codeseeker 1.4.0

package/dist/cli/commands/handlers/search-command-handler.js

@@ -0,0 +1,500 @@
+"use strict";
+/**
+ * Search Command Handler
+ * Single Responsibility: Handle search commands including semantic search
+ *
+ * STORAGE MODES:
+ * - Embedded (default): Uses SQLite vector store via StorageManager
+ * - Server: Uses PostgreSQL via analysisRepository
+ */
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.SearchCommandHandler = void 0;
+const base_command_handler_1 = require("../base-command-handler");
+const embedding_service_1 = require("../../services/data/embedding/embedding-service");
+const analysis_repository_consolidated_1 = require("../../../shared/analysis-repository-consolidated");
+const storage_1 = require("../../../storage");
+const logger_1 = require("../../../utils/logger");
+const path_1 = __importDefault(require("path"));
+const fast_glob_1 = require("fast-glob");
+const fs = __importStar(require("fs/promises"));
+class SearchCommandHandler extends base_command_handler_1.BaseCommandHandler {
+    logger = logger_1.Logger.getInstance();
+    /**
+     * Convert similarity score (0-1) to star rating display
+     * ★★★★★ = 90-100% (Excellent match)
+     * ★★★★☆ = 75-89%  (Very good match)
+     * ★★★☆☆ = 60-74%  (Good match)
+     * ★★☆☆☆ = 45-59%  (Fair match)
+     * ★☆☆☆☆ = 30-44%  (Weak match)
+     * ☆☆☆☆☆ = 0-29%   (Poor match)
+     */
+    getStarRating(score) {
+        // Ensure score is in 0-1 range
+        const normalizedScore = Math.max(0, Math.min(1, score));
+        const percentage = normalizedScore * 100;
+        if (percentage >= 90)
+            return '★★★★★';
+        if (percentage >= 75)
+            return '★★★★☆';
+        if (percentage >= 60)
+            return '★★★☆☆';
+        if (percentage >= 45)
+            return '★★☆☆☆';
+        if (percentage >= 30)
+            return '★☆☆☆☆';
+        return '☆☆☆☆☆';
+    }
+    async handle(args) {
+        // Parse arguments first to check for --index flag
+        const parts = args.trim() ? args.split(' ') : [];
+        const isIndex = parts.includes('--index');
+        // Allow args with only flags if indexing
+        const nonFlagParts = parts.filter(p => !p.startsWith('--'));
+        if (nonFlagParts.length === 0 && !isIndex) {
+            return {
+                success: false,
+                message: 'Usage: search <query> [--index] [--threshold=0.7] [--limit=10] [--verbose]'
+            };
+        }
+        const isVerbose = parts.includes('--verbose');
+        // Extract threshold and limit
+        const thresholdArg = parts.find(p => p.startsWith('--threshold='));
+        const limitArg = parts.find(p => p.startsWith('--limit='));
+        const threshold = thresholdArg ? parseFloat(thresholdArg.split('=')[1]) : 0.7;
+        const limit = limitArg ? parseInt(limitArg.split('=')[1]) : 10;
+        // Get query (remove flags)
+        const query = parts.filter(p => !p.startsWith('--')).join(' ');
+        try {
+            const projectPath = this.context.currentProject?.projectPath || process.cwd();
+            this.logger.info(`Using project path: ${projectPath}`);
+            this.logger.info(`Context project ID: ${this.context.currentProject?.projectId}`);
+            const projectId = this.context.currentProject?.projectId || await this.generateProjectId(projectPath);
+            this.logger.info(`Final project ID for search: ${projectId}`);
+            if (isIndex) {
+                return await this.indexProject(projectPath, projectId);
+            }
+            else if (query) {
+                return await this.searchCode(query, projectId, { threshold, limit, verbose: isVerbose });
+            }
+            else {
+                return {
+                    success: false,
+                    message: 'Please provide a search query or use --index to index the codebase'
+                };
+            }
+        }
+        catch (error) {
+            this.logger.error('Search failed:', error);
+            return {
+                success: false,
+                message: `Search failed: ${error instanceof Error ? error.message : 'Unknown error'}`
+            };
+        }
+    }
+    /**
+     * Index the current project for semantic search (incremental)
+     * Only reindexes files that have changed based on content hash
+     */
+    async indexProject(projectPath, projectId) {
+        console.log('🔄 Indexing codebase for semantic search...');
+        console.log(`📁 Project: ${projectPath}`);
+        try {
+            // Get all code files
+            const files = await (0, fast_glob_1.glob)(['**/*.{ts,js,jsx,tsx,py,java,cs,cpp,c,h,hpp}'], {
+                cwd: projectPath,
+                ignore: ['**/node_modules/**', '**/dist/**', '**/build/**', '**/.git/**']
+            });
+            console.log(`📂 Found ${files.length} files to scan`);
+            if (files.length === 0) {
+                return {
+                    success: false,
+                    message: 'No code files found to index'
+                };
+            }
+            // Get existing file hashes from database to enable incremental indexing
+            const existingHashes = await this.getExistingFileHashes(projectId);
+            console.log(`   📊 Found ${existingHashes.size} previously indexed files`);
+            // Compute current file hashes and determine what needs updating
+            const crypto = require('crypto');
+            const filesToProcess = [];
+            const filesToDelete = [];
+            const currentFiles = new Set();
+            for (const file of files) {
+                currentFiles.add(file);
+                const filePath = path_1.default.join(projectPath, file);
+                try {
+                    const content = await fs.readFile(filePath, 'utf-8');
+                    if (content.length < 50)
+                        continue; // Skip very small files
+                    const fileHash = crypto.createHash('md5').update(content).digest('hex');
+                    const existingHash = existingHashes.get(file);
+                    if (!existingHash || existingHash !== fileHash) {
+                        filesToProcess.push(file);
+                        if (existingHash) {
+                            filesToDelete.push(file); // File changed, delete old embeddings first
+                        }
+                    }
+                }
+                catch (error) {
+                    this.logger.warn(`Failed to read file ${file}:`, error);
+                }
+            }
+            // Find deleted files (in DB but not in current file system)
+            for (const [file] of existingHashes) {
+                if (!currentFiles.has(file)) {
+                    filesToDelete.push(file);
+                }
+            }
+            // Delete old embeddings for changed/deleted files
+            if (filesToDelete.length > 0) {
+                await this.deleteFileEmbeddings(projectId, filesToDelete);
+                console.log(`   🗑️  Removed embeddings for ${filesToDelete.length} changed/deleted files`);
+            }
+            if (filesToProcess.length === 0) {
+                console.log(`✅ All ${files.length} files are up to date - no reindexing needed`);
+                return {
+                    success: true,
+                    message: `Project already indexed: ${files.length} files up to date`,
+                    data: { segments: 0, files: 0, unchanged: files.length }
+                };
+            }
+            console.log(`   📝 Processing ${filesToProcess.length} new/changed files...`);
+            // Initialize embedding service
+            const embeddingService = new embedding_service_1.EmbeddingService({
+                provider: 'xenova',
+                model: 'Xenova/all-MiniLM-L6-v2'
+            });
+            const embeddings = [];
+            let processedFiles = 0;
+            for (const file of filesToProcess.slice(0, 50)) { // Limit to 50 files for MVP
+                try {
+                    const filePath = path_1.default.join(projectPath, file);
+                    const content = await fs.readFile(filePath, 'utf-8');
+                    if (content.length < 50)
+                        continue;
+                    // Create simple chunks (split by lines for now)
+                    const lines = content.split('\n');
+                    const chunks = [];
+                    for (let i = 0; i < lines.length; i += 20) {
+                        const chunk = lines.slice(i, i + 20).join('\n');
+                        if (chunk.trim().length > 20) {
+                            chunks.push(chunk);
+                        }
+                    }
+                    // Compute full file hash for incremental indexing comparison
+                    const fullFileHash = crypto.createHash('md5').update(content).digest('hex');
+                    // Generate embeddings for each chunk
+                    for (let chunkIndex = 0; chunkIndex < chunks.length; chunkIndex++) {
+                        const chunk = chunks[chunkIndex];
+                        try {
+                            // Generate the actual embedding vector
+                            const embeddingVector = await embeddingService.generateEmbedding(chunk, file);
+                            const embedding = {
+                                project_id: projectId,
+                                file_path: file,
+                                chunk_index: chunkIndex,
+                                content_type: 'code',
+                                content_text: chunk,
+                                content_hash: crypto.createHash('md5').update(chunk).digest('hex'),
+                                embedding: embeddingVector, // Include the actual embedding vector
+                                // Store full file hash in metadata for incremental indexing
+                                metadata: {
+                                    full_file_hash: fullFileHash,
+                                    total_chunks: chunks.length
+                                }
+                            };
+                            embeddings.push(embedding);
+                        }
+                        catch (error) {
+                            this.logger.warn(`Failed to process chunk ${chunkIndex} in ${file}:`, error);
+                        }
+                    }
+                    processedFiles++;
+                    if (processedFiles % 10 === 0) {
+                        console.log(`   Processed ${processedFiles}/${filesToProcess.length} files...`);
+                    }
+                }
+                catch (error) {
+                    this.logger.warn(`Failed to process file ${file}:`, error);
+                }
+            }
+            // Save embeddings to appropriate storage (embedded or server)
+            if (embeddings.length > 0) {
+                // Get storage manager first to ensure singleton is initialized
+                const storageManager = await (0, storage_1.getStorageManager)();
+                if (storageManager.getMode() === 'embedded') {
+                    // Use embedded SQLite vector store
+                    const vectorStore = storageManager.getVectorStore();
+                    // Convert to VectorDocument format and upsert
+                    const docs = embeddings.map(e => ({
+                        id: `${e.project_id}-${e.file_path}-${e.chunk_index}`,
+                        projectId: e.project_id,
+                        filePath: e.file_path,
+                        content: e.content_text,
+                        embedding: e.embedding || [],
+                        metadata: e.metadata
+                    }));
+                    await vectorStore.upsertMany(docs);
+                }
+                else {
+                    // Use PostgreSQL (server mode)
+                    await analysis_repository_consolidated_1.analysisRepository.saveMultipleEmbeddings(embeddings);
+                }
+                console.log(`✅ Generated embeddings for ${embeddings.length} code segments`);
+                console.log(`📊 Processed ${processedFiles} new/changed files (${files.length - filesToProcess.length} unchanged)`);
+                return {
+                    success: true,
+                    message: `Project indexed: ${embeddings.length} segments from ${processedFiles} files`,
+                    data: {
+                        segments: embeddings.length,
+                        files: processedFiles,
+                        unchanged: files.length - filesToProcess.length,
+                        deleted: filesToDelete.length
+                    }
+                };
+            }
+            else {
+                return {
+                    success: true,
+                    message: 'No new code segments to index',
+                    data: { segments: 0, files: 0 }
+                };
+            }
+        }
+        catch (error) {
+            this.logger.error('Indexing failed:', error);
+            return {
+                success: false,
+                message: `Indexing failed: ${error instanceof Error ? error.message : 'Unknown error'}`
+            };
+        }
+    }
+    /**
+     * Get existing file hashes from database for incremental indexing
+     */
+    async getExistingFileHashes(projectId) {
+        try {
+            const storageManager = await (0, storage_1.getStorageManager)();
+            if (storageManager.getMode() === 'embedded') {
+                // For embedded mode, return empty map (always reindex for now)
+                // TODO: Add incremental indexing support for embedded storage
+                return new Map();
+            }
+            return await analysis_repository_consolidated_1.analysisRepository.getFileHashes(projectId);
+        }
+        catch (error) {
+            this.logger.warn('Could not get existing file hashes:', error);
+            return new Map();
+        }
+    }
+    /**
+     * Delete embeddings for specified files
+     */
+    async deleteFileEmbeddings(projectId, files) {
+        if (files.length === 0)
+            return;
+        try {
+            const storageManager = await (0, storage_1.getStorageManager)();
+            if (storageManager.getMode() === 'embedded') {
+                // For embedded mode, we'll delete all and re-add during upsert
+                const vectorStore = storageManager.getVectorStore();
+                await vectorStore.deleteByProject(projectId);
+            }
+            else {
+                await analysis_repository_consolidated_1.analysisRepository.deleteEmbeddingsForFiles(projectId, files);
+            }
+        }
+        catch (error) {
+            this.logger.warn('Could not delete file embeddings:', error);
+        }
+    }
+    /**
+     * Search for code using semantic similarity
+     */
+    async searchCode(query, projectId, options) {
+        console.log(`🔍 Searching for: "${query}"`);
+        try {
+            // Get storage manager first to ensure singleton is initialized
+            const storageManager = await (0, storage_1.getStorageManager)();
+            let results = [];
+            if (storageManager.getMode() === 'embedded') {
+                // Use embedded SQLite + MiniSearch for text search
+                const vectorStore = storageManager.getVectorStore();
+                const searchResults = await vectorStore.searchByText(query, projectId, options.limit);
+                if (searchResults.length === 0) {
+                    console.log('   No indexed content found - run "search --index" first');
+                    return {
+                        success: false,
+                        message: 'No indexed content found. Please run "search --index" first to index the codebase.'
+                    };
+                }
+                console.log(`🧠 Found ${searchResults.length} matching code segments`);
+                results = searchResults
+                    .filter(r => r.score >= options.threshold)
+                    .map(r => ({
+                    file_path: r.document.filePath,
+                    content_type: 'code',
+                    content_text: r.document.content,
+                    similarity_score: r.score,
+                    chunk_index: 0
+                }));
+            }
+            else {
+                // Use PostgreSQL (server mode)
+                const embeddings = await analysis_repository_consolidated_1.analysisRepository.getEmbeddings(projectId, {
+                    limit: options.limit
+                });
+                if (embeddings.length === 0) {
+                    console.log('   No embeddings found - run "search --index" first');
+                    return {
+                        success: false,
+                        message: 'No embeddings found. Please run "search --index" first to index the codebase.'
+                    };
+                }
+                console.log(`🧠 Found ${embeddings.length} code segments to search`);
+                // For server mode, do simple text-based search
+                const queryLower = query.toLowerCase();
+                results = embeddings
+                    .map((embedding) => ({
+                    file_path: embedding.file_path,
+                    content_type: embedding.content_type,
+                    content_text: embedding.content_text,
+                    similarity_score: this.calculateTextSimilarity(queryLower, embedding.content_text?.toLowerCase() || ''),
+                    chunk_index: embedding.chunk_index
+                }))
+                    .filter(result => result.similarity_score >= options.threshold)
+                    .sort((a, b) => b.similarity_score - a.similarity_score)
+                    .slice(0, options.limit);
+            }
+            console.log(`\n🔍 Search Results (${results.length} found):`);
+            if (results.length === 0) {
+                console.log('   No similar code segments found');
+                console.log('   Try lowering the similarity threshold or using different search terms');
+            }
+            else {
+                results.forEach((result, index) => {
+                    const stars = this.getStarRating(result.similarity_score);
+                    console.log(`\n📄 Result ${index + 1}:`);
+                    console.log(`   File: ${result.file_path}`);
+                    console.log(`   Type: ${result.content_type}`);
+                    console.log(`   Match: ${stars}`);
+                    if (options.verbose) {
+                        const percentage = Math.min(100, result.similarity_score * 100).toFixed(0);
+                        console.log(`   Score: ${percentage}%`);
+                        console.log(`   Content Preview:`);
+                        const preview = result.content_text.substring(0, 200);
+                        console.log(`   ${preview}${result.content_text.length > 200 ? '...' : ''}`);
+                    }
+                });
+            }
+            console.log(`\n💡 Tips:`);
+            console.log(`   • Use --verbose for more details`);
+            console.log(`   • Use --threshold to adjust similarity filtering`);
+            console.log(`   • Use search --index to index your codebase first`);
+            return {
+                success: true,
+                message: `Found ${results.length} matches`,
+                data: { query, results }
+            };
+        }
+        catch (error) {
+            this.logger.error('Search failed:', error);
+            return {
+                success: false,
+                message: `Search failed: ${error instanceof Error ? error.message : 'Unknown error'}`
+            };
+        }
+    }
+    /**
+     * Calculate simple text-based similarity for MVP
+     */
+    calculateTextSimilarity(query, content) {
+        if (!query || !content)
+            return 0;
+        const queryWords = query.split(/\s+/).filter(w => w.length > 2);
+        const contentWords = content.split(/\s+/).map(w => w.toLowerCase());
+        if (queryWords.length === 0)
+            return 0;
+        let matches = 0;
+        for (const word of queryWords) {
+            if (contentWords.some(cw => cw.includes(word) || word.includes(cw))) {
+                matches++;
+            }
+        }
+        return matches / queryWords.length;
+    }
+    /**
+     * Get existing project ID from database
+     */
+    async generateProjectId(projectPath) {
+        try {
+            // Normalize the path for consistent lookup
+            const normalizedPath = path_1.default.resolve(projectPath);
+            this.logger.info(`Looking up project with path: ${normalizedPath}`);
+            // Try to find existing project by path
+            const projects = await analysis_repository_consolidated_1.analysisRepository.getProjects({ projectPath: normalizedPath });
+            this.logger.info(`Found ${projects.length} projects matching path`);
+            if (projects.length > 0) {
+                this.logger.info(`Using project ID: ${projects[0].id}`);
+                return projects[0].id;
+            }
+            // Also try without normalization in case paths were stored differently
+            const projectsOrig = await analysis_repository_consolidated_1.analysisRepository.getProjects({ projectPath });
+            if (projectsOrig.length > 0) {
+                this.logger.info(`Found project with original path, using ID: ${projectsOrig[0].id}`);
+                return projectsOrig[0].id;
+            }
+            // Get all projects to debug
+            const allProjects = await analysis_repository_consolidated_1.analysisRepository.getProjects({});
+            this.logger.info(`Total projects in database: ${allProjects.length}`);
+            allProjects.forEach(p => {
+                this.logger.info(`Project: ${p.project_name}, Path: ${p.project_path}, ID: ${p.id}`);
+            });
+            // Fallback: this should not happen if init was run properly
+            this.logger.error(`No project found for path: ${projectPath} (normalized: ${normalizedPath})`);
+            throw new Error(`Project not found for path: ${projectPath}. Please run "codeseeker setup" first.`);
+        }
+        catch (error) {
+            this.logger.error('Could not retrieve project ID:', error);
+            throw error;
+        }
+    }
+}
+exports.SearchCommandHandler = SearchCommandHandler;
+//# sourceMappingURL=search-command-handler.js.map

package/dist/cli/commands/handlers/search-command-handler.js.map

@@ -0,0 +1 @@
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package/dist/cli/commands/handlers/setup-command-handler.d.ts

@@ -0,0 +1,103 @@
+/**
+ * Project Initialization Command Handler - Fully Implemented
+ * Single Responsibility: Handle project initialization commands (per-project setup)
+ * Implements project registration, indexing, and knowledge graph creation
+ */
+import { BaseCommandHandler } from '../base-command-handler';
+import { CommandResult } from '../command-context';
+export declare class SetupCommandHandler extends BaseCommandHandler {
+    private logger;
+    /**
+     * Handle setup/init commands
+     */
+    handle(args: string): Promise<CommandResult>;
+    /**
+     * Check if project.json has a path mismatch with current directory
+     * This happens when a project folder is copied from another location
+     */
+    private checkProjectPathMismatch;
+    /**
+     * Perform complete database cleanup and reinitialization
+     * Uses storage abstraction for both embedded and server modes
+     */
+    private handleCompleteReset;
+    /**
+     * Clean up Neo4j knowledge graph data for a project
+     */
+    private cleanupNeo4jData;
+    /**
+     * Initialize a CodeSeeker project
+     */
+    private handleInit;
+    /**
+     * Setup system-wide configuration
+     */
+    private handleSetup;
+    /**
+     * Initialize database connection and basic tables
+     */
+    private initializeDatabase;
+    /**
+     * Build initial knowledge graph for the project
+     * Uses embedded Graphology store by default, Neo4j if in server mode
+     */
+    private buildInitialKnowledgeGraph;
+    /**
+     * Generate coding standards file from detected patterns
+     */
+    private generateCodingStandards;
+    /**
+     * Apply the consolidated database schema
+     * Uses embedded storage by default (no Docker required)
+     */
+    private applyConsolidatedSchema;
+    /**
+     * Create basic tables if schema file is not available
+     */
+    private createBasicTables;
+    /**
+     * Initialize project record in database
+     * Uses embedded storage by default, PostgreSQL in server mode
+     */
+    private initializeProject;
+    /**
+     * Generate initial embeddings for the project (basic implementation)
+     */
+    private generateInitialEmbeddings;
+    /**
+     * Create CODESEEKER.md instructions file with detected platforms
+     */
+    private createInstructionsFile;
+    /**
+     * Append platform detection to existing CODESEEKER.md
+     */
+    private appendPlatformDetection;
+    /**
+     * Unified CodeSeeker MCP guidance section for ALL agent instruction files
+     * Used for CLAUDE.md, AGENTS.md, .cursorrules, COPILOT.md, GEMINI.md, GROK.md, etc.
+     * This tells AI assistants to prefer CodeSeeker MCP tools over grep/glob
+     */
+    private readonly CODESEEKER_MCP_GUIDANCE;
+    /**
+     * Common agent instruction files to check and update with CodeSeeker MCP guidance
+     * These are files that AI tools (Claude, Cursor, Copilot, Gemini, Grok, etc.) use for instructions
+     * All agents get the same unified CODESEEKER_MCP_GUIDANCE template
+     */
+    private readonly AGENT_INSTRUCTION_FILES;
+    /**
+     * Update agent instruction files (AGENTS.md, .cursorrules, etc.) with CodeSeeker guidance
+     * Only updates files that already exist - doesn't create new ones
+     * Uses the same unified CODESEEKER_MCP_GUIDANCE as CLAUDE.md
+     * If no files found, prompts user to create or specify one
+     */
+    private updateAgentInstructionFiles;
+    /**
+     * Update local project configuration file
+     */
+    private updateLocalProjectConfig;
+    /**
+     * Index codebase for semantic search by delegating to search handler
+     */
+    private indexCodebase;
+}
+//# sourceMappingURL=setup-command-handler.d.ts.map

package/dist/cli/commands/handlers/setup-command-handler.d.ts.map

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