code-auditor-mcp 2.0.2 → 2.2.0

package/dist/codeIndexDB-enhanced.js.map

@@ -1 +1 @@
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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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+{"version":3,"file":"codeIndexDB.d.ts","sourceRoot":"","sources":["../src/codeIndexDB.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,IAAoB,MAAM,QAAQ,CAAC;AAI1C,OAAO,KAAK,EACV,sBAAsB,EACtB,WAAW,EAEX,iBAAiB,EACjB,iBAAiB,EAClB,MAAM,wBAAwB,CAAC;AAEhC,OAAO,EACL,wBAAwB,EACxB,gBAAgB,EAChB,YAAY,EACZ,aAAa,EAGb,gBAAgB,EAChB,mBAAmB,EACnB,WAAW,EACZ,MAAM,YAAY,CAAC;AAIpB,OAAO,EACL,cAAc,EACd,aAAa,EACb,eAAe,EACf,mBAAmB,EACpB,MAAM,sBAAsB,CAAC;AAU9B,qBAAa,WAAW;IACtB,OAAO,CAAC,MAAM,CAAC,QAAQ,CAAc;IACrC,gGAAgG;IAChG,SAAS,CAAC,EAAE,EAAE,IAAI,CAAC;IACnB,OAAO,CAAC,mBAAmB,CAA6C;IACxE,OAAO,CAAC,mBAAmB,CAAgC;IAC3D,OAAO,CAAC,sBAAsB,CAAgC;IAC9D,OAAO,CAAC,wBAAwB,CAAgC;IAChE,OAAO,CAAC,iBAAiB,CAAgC;IACzD,OAAO,CAAC,gBAAgB,CAAgC;IACxD,OAAO,CAAC,qBAAqB,CAAgC;IAC7D,iEAAiE;IACjE,OAAO,CAAC,eAAe,CAAgD;IACvE,OAAO,CAAC,cAAc,CAAsC;IAC5D,OAAO,CAAC,WAAW,CAAM;IACzB,OAAO,CAAC,MAAM,CAAS;IACvB,OAAO,CAAC,aAAa,CAAS;gBAElB,MAAM,GAAE,MAAmB;IAsGvC,MAAM,CAAC,WAAW,CAAC,MAAM,CAAC,EAAE,MAAM,GAAG,WAAW;IAW1C,UAAU,IAAI,OAAO,CAAC,IAAI,CAAC;IA2IjC,OAAO,CAAC,iBAAiB;IAMzB;;;OAGG;IACH,OAAO,CAAC,qBAAqB;IA+B7B;;;OAGG;IACH,OAAO,CAAC,oBAAoB;IAkBtB,gBAAgB,CAAC,IAAI,EAAE,gBAAgB,GAAG,wBAAwB,GAAG,OAAO,CAAC,IAAI,CAAC;IA+BlF,iBAAiB,CAAC,SAAS,EAAE,CAAC,gBAAgB,GAAG,wBAAwB,CAAC,EAAE,GAAG,OAAO,CAAC;QAC3F,OAAO,EAAE,OAAO,CAAC;QACjB,UAAU,EAAE,MAAM,CAAC;QACnB,MAAM,EAAE,MAAM,CAAC;QACf,MAAM,CAAC,EAAE,KAAK,CAAC;YAAE,QAAQ,EAAE,MAAM,CAAC;YAAC,KAAK,EAAE,MAAM,CAAA;SAAE,CAAC,CAAC;KACrD,CAAC;IA4BF;;;;;OAKG;IACG,aAAa,CAAC,QAAQ,EAAE,MAAM,EAAE,gBAAgB,EAAE,CAAC,gBAAgB,GAAG,wBAAwB,CAAC,EAAE,GAAG,OAAO,CAAC;QAChH,KAAK,EAAE,MAAM,CAAC;QACd,OAAO,EAAE,MAAM,CAAC;QAChB,OAAO,EAAE,MAAM,CAAC;KACjB,CAAC;IAmEF;;;OAGG;IACG,qBAAqB,CAAC,QAAQ,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC;IA6C7D;;OAEG;IACH,OAAO,CAAC,2BAA2B;IAcnC;;OAEG;IACH,OAAO,CAAC,wBAAwB;IAIhC;;;;;OAKG;IACG,yBAAyB,CAC7B,YAAY,EAAE,MAAM,EACpB,QAAQ,GAAE,MAAW,GACpB,OAAO,CAAC,KAAK,CAAC;QAAE,IAAI,EAAE,MAAM,CAAC;QAAC,KAAK,EAAE,MAAM,CAAA;KAAE,CAAC,CAAC;IAyBlD;;;;;OAKG;IACG,oBAAoB,CACxB,YAAY,EAAE,MAAM,EACpB,QAAQ,GAAE,MAAW,GACpB,OAAO,CAAC,KAAK,CAAC;QAAE,IAAI,EAAE,MAAM,CAAC;QAAC,KAAK,EAAE,MAAM,CAAA;KAAE,CAAC,CAAC;IAyBlD;;;OAGG;IACG,0BAA0B,IAAI,OAAO,CAAC,KAAK,CAAC,MAAM,EAAE,CAAC,CAAC;IAoD5D;;;OAGG;IACG,yBAAyB,IAAI,OAAO,CAAC,IAAI,CAAC;IAwBhD;;OAEG;IACG,eAAe,IAAI,OAAO,CAAC,wBAAwB,EAAE,CAAC;IAoCtD,eAAe,CAAC,OAAO,EAAE,aAAa,GAAG,OAAO,CAAC,YAAY,CAAC;IA+IpE;;;;;OAKG;YACW,0BAA0B;IAuFxC;;OAEG;YACW,oBAAoB;IA6BlC;;OAEG;IACH,OAAO,CAAC,kBAAkB;IAkB1B;;OAEG;IACH,OAAO,CAAC,wBAAwB;IAqBhC;;OAEG;IACH,OAAO,CAAC,kBAAkB;IAa1B;;OAEG;IACH,OAAO,CAAC,qBAAqB;IAe7B;;OAEG;IACH,OAAO,CAAC,WAAW;IAKnB;;OAEG;IACH,OAAO,CAAC,uBAAuB;IAU/B;;OAEG;IACH,OAAO,CAAC,aAAa;IAgBrB;;OAEG;IACH,OAAO,CAAC,YAAY;IAyBpB;;OAEG;IACH,OAAO,CAAC,YAAY;IA6Jd,cAAc,CAAC,IAAI,EAAE,MAAM,EAAE,QAAQ,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC,wBAAwB,GAAG,IAAI,CAAC;IAezF,QAAQ,IAAI,OAAO,CAAC;QACxB,cAAc,EAAE,MAAM,CAAC;QACvB,SAAS,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;QAClC,eAAe,EAAE,KAAK,CAAC;YAAE,IAAI,EAAE,MAAM,CAAC;YAAC,KAAK,EAAE,MAAM,CAAA;SAAE,CAAC,CAAC;QACxD,YAAY,EAAE,MAAM,CAAC;QACrB,WAAW,EAAE,IAAI,CAAC;KACnB,CAAC;IAwCF;;;;;;;;;OASG;IACG,UAAU,IAAI,OAAO,CAAC,IAAI,CAAC;IAc3B,KAAK,IAAI,OAAO,CAAC,IAAI,CAAC;IAQ5B,OAAO,CAAC,iBAAiB;IAWzB;;;OAGG;IACG,eAAe,CAAC,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC;QAC/C,KAAK,EAAE,MAAM,CAAC;QACd,OAAO,EAAE,MAAM,CAAC;QAChB,OAAO,EAAE,MAAM,CAAC;KACjB,GAAG,IAAI,CAAC;IAuET;;;OAGG;IACG,WAAW,IAAI,OAAO,CAAC;QAC3B,YAAY,EAAE,MAAM,CAAC;QACrB,YAAY,EAAE,MAAM,CAAC;QACrB,YAAY,EAAE,MAAM,EAAE,CAAC;QACvB,MAAM,EAAE,KAAK,CAAC;YAAE,IAAI,EAAE,MAAM,CAAC;YAAC,KAAK,EAAE,MAAM,CAAA;SAAE,CAAC,CAAC;KAChD,CAAC;IAmDF;;;OAGG;IACG,QAAQ,CACZ,gBAAgB,CAAC,EAAE,CAAC,QAAQ,EAAE;QAAE,OAAO,EAAE,MAAM,CAAC;QAAC,KAAK,EAAE,MAAM,CAAC;QAAC,IAAI,EAAE,MAAM,CAAA;KAAE,KAAK,IAAI,GACtF,OAAO,CAAC;QACT,WAAW,EAAE,MAAM,CAAC;QACpB,cAAc,EAAE,MAAM,CAAC;QACvB,gBAAgB,EAAE,MAAM,CAAC;QACzB,gBAAgB,EAAE,MAAM,CAAC;QACzB,MAAM,EAAE,KAAK,CAAC;YAAE,IAAI,EAAE,MAAM,CAAC;YAAC,KAAK,EAAE,MAAM,CAAA;SAAE,CAAC,CAAC;KAChD,CAAC;IAuDF;;OAEG;YACW,oBAAoB;IAmIlC;;OAEG;YACW,2BAA2B;IAwEzC;;OAEG;IACG,YAAY,CAAC,IAAI,CAAC,EAAE,aAAa,EAAE,MAAM,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,cAAc,EAAE,CAAC;IAU7F;;OAEG;IACG,iBAAiB,CAAC,KAAK,EAAE,IAAI,CAAC,cAAc,EAAE,IAAI,GAAG,SAAS,CAAC,GAAG,OAAO,CAAC,cAAc,CAAC;IAW/F;;OAEG;IACG,qBAAqB,CAAC,IAAI,EAAE,MAAM,EAAE,MAAM,EAAE,eAAe,GAAG,OAAO,CAAC,IAAI,CAAC;IAWjF;;OAEG;IACH,aAAa,CAAC,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,aAAa,GAAG,OAAO;IA2BzD;;OAEG;IACG,yBAAyB,IAAI,OAAO,CAAC,mBAAmB,EAAE,CAAC;IAQjE;;OAEG;IACG,iBAAiB,CAAC,WAAW,EAAE,GAAG,EAAE,WAAW,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,CAAC;IAwB/E;;OAEG;IACG,eAAe,CAAC,OAAO,EAAE,MAAM,GAAG,OAAO,CAAC,GAAG,GAAG,IAAI,CAAC;IAiB3D;;OAEG;IACH,OAAO,CAAC,oBAAoB;IAa5B;;OAEG;IACG,mBAAmB,CACvB,YAAY,EAAE,MAAM,EACpB,MAAM,EAAE,MAAM,CAAC,MAAM,EAAE,GAAG,CAAC,EAC3B,OAAO,CAAC,EAAE;QACR,WAAW,CAAC,EAAE,MAAM,CAAC;QACrB,QAAQ,CAAC,EAAE,OAAO,CAAC;QACnB,QAAQ,CAAC,EAAE,GAAG,CAAC;KAChB,GACA,OAAO,CAAC,MAAM,CAAC;IAoClB;;OAEG;IACG,iBAAiB,CACrB,YAAY,EAAE,MAAM,EACpB,WAAW,CAAC,EAAE,MAAM,GACnB,OAAO,CAAC,MAAM,CAAC,MAAM,EAAE,GAAG,CAAC,GAAG,IAAI,CAAC;IAsBtC;;OAEG;IACG,qBAAqB,CAAC,WAAW,CAAC,EAAE,MAAM,GAAG,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package/dist/codeIndexDb.js

@@ -6,11 +6,15 @@ import Loki from 'lokijs';
 import * as FlexSearch from 'flexsearch';
 import { promises as fs } from 'fs';
 import path from 'path';
+import { ProjectTaskRepository } from './services/ProjectTaskRepository.js';
 import { QueryParser } from './search/QueryParser.js';
+import { getPersistedStorageRoot, resolvePersistedIndexPath } from './dataPaths.js';
+import { ContextualError, getErrnoCode } from './mcpToolErrors.js';
 import { WhitelistType, WhitelistStatus } from './types/whitelist.js';
 // Using SearchOptions and SearchResult from types.ts
 export class CodeIndexDB {
     static instance;
+    /** Subclasses (e.g. EnhancedCodeIndexDB) need access for extra collections without `as any`. */
     db;
     functionsCollection = null;
     whitelistCollection = null;
@@ -19,6 +23,9 @@ export class CodeIndexDB {
     codeMapCollection = null;
     schemaCollection = null;
     schemaUsageCollection = null;
+    /** User tasks: NOT cleared by clearIndex() — see clearIndex() */
+    tasksCollection = null;
+    taskRepository = null;
     searchIndex; // FlexSearch Document instance
     dbPath;
     isInitialized = false;
@@ -124,25 +131,73 @@ export class CodeIndexDB {
     }
     static getInstance(dbPath) {
         if (!CodeIndexDB.instance) {
-            CodeIndexDB.instance = new CodeIndexDB(dbPath || './.code-index/index.db');
+            const resolved = dbPath !== undefined && dbPath !== ''
+                ? path.resolve(dbPath)
+                : resolvePersistedIndexPath();
+            CodeIndexDB.instance = new CodeIndexDB(resolved);
         }
         return CodeIndexDB.instance;
     }
     async initialize() {
         if (this.isInitialized)
             return;
-        // Ensure directory exists
         const dir = path.dirname(this.dbPath);
-        await fs.mkdir(dir, { recursive: true });
-        // Load database
-        await new Promise((resolve, reject) => {
-            this.db.loadDatabase({}, (err) => {
-                if (err)
-                    reject(err);
-                else
-                    resolve();
+        const storageRoot = getPersistedStorageRoot();
+        try {
+            let st;
+            try {
+                st = await fs.stat(dir);
+            }
+            catch (e) {
+                const code = getErrnoCode(e);
+                if (code && code !== 'ENOENT') {
+                    throw new ContextualError(`Cannot access code index storage directory (${code}): ${dir}`, {
+                        errnoCode: code,
+                        storageRoot,
+                        dbPath: this.dbPath,
+                        hint: 'Fix permissions or set CODE_AUDITOR_DATA_DIR / --data-dir to a writable directory.',
+                    }, e instanceof Error ? e : undefined);
+                }
+            }
+            if (st && !st.isDirectory()) {
+                throw new ContextualError(`Code index storage path exists but is not a directory: ${dir}`, {
+                    storageRoot,
+                    dbPath: this.dbPath,
+                    hint: 'Remove the conflicting file/path or choose a different CODE_AUDITOR_DATA_DIR / --data-dir.',
+                });
+            }
+            await fs.mkdir(dir, { recursive: true });
+        }
+        catch (e) {
+            if (e instanceof ContextualError)
+                throw e;
+            const code = getErrnoCode(e);
+            throw new ContextualError(`Failed to prepare code index storage: ${e instanceof Error ? e.message : String(e)}`, {
+                ...(code && { errnoCode: code }),
+                storageRoot,
+                dbPath: this.dbPath,
+                hint: 'Ensure the storage directory is writable (default: <cwd>/.code-index when CODE_AUDITOR_DATA_DIR is unset).',
+            }, e instanceof Error ? e : undefined);
+        }
+        try {
+            await new Promise((resolve, reject) => {
+                this.db.loadDatabase({}, (err) => {
+                    if (err)
+                        reject(err);
+                    else
+                        resolve();
+                });
             });
-        });
+        }
+        catch (e) {
+            const code = getErrnoCode(e);
+            throw new ContextualError(`Failed to load code index database: ${e instanceof Error ? e.message : String(e)}`, {
+                ...(code && { errnoCode: code }),
+                storageRoot,
+                dbPath: this.dbPath,
+                hint: 'The index file may be corrupted, locked by another process, or on a read-only volume. Try a different CODE_AUDITOR_DATA_DIR or delete index.db if safe.',
+            }, e instanceof Error ? e : undefined);
+        }
         // Get or create functions collection
         this.functionsCollection = this.db.getCollection('functions') ||
             this.db.addCollection('functions', {
@@ -178,6 +233,10 @@ export class CodeIndexDB {
             this.db.addCollection('schemaUsage', {
                 indices: ['tableName', 'filePath', 'functionName', 'usageType']
             });
+        this.tasksCollection = this.db.getCollection('projectTasks') ||
+            this.db.addCollection('projectTasks', {
+                indices: ['taskId', 'projectPath', 'status', 'source', 'sortOrder']
+            });
         // Initialize default whitelists if empty
         if (this.whitelistCollection.count() === 0) {
             await this.initializeDefaultWhitelists();
@@ -191,7 +250,7 @@ export class CodeIndexDB {
         this.isInitialized = true;
     }
     ensureInitialized() {
-        if (!this.isInitialized || !this.functionsCollection) {
+        if (!this.isInitialized || !this.functionsCollection || !this.tasksCollection) {
             throw new Error('Database not initialized. Call initialize() first.');
         }
     }
@@ -1121,18 +1180,40 @@ export class CodeIndexDB {
             lastUpdated: new 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).
+     */
     async clearIndex() {
         this.ensureInitialized();
         this.functionsCollection.clear();
         this.searchIndex.clear();
+        this.auditResultsCollection.clear();
+        this.codeMapCollection.clear();
+        this.schemaCollection.clear();
+        this.schemaUsageCollection.clear();
         this.db.saveDatabase();
     }
     async close() {
         if (this.isInitialized) {
+            this.taskRepository = null;
             this.db.close();
             this.isInitialized = false;
         }
     }
+    getTaskRepository() {
+        this.ensureInitialized();
+        if (!this.taskRepository) {
+            this.taskRepository = new ProjectTaskRepository(() => this.tasksCollection, () => this.db.saveDatabase());
+        }
+        return this.taskRepository;
+    }
     /**
      * Synchronize a single file's functions with the index
      * Adds new functions, updates existing ones, and removes deleted ones
@@ -1553,13 +1634,13 @@ export class CodeIndexDB {
         this.ensureInitialized();
         // Generate unique audit ID
         const auditId = `audit_${Date.now()}_${Math.random().toString(36).substr(2, 9)}`;
-        // Store the full audit result structure to preserve all data
+        // Store the entire result to preserve analyzer structure; auditId must come last so
+        // a stray auditResult.auditId cannot break pagination lookups.
         const auditRecord = {
+            ...auditResult,
             auditId,
             timestamp: new Date(),
             projectPath,
-            // Store the entire result to preserve analyzer structure
-            ...auditResult,
             expiresAt: new Date(Date.now() + 24 * 60 * 60 * 1000) // Expire after 24 hours
         };
         this.auditResultsCollection.insert(auditRecord);
@@ -1972,5 +2053,23 @@ export class CodeIndexDB {
             schemaContext
         };
     }
+    async createProjectTask(input) {
+        return this.getTaskRepository().create(input);
+    }
+    async getProjectTask(taskId) {
+        return this.getTaskRepository().getById(taskId);
+    }
+    async listProjectTasks(projectPath, options) {
+        return this.getTaskRepository().list(projectPath, options);
+    }
+    /**
+     * @param patch Raw JSON-shaped update; unknown keys are ignored (see sanitizeUpdatePatch).
+     */
+    async updateProjectTask(taskId, patch) {
+        return this.getTaskRepository().update(taskId, patch);
+    }
+    async deleteProjectTask(taskId) {
+        return this.getTaskRepository().delete(taskId);
+    }
 }
 //# sourceMappingURL=codeIndexDB.js.map