/**
 * 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
     *
     * IMPORTANT: This now updates existing guidance to the latest version if it's outdated
     */
    private updateAgentInstructionFiles;
    /**
     * Update local project configuration file
     */
    private updateLocalProjectConfig;
    /**
     * Index codebase for semantic search by delegating to search handler
     */
    private indexCodebase;
}
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