_index` reset**: clearing the analysis index removes indexed functions, cached audits, code maps, and schema overlays so you do not keep “ghost” references to deleted code—it does **not** delete your task list or analyzer configs.
+
 ## Real Examples
 
 ### Example 1: Finding Authentication Patterns
@@ -89,18 +92,30 @@ Claude: Found 4 similar components:
 
 ## Installation Options
 
-### Global Install
+### Published package (npm / pnpm / yarn)
 ```bash
 npm install -g code-auditor-mcp
+# or: pnpm add -g code-auditor-mcp
 code-audit  # Run analysis
 ```
 
-### Project Install
+### Project install
 ```bash
-npm install --save-dev code-auditor
+npm install --save-dev code-auditor-mcp
 npx code-audit
 ```
 
+### Developing from this repository
+Requires **Node.js 18+**. From the `app/` directory:
+
+```bash
+pnpm install
+pnpm run build
+pnpm test
+```
+
+The package manager in use is **pnpm** (see `packageManager` in `package.json`). Use `pnpm run test:parity` only if you need the legacy vs universal analyzer parity suite.
+
 ### CI/CD Integration
 ```yaml
 # GitHub Actions
@@ -108,6 +123,29 @@ npx code-audit
   run: npx code-audit --fail-on-critical
 ```
 
+### MCP server: where the index is stored
+
+The Loki index file defaults to **`<current working directory>/.code-index/index.db`**. If your MCP host runs with an unexpected or shared `cwd`, point at a dedicated folder:
+
+- **Environment variable** `CODE_AUDITOR_DATA_DIR` — directory to use as the storage root (absolute or relative to the process cwd when the server starts). The database file is **`<resolved>/index.db`** (no extra `.code-index` segment).
+- **CLI** — `node dist/mcp-index.js --data-dir /path/to/data` (equivalent to setting the env var). The published binary `code-auditor-mcp` also accepts `--data-dir` because it loads the same bootstrap.
+
+Example **Cursor** `.cursor/mcp.json` fragment:
+
+```json
+{
+  "mcpServers": {
+    "code-auditor": {
+      "command": "node",
+      "args": ["/absolute/path/to/code-auditor/app/dist/mcp-index.js", "--stdio"],
+      "env": {
+        "CODE_AUDITOR_DATA_DIR": "/Users/you/Library/Application Support/code-auditor"
+      }
+    }
+  }
+}
+```
+
 ## Key Commands
 
 ```bash

package/dist/applyDataDirEnv.d.ts

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=applyDataDirEnv.d.ts.map

package/dist/applyDataDirEnv.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"applyDataDirEnv.d.ts","sourceRoot":"","sources":["../src/applyDataDirEnv.ts"],"names":[],"mappings":""}

package/dist/applyDataDirEnv.js

@@ -0,0 +1,21 @@
+/**
+ * Parse --data-dir before any module loads CodeIndexDB.getInstance().
+ * Sets CODE_AUDITOR_DATA_DIR to an absolute path (resolved from cwd if relative).
+ */
+import path from 'node:path';
+const argv = process.argv.slice(2);
+for (let i = 0; i < argv.length; i++) {
+    const a = argv[i];
+    if (a === '--data-dir' || a === '--dataDir') {
+        const val = argv[i + 1];
+        if (val && !val.startsWith('-')) {
+            process.env.CODE_AUDITOR_DATA_DIR = path.resolve(val);
+        }
+        else {
+            // stderr only; avoids silent failure when e.g. `--data-dir --ui` skips the path
+            console.error('[code-auditor] --data-dir requires a directory path (next argv). Using CODE_AUDITOR_DATA_DIR env or default .code-index/.');
+        }
+        break;
+    }
+}
+//# sourceMappingURL=applyDataDirEnv.js.map

package/dist/applyDataDirEnv.js.map

@@ -0,0 +1 @@
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package/dist/auditRunner.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"auditRunner.d.ts","sourceRoot":"","sources":["../src/auditRunner.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAIH,OAAO,EACL,WAAW,EACX,kBAAkB,EAClB,kBAAkB,EAKnB,MAAM,YAAY,CAAC;AAgCpB;;GAEG;AACH,wBAAgB,iBAAiB,CAAC,OAAO,GAAE,kBAAuB;iCAM5B,kBAAkB,KAAG,IAAI;oCAOhB,MAAM,KAAG,OAAO,CAAC,kBAAkB,CAAC;uBAQjD,kBAAkB,KAAG,OAAO,CAAC,WAAW,CAAC;6BA0K1B,WAAW,UAAU,MAAM,KAAG,OAAO,CAAC,MAAM,CAAC;EAU7F;AAgGD;;GAEG;AACH,wBAAsB,QAAQ,CAAC,OAAO,CAAC,EAAE,kBAAkB,GAAG,OAAO,CAAC,WAAW,CAAC,CAGjF;AAED,OAAO,EAAE,aAAa,EAAE,kBAAkB,EAAE,MAAM,YAAY,CAAC"}

package/dist/auditRunner.js

@@ -2,10 +2,12 @@
  * Audit Runner (Functional)
  * Main orchestrator for running code audits
  */
+import path from 'path';
 import { discoverFiles } from './utils/fileDiscovery.js';
 import { loadConfig } from './config/configLoader.js';
 import { generateReport } from './reporting/reportGenerator.js';
 import { extractFunctionsFromFile } from './functionScanner.js';
+import { isMcpDebugEnabled, logMcpDebug, logMcpInfo } from './mcpDiagnostics.js';
 // Import analyzer definitions
 // Use compatibility layers for refactored analyzers
 import { createSOLIDAnalyzer } from './adapters/solidAnalyzerCompat.js';
@@ -60,6 +62,12 @@ export function createAuditRunner(options = {}) {
         });
         // Discover files
         const files = await discoverProjectFiles(mergedOptions);
+        const root = mergedOptions.projectRoot || process.cwd();
+        logMcpInfo('discovery', 'file discovery finished', {
+            projectRoot: path.resolve(root),
+            totalFiles: files.length,
+            indexFunctions: !!mergedOptions.indexFunctions
+        });
         // Collect functions if enabled
         let collectedFunctions = [];
         const fileToFunctionsMap = new Map(); // Track functions per file for sync
@@ -72,8 +80,17 @@ export function createAuditRunner(options = {}) {
             // Note: Go files will be indexed by the Universal SOLID analyzer directly
             const scriptFiles = files.filter(f => f.endsWith('.ts') || f.endsWith('.tsx') ||
                 f.endsWith('.js') || f.endsWith('.jsx'));
+            logMcpInfo('function-indexing', 'extracting functions from script files', {
+                scriptFileCount: scriptFiles.length
+            });
             for (let i = 0; i < scriptFiles.length; i++) {
                 try {
+                    if (i > 0 && i % 50 === 0) {
+                        logMcpInfo('function-indexing', 'progress', {
+                            current: i,
+                            total: scriptFiles.length
+                        });
+                    }
                     const fileFunctions = await extractFunctionsFromFile(scriptFiles[i], {
                         unusedImportsConfig: mergedOptions.unusedImportsConfig
                     });
@@ -85,23 +102,33 @@ export function createAuditRunner(options = {}) {
                         total: scriptFiles.length,
                         message: `Collected ${fileFunctions.length} items from ${scriptFiles[i]}`
                     });
+                    if (isMcpDebugEnabled()) {
+                        logMcpDebug('function-indexing', scriptFiles[i], {
+                            symbols: fileFunctions.length
+                        });
+                    }
                 }
                 catch (error) {
-                    // Log error but continue with other files
-                    console.warn(`Failed to extract functions from ${scriptFiles[i]}:`, error);
+                    logMcpInfo('function-indexing', 'extract failed (continuing)', {
+                        file: scriptFiles[i],
+                        error: error instanceof Error ? error.message : String(error)
+                    });
                 }
             }
         }
         // Run analyzers
         const analyzerResults = {};
         const enabledAnalyzers = getEnabledAnalyzers(mergedOptions, analyzerRegistry);
-        console.log('[DEBUG] Enabled analyzers:', enabledAnalyzers);
-        console.log('[DEBUG] Available analyzers in registry:', Object.keys(analyzerRegistry));
+        logMcpInfo('analysis', 'enabled analyzers', {
+            names: enabledAnalyzers,
+            fileCount: files.length
+        });
+        logMcpDebug('analysis', 'registry keys', { keys: Object.keys(analyzerRegistry) });
         for (const analyzerName of enabledAnalyzers) {
             const analyzer = analyzerRegistry[analyzerName];
-            console.log(`[DEBUG] Processing analyzer: ${analyzerName}, found: ${!!analyzer}`);
+            logMcpDebug('analysis', `starting analyzer ${analyzerName}`, { found: !!analyzer });
             if (!analyzer) {
-                console.warn(`Unknown analyzer: ${analyzerName}`);
+                logMcpInfo('analysis', `unknown analyzer skipped: ${analyzerName}`, {});
                 continue;
             }
             reportProgress(mergedOptions, {
@@ -109,11 +136,7 @@ export function createAuditRunner(options = {}) {
                 analyzer: analyzerName,
                 message: `Running ${analyzerName} analyzer...`
             });
-            console.log(`[DEBUG] About to call ${analyzerName}.analyze()`);
-            console.log(`[DEBUG] Analyzer object:`, analyzer);
-            console.log(`[DEBUG] Analyzer.analyze type:`, typeof analyzer.analyze);
-            console.log(`[DEBUG] Files to analyze:`, files);
-            console.log(`[DEBUG] Config for analyzer:`, mergedOptions.analyzerConfigs?.[analyzerName] || {});
+            logMcpInfo('analysis', `running ${analyzerName}`, { fileCount: files.length });
             try {
                 const result = await analyzer.analyze(files, mergedOptions.analyzerConfigs?.[analyzerName] || {}, mergedOptions, (progress) => {
                     reportProgress(mergedOptions, {
@@ -123,8 +146,19 @@ export function createAuditRunner(options = {}) {
                         total: progress.total,
                         message: `Analyzing ${progress.file}...`
                     });
+                    if (isMcpDebugEnabled() && progress.current && progress.total) {
+                        if (progress.current % 20 === 0 || progress.current === progress.total) {
+                            logMcpDebug('analysis', `${analyzerName} file progress`, {
+                                current: progress.current,
+                                total: progress.total,
+                                file: progress.file
+                            });
+                        }
+                    }
+                });
+                logMcpDebug('analysis', `${analyzerName} completed`, {
+                    violations: result.violations?.length ?? 0
                 });
-                console.log(`[DEBUG] ${analyzerName}.analyze() returned:`, result);
                 analyzerResults[analyzerName] = result;
             }
             catch (error) {
@@ -192,7 +226,8 @@ async function discoverProjectFiles(options) {
  * Get list of enabled analyzers
  */
 function getEnabledAnalyzers(options, registry) {
-    if (options.enabledAnalyzers && options.enabledAnalyzers.length > 0) {
+    // Explicit array (including empty = run no analyzers, e.g. index-only harness)
+    if (options.enabledAnalyzers !== undefined) {
         return options.enabledAnalyzers;
     }
     return Object.keys(registry);

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package/dist/codeIndexDB-enhanced.d.ts

@@ -2,7 +2,6 @@
  * Enhanced Code Index Database for Cross-Language Support
  * Extends the existing CodeIndexDB with multi-language capabilities
  */
-import Loki from 'lokijs';
 import { CodeIndexDB } from './codeIndexDB.js';
 import { CrossLanguageEntity, CrossReference, APIContract, CrossLanguageSearchOptions, CrossLanguageSearchResult, CrossLanguageAnalysisResult, DependencyGraph, MigrationOptions } from './types/crossLanguage.js';
 /**
@@ -73,8 +72,8 @@ export declare class EnhancedCodeIndexDB extends CodeIndexDB {
      */
     private generateSearchTokens;
     /**
-     * Get access to the underlying database for advanced operations
+     * Also clears cross-language derived collections and their FlexSearch mirror when present.
      */
-    getDatabase(): Loki;
+    clearIndex(): Promise<void>;
 }
 //# sourceMappingURL=codeIndexDB-enhanced.d.ts.map

package/dist/codeIndexDB-enhanced.d.ts.map

@@ -1 +1 @@
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package/dist/codeIndexDB-enhanced.js

@@ -90,17 +90,28 @@ export class EnhancedCodeIndexDB extends CodeIndexDB {
      */
     async initializeEnhanced() {
         await this.initialize(); // Initialize base collections first
-        // Initialize cross-language collections
-        this.crossLanguageEntitiesCollection = this.getDatabase().addCollection('crossLanguageEntities', {
-            indices: ['id', 'name', 'language', 'type', 'file'],
-            unique: ['id']
-        });
-        this.crossReferencesCollection = this.getDatabase().addCollection('crossReferences', {
-            indices: ['sourceId', 'targetId', 'sourceLanguage', 'targetLanguage', 'type']
-        });
-        this.apiContractsCollection = this.getDatabase().addCollection('apiContracts', {
-            indices: ['entityId', 'version']
-        });
+        this.crossLanguageEntitiesCollection =
+            this.db.getCollection('crossLanguageEntities') ||
+                this.db.addCollection('crossLanguageEntities', {
+                    indices: ['id', 'name', 'language', 'type', 'file'],
+                    unique: ['id']
+                });
+        this.crossReferencesCollection =
+            this.db.getCollection('crossReferences') ||
+                this.db.addCollection('crossReferences', {
+                    indices: [
+                        'sourceId',
+                        'targetId',
+                        'sourceLanguage',
+                        'targetLanguage',
+                        'type'
+                    ]
+                });
+        this.apiContractsCollection =
+            this.db.getCollection('apiContracts') ||
+                this.db.addCollection('apiContracts', {
+                    indices: ['entityId', 'version']
+                });
         console.log('[EnhancedCodeIndexDB] Cross-language collections initialized');
     }
     /**
@@ -402,11 +413,26 @@ export class EnhancedCodeIndexDB extends CodeIndexDB {
         return Array.from(tokens);
     }
     /**
-     * Get access to the underlying database for advanced operations
+     * Also clears cross-language derived collections and their FlexSearch mirror when present.
      */
-    getDatabase() {
-        // Protected method to access the underlying database
-        return this.db;
+    async clearIndex() {
+        await super.clearIndex();
+        const ldb = this.db;
+        const names = [
+            'crossLanguageEntities',
+            'crossReferences',
+            'apiContracts'
+        ];
+        for (const n of names) {
+            const c = ldb.getCollection(n);
+            if (c) {
+                c.clear();
+            }
+        }
+        if (this.crossLanguageSearchIndex) {
+            this.crossLanguageSearchIndex.clear();
+        }
+        ldb.saveDatabase();
     }
 }
 /**

package/dist/codeIndexDB-enhanced.js.map

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package/dist/codeIndexDb.d.ts

@@ -2,11 +2,14 @@
  * Code Index Database using LokiJS + FlexSearch
  * Pure JavaScript implementation with no native dependencies
  */
+import Loki from 'lokijs';
+import type { CreateProjectTaskInput, ProjectTask, ProjectTaskSource, ProjectTaskStatus } from './types/projectTask.js';
 import { EnhancedFunctionMetadata, FunctionMetadata, SearchResult, SearchOptions, SchemaDefinition, SchemaIndexMetadata, SchemaUsage } from './types.js';
 import { WhitelistEntry, WhitelistType, WhitelistStatus, WhitelistSuggestion } from './types/whitelist.js';
 export declare class CodeIndexDB {
     private static instance;
-    private db;
+    /** Subclasses (e.g. EnhancedCodeIndexDB) need access for extra collections without `as any`. */
+    protected db: Loki;
     private functionsCollection;
     private whitelistCollection;
     private auditResultsCollection;
@@ -14,6 +17,9 @@ export declare class CodeIndexDB {
     private codeMapCollection;
     private schemaCollection;
     private schemaUsageCollection;
+    /** User tasks: NOT cleared by clearIndex() — see clearIndex() */
+    private tasksCollection;
+    private taskRepository;
     private searchIndex;
     private dbPath;
     private isInitialized;
@@ -158,8 +164,19 @@ export declare class CodeIndexDB {
         filesIndexed: number;
         lastUpdated: Date;
     }>;
+    /**
+     * Drops analysis-derived data so search, cached audits, code maps, and schema overlays
+     * cannot reference removed or stale code ("ghost" analysis).
+     *
+     * Clears: indexed functions, FlexSearch, auditResults, codeMaps, schemas, schemaUsage.
+     * Preserves: projectTasks, analyzerConfigs, whitelist (user rules, not mirrored code).
+     *
+     * When adding collections that store derived code intelligence, clear them here unless
+     * they are durable user preferences (same category as analyzerConfigs).
+     */
     clearIndex(): Promise<void>;
     close(): Promise<void>;
+    private getTaskRepository;
     /**
      * Synchronize a single file's functions with the index
      * Adds new functions, updates existing ones, and removes deleted ones
@@ -361,5 +378,17 @@ export declare class CodeIndexDB {
             usageType: string;
         }>;
     }>;
+    createProjectTask(input: CreateProjectTaskInput): Promise<ProjectTask>;
+    getProjectTask(taskId: string): Promise<ProjectTask | null>;
+    listProjectTasks(projectPath: string, options?: {
+        status?: ProjectTaskStatus;
+        source?: ProjectTaskSource;
+        limit?: number;
+    }): Promise<ProjectTask[]>;
+    /**
+     * @param patch Raw JSON-shaped update; unknown keys are ignored (see sanitizeUpdatePatch).
+     */
+    updateProjectTask(taskId: string, patch: unknown): Promise<ProjectTask | null>;
+    deleteProjectTask(taskId: string): Promise<boolean>;
 }
 //# sourceMappingURL=codeIndexDB.d.ts.map

package/dist/codeIndexDb.d.ts.map

@@ -1 +1 @@
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