@grafema/core 0.1.0-alpha.5 → 0.2.0-beta

package/README.md

@@ -52,7 +52,6 @@ The orchestrator runs analysis in 5 phases:
 ### Indexing
 - `JSModuleIndexer` - JavaScript/TypeScript module resolution
 - `RustModuleIndexer` - Rust crate analysis
-- `ServiceDetector` - Monorepo service discovery
 
 ### Analysis
 - `JSASTAnalyzer` - Core JS/TS AST analysis

package/dist/Orchestrator.d.ts

@@ -2,8 +2,9 @@
  * Orchestrator - управляет процессом анализа через фазы
  * Полностью абстрактный - специфичная логика в плагинах
  */
+import { DiagnosticCollector } from './diagnostics/DiagnosticCollector.js';
 import type { Plugin, PluginContext } from './plugins/Plugin.js';
-import type { GraphBackend } from '@grafema/types';
+import type { GraphBackend, Logger, LogLevel, ServiceDefinition } from '@grafema/types';
 /**
  * Progress callback info
  */
@@ -37,8 +38,24 @@ export interface OrchestratorOptions {
     onProgress?: ProgressCallback;
     forceAnalysis?: boolean;
     serviceFilter?: string | null;
+    /** Override entrypoint, bypasses auto-detection. Path relative to project root. */
+    entrypoint?: string;
     indexOnly?: boolean;
     parallel?: ParallelConfig | null;
+    /** Logger instance for structured logging. */
+    logger?: Logger;
+    /** Log level for the default logger. Ignored if logger is provided. */
+    logLevel?: LogLevel;
+    /**
+     * Config-provided services (REG-174).
+     * If provided and non-empty, discovery plugins are skipped.
+     */
+    services?: ServiceDefinition[];
+    /**
+     * Enable strict mode for fail-fast debugging.
+     * When true, enrichers report unresolved references as fatal errors.
+     */
+    strictMode?: boolean;
 }
 /**
  * Service info from discovery
@@ -93,12 +110,19 @@ export declare class Orchestrator {
     private onProgress;
     private forceAnalysis;
     private serviceFilter;
+    private entrypoint;
     private indexOnly;
     private profiler;
     private parallelConfig;
     private analysisQueue;
     private rfdbServerProcess;
     private _serverWasExternal;
+    private diagnosticCollector;
+    private logger;
+    /** Config-provided services (REG-174) */
+    private configServices;
+    /** Strict mode flag (REG-330) */
+    private strictMode;
     constructor(options?: OrchestratorOptions);
     /**
      * Запустить анализ проекта
@@ -110,7 +134,8 @@ export declare class Orchestrator {
      */
     buildIndexingUnits(manifest: DiscoveryManifest): IndexingUnit[];
     /**
-     * PHASE 0: Discovery - запуск плагинов DISCOVERY фазы
+     * PHASE 0: Discovery - запуск плагинов DISCOVERY фазы.
+     * If config services are provided, they take precedence and plugins are skipped.
      */
     discover(projectPath: string): Promise<DiscoveryManifest>;
     /**
@@ -119,6 +144,10 @@ export declare class Orchestrator {
     runPhase(phaseName: string, context: Partial<PluginContext> & {
         graph: PluginContext['graph'];
     }): Promise<void>;
+    /**
+     * Get the diagnostic collector for retrieving all collected diagnostics
+     */
+    getDiagnostics(): DiagnosticCollector;
     /**
      * Run queue-based parallel analysis using worker_threads and RFDB server
      *

package/dist/Orchestrator.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"Orchestrator.d.ts","sourceRoot":"","sources":["../src/Orchestrator.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAWH,OAAO,EAAE,mBAAmB,EAAE,MAAM,sCAAsC,CAAC;AAC3E,OAAO,KAAK,EAAE,MAAM,EAAE,aAAa,EAAE,MAAM,qBAAqB,CAAC;AACjE,OAAO,KAAK,EAAE,YAAY,EAAe,MAAM,EAAE,QAAQ,EAAa,iBAAiB,EAAE,MAAM,gBAAgB,CAAC;AAKhH;;GAEG;AACH,MAAM,WAAW,YAAY;IAC3B,KAAK,EAAE,MAAM,CAAC;IACd,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,cAAc,CAAC,EAAE,MAAM,CAAC;IACxB,gBAAgB,CAAC,EAAE,MAAM,CAAC;CAC3B;AAED;;GAEG;AACH,MAAM,MAAM,gBAAgB,GAAG,CAAC,IAAI,EAAE,YAAY,KAAK,IAAI,CAAC;AAE5D;;GAEG;AACH,MAAM,WAAW,cAAc;IAC7B,OAAO,EAAE,OAAO,CAAC;IACjB,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,UAAU,CAAC,EAAE,MAAM,CAAC;CACrB;AAED;;GAEG;AACH,MAAM,WAAW,mBAAmB;IAClC,KAAK,CAAC,EAAE,YAAY,CAAC;IACrB,OAAO,CAAC,EAAE,MAAM,EAAE,CAAC;IACnB,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,UAAU,CAAC,EAAE,gBAAgB,CAAC;IAC9B,aAAa,CAAC,EAAE,OAAO,CAAC;IACxB,aAAa,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IAC9B,mFAAmF;IACnF,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,SAAS,CAAC,EAAE,OAAO,CAAC;IACpB,QAAQ,CAAC,EAAE,cAAc,GAAG,IAAI,CAAC;IACjC,8CAA8C;IAC9C,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,uEAAuE;IACvE,QAAQ,CAAC,EAAE,QAAQ,CAAC;IACpB;;;OAGG;IACH,QAAQ,CAAC,EAAE,iBAAiB,EAAE,CAAC;IAC/B;;;OAGG;IACH,UAAU,CAAC,EAAE,OAAO,CAAC;CACtB;AAED;;GAEG;AACH,MAAM,WAAW,WAAW;IAC1B,EAAE,EAAE,MAAM,CAAC;IACX,IAAI,EAAE,MAAM,CAAC;IACb,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,QAAQ,CAAC,EAAE;QACT,UAAU,CAAC,EAAE,MAAM,CAAC;QACpB,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC;KACxB,CAAC;IACF,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC;CACxB;AAED;;GAEG;AACH,MAAM,WAAW,cAAc;IAC7B,EAAE,EAAE,MAAM,CAAC;IACX,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,IAAI,EAAE,MAAM,CAAC;IACb,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC;CACxB;AAED;;GAEG;AACH,MAAM,WAAW,iBAAiB;IAChC,QAAQ,EAAE,WAAW,EAAE,CAAC;IACxB,WAAW,EAAE,cAAc,EAAE,CAAC;IAC9B,WAAW,EAAE,MAAM,CAAC;IACpB,OAAO,CAAC,EAAE,OAAO,EAAE,CAAC;CACrB;AAED;;GAEG;AACH,MAAM,WAAW,YAAY;IAC3B,EAAE,EAAE,MAAM,CAAC;IACX,IAAI,EAAE,MAAM,CAAC;IACb,IAAI,EAAE,MAAM,CAAC;IACb,IAAI,EAAE,SAAS,GAAG,YAAY,CAAC;IAC/B,cAAc,CAAC,EAAE,MAAM,CAAC;IACxB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC;CACxB;AAgBD,qBAAa,YAAY;IACvB,OAAO,CAAC,KAAK,CAAe;IAC5B,OAAO,CAAC,MAAM,CAAsB;IACpC,OAAO,CAAC,OAAO,CAAW;IAC1B,OAAO,CAAC,WAAW,CAAS;IAC5B,OAAO,CAAC,UAAU,CAAmB;IACrC,OAAO,CAAC,aAAa,CAAU;IAC/B,OAAO,CAAC,aAAa,CAAgB;IACrC,OAAO,CAAC,UAAU,CAAqB;IACvC,OAAO,CAAC,SAAS,CAAU;IAC3B,OAAO,CAAC,QAAQ,CAAW;IAC3B,OAAO,CAAC,cAAc,CAAwB;IAC9C,OAAO,CAAC,aAAa,CAAuB;IAC5C,OAAO,CAAC,iBAAiB,CAAsB;IAC/C,OAAO,CAAC,kBAAkB,CAAU;IACpC,OAAO,CAAC,mBAAmB,CAAsB;IACjD,OAAO,CAAC,MAAM,CAAS;IACvB,yCAAyC;IACzC,OAAO,CAAC,cAAc,CAAkC;IACxD,iCAAiC;IACjC,OAAO,CAAC,UAAU,CAAU;gBAEhB,OAAO,GAAE,mBAAwB;IAwC7C;;OAEG;IACG,GAAG,CAAC,WAAW,EAAE,MAAM,GAAG,OAAO,CAAC,iBAAiB,CAAC;IAoQ1D;;;OAGG;IACH,kBAAkB,CAAC,QAAQ,EAAE,iBAAiB,GAAG,YAAY,EAAE;IAwC/D;;;OAGG;IACG,QAAQ,CAAC,WAAW,EAAE,MAAM,GAAG,OAAO,CAAC,iBAAiB,CAAC;IA6H/D;;OAEG;IACG,QAAQ,CAAC,SAAS,EAAE,MAAM,EAAE,OAAO,EAAE,OAAO,CAAC,aAAa,CAAC,GAAG;QAAE,KAAK,EAAE,aAAa,CAAC,OAAO,CAAC,CAAA;KAAE,GAAG,OAAO,CAAC,IAAI,CAAC;IAuGrH;;OAEG;IACH,cAAc,IAAI,mBAAmB;IAIrC;;;;;;;OAOG;IACG,mBAAmB,CAAC,QAAQ,EAAE,iBAAiB,GAAG,OAAO,CAAC,IAAI,CAAC;IAwErE;;;;OAIG;IACG,eAAe,CAAC,UAAU,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC;IAgExE;;OAEG;IACG,cAAc,IAAI,OAAO,CAAC,IAAI,CAAC;CActC"}

package/dist/Orchestrator.js

@@ -2,14 +2,18 @@
  * Orchestrator - управляет процессом анализа через фазы
  * Полностью абстрактный - специфичная логика в плагинах
  */
-import { existsSync, unlinkSync } from 'fs';
+import { readFileSync, existsSync, unlinkSync } from 'fs';
 import { join, dirname, resolve } from 'path';
 import { fileURLToPath } from 'url';
 import { spawn, execSync } from 'child_process';
 import { setTimeout as sleep } from 'timers/promises';
 import { SimpleProjectDiscovery } from './plugins/discovery/SimpleProjectDiscovery.js';
+import { resolveSourceEntrypoint } from './plugins/discovery/resolveSourceEntrypoint.js';
 import { Profiler } from './core/Profiler.js';
 import { AnalysisQueue } from './core/AnalysisQueue.js';
+import { DiagnosticCollector } from './diagnostics/DiagnosticCollector.js';
+import { createLogger } from './logging/Logger.js';
+import { NodeFactory } from './core/NodeFactory.js';
 export class Orchestrator {
     graph;
     config;
@@ -18,12 +22,19 @@ export class Orchestrator {
     onProgress;
     forceAnalysis;
     serviceFilter;
+    entrypoint;
     indexOnly;
     profiler;
     parallelConfig;
     analysisQueue;
     rfdbServerProcess;
     _serverWasExternal;
+    diagnosticCollector;
+    logger;
+    /** Config-provided services (REG-174) */
+    configServices;
+    /** Strict mode flag (REG-330) */
+    strictMode;
     constructor(options = {}) {
         this.graph = options.graph;
         this.config = options;
@@ -32,6 +43,7 @@ export class Orchestrator {
         this.onProgress = options.onProgress || (() => { }); // Callback для прогресса
         this.forceAnalysis = options.forceAnalysis || false; // Флаг для игнорирования кэша
         this.serviceFilter = options.serviceFilter || null; // Фильтр для одного сервиса
+        this.entrypoint = options.entrypoint; // Override entrypoint, bypasses discovery
         this.indexOnly = options.indexOnly || false; // Только DISCOVERY + INDEXING (для coverage)
         this.profiler = new Profiler('Orchestrator');
         // Parallel/queue-based analysis config
@@ -39,9 +51,19 @@ export class Orchestrator {
         this.analysisQueue = null;
         this.rfdbServerProcess = null;
         this._serverWasExternal = false;
-        // Auto-add default discovery if no discovery plugins provided
+        // Initialize diagnostic collector
+        this.diagnosticCollector = new DiagnosticCollector();
+        // Initialize logger (use provided or create default)
+        this.logger = options.logger ?? createLogger(options.logLevel ?? 'info');
+        // Store config-provided services (REG-174)
+        this.configServices = options.services;
+        // Strict mode configuration (REG-330)
+        this.strictMode = options.strictMode ?? false;
+        // Modified auto-add logic: SKIP auto-add if config services provided (REG-174)
         const hasDiscovery = this.plugins.some(p => p.metadata?.phase === 'DISCOVERY');
-        if (!hasDiscovery) {
+        const hasConfigServices = this.configServices && this.configServices.length > 0;
+        if (!hasDiscovery && !hasConfigServices) {
+            // Only auto-add if NO discovery plugins AND NO config services
             this.plugins.unshift(new SimpleProjectDiscovery());
         }
     }
@@ -52,10 +74,37 @@ export class Orchestrator {
         const totalStartTime = Date.now();
         // Resolve to absolute path
         const absoluteProjectPath = projectPath.startsWith('/') ? projectPath : resolve(projectPath);
+        // RADICAL SIMPLIFICATION: Clear entire graph once at the start if forceAnalysis
+        if (this.forceAnalysis && this.graph.clear) {
+            this.logger.info('Clearing entire graph (forceAnalysis=true)');
+            await this.graph.clear();
+            this.logger.info('Graph cleared successfully');
+        }
         this.onProgress({ phase: 'discovery', currentPlugin: 'Starting discovery...', message: 'Discovering services...', totalFiles: 0, processedFiles: 0 });
-        // PHASE 0: DISCOVERY - запуск плагинов фазы DISCOVERY
+        // PHASE 0: DISCOVERY - запуск плагинов фазы DISCOVERY (or use entrypoint override)
         this.profiler.start('DISCOVERY');
-        const manifest = await this.discover(absoluteProjectPath);
+        let manifest;
+        if (this.entrypoint) {
+            // Skip discovery, create synthetic manifest with single service
+            const entrypointPath = this.entrypoint.startsWith('/')
+                ? this.entrypoint
+                : join(absoluteProjectPath, this.entrypoint);
+            const serviceName = this.entrypoint.split('/').pop()?.replace(/\.[^.]+$/, '') || 'main';
+            manifest = {
+                services: [{
+                        id: `service:${serviceName}`,
+                        name: serviceName,
+                        path: entrypointPath,
+                        metadata: { entrypoint: entrypointPath }
+                    }],
+                entrypoints: [],
+                projectPath: absoluteProjectPath
+            };
+            this.logger.info('Using entrypoint override', { entrypoint: this.entrypoint, resolved: entrypointPath });
+        }
+        else {
+            manifest = await this.discover(absoluteProjectPath);
+        }
         this.profiler.end('DISCOVERY');
         const epCount = manifest.entrypoints?.length || 0;
         const svcCount = manifest.services?.length || 0;
@@ -66,7 +115,7 @@ export class Orchestrator {
             totalFiles: 0,
             processedFiles: 0
         });
-        console.log(`[Orchestrator] Discovery: ${svcCount} services, ${epCount} entrypoints`);
+        this.logger.info('Discovery complete', { services: svcCount, entrypoints: epCount });
         // Build unified list of indexing units from services AND entrypoints
         const indexingUnits = this.buildIndexingUnits(manifest);
         // Filter if specified
@@ -76,13 +125,12 @@ export class Orchestrator {
                 u.path === this.serviceFilter ||
                 u.name.includes(this.serviceFilter) ||
                 u.path.includes(this.serviceFilter));
-            console.log(`[Orchestrator] Filtering: ${this.serviceFilter} (found ${unitsToProcess.length} of ${indexingUnits.length})`);
+            this.logger.info('Filtering services', { filter: this.serviceFilter, found: unitsToProcess.length, total: indexingUnits.length });
         }
         else {
             unitsToProcess = indexingUnits;
         }
-        console.log(`[Orchestrator] Processing ${unitsToProcess.length} indexing units (services + entrypoints)`);
-        console.log(`[Orchestrator] Strategy: Phase-by-phase with DFS dependency tree per entrypoint`);
+        this.logger.info('Processing indexing units', { count: unitsToProcess.length, strategy: 'Phase-by-phase with DFS' });
         // PHASE 1: INDEXING - каждый сервис строит своё дерево зависимостей от entrypoint
         const indexingStart = Date.now();
         this.profiler.start('INDEXING');
@@ -118,9 +166,13 @@ export class Orchestrator {
                     },
                     modules: []
                 };
-                await this.runPhase('INDEXING', { manifest: unitManifest, graph: this.graph, workerCount: 1 });
+                await this.runPhase('INDEXING', {
+                    manifest: unitManifest,
+                    graph: this.graph,
+                    workerCount: 1,
+                });
                 const unitTime = ((Date.now() - unitStart) / 1000).toFixed(2);
-                console.log(`[Orchestrator] ⏱️ INDEXING ${unit.name}: ${unitTime}s`);
+                this.logger.debug('INDEXING complete', { unit: unit.name, duration: unitTime });
                 this.onProgress({
                     phase: 'indexing',
                     currentPlugin: 'JSModuleIndexer',
@@ -133,12 +185,11 @@ export class Orchestrator {
             processedUnits += batch.length;
         }
         this.profiler.end('INDEXING');
-        console.log(`[Orchestrator] ⏱️ INDEXING phase total: ${((Date.now() - indexingStart) / 1000).toFixed(2)}s`);
+        this.logger.info('INDEXING phase complete', { duration: ((Date.now() - indexingStart) / 1000).toFixed(2) });
         // Skip remaining phases if indexOnly mode (for coverage)
         if (this.indexOnly) {
             const totalTime = ((Date.now() - totalStartTime) / 1000).toFixed(2);
-            console.log(`[Orchestrator] ⏱️ indexOnly mode - skipping ANALYSIS/ENRICHMENT/VALIDATION`);
-            console.log(`[Orchestrator] ⏱️ Total time: ${totalTime}s for ${unitsToProcess.length} units`);
+            this.logger.info('indexOnly mode - skipping remaining phases', { duration: totalTime, units: unitsToProcess.length });
             return manifest;
         }
         // PHASE 2: ANALYSIS - все units (параллельно батчами)
@@ -180,9 +231,13 @@ export class Orchestrator {
                         },
                         modules: []
                     };
-                    await this.runPhase('ANALYSIS', { manifest: unitManifest, graph: this.graph, workerCount: 1 });
+                    await this.runPhase('ANALYSIS', {
+                        manifest: unitManifest,
+                        graph: this.graph,
+                        workerCount: 1,
+                    });
                     const unitTime = ((Date.now() - unitStart) / 1000).toFixed(2);
-                    console.log(`[Orchestrator] ⏱️ ANALYSIS ${unit.name}: ${unitTime}s`);
+                    this.logger.debug('ANALYSIS complete', { unit: unit.name, duration: unitTime });
                     this.onProgress({
                         phase: 'analysis',
                         currentPlugin: 'Analyzers',
@@ -196,27 +251,44 @@ export class Orchestrator {
             }
         }
         this.profiler.end('ANALYSIS');
-        console.log(`[Orchestrator] ⏱️ ANALYSIS phase total: ${((Date.now() - analysisStart) / 1000).toFixed(2)}s`);
+        this.logger.info('ANALYSIS phase complete', { duration: ((Date.now() - analysisStart) / 1000).toFixed(2) });
         // PHASE 3: ENRICHMENT - post-processing, граф traversal, вычисления (глобально)
         const enrichmentStart = Date.now();
         this.profiler.start('ENRICHMENT');
         this.onProgress({ phase: 'enrichment', currentPlugin: 'Starting enrichment...', message: 'Enriching graph data...', totalFiles: 0, processedFiles: 0 });
         await this.runPhase('ENRICHMENT', { manifest, graph: this.graph, workerCount: this.workerCount });
         this.profiler.end('ENRICHMENT');
-        console.log(`[Orchestrator] ⏱️ ENRICHMENT phase: ${((Date.now() - enrichmentStart) / 1000).toFixed(2)}s`);
+        this.logger.info('ENRICHMENT phase complete', { duration: ((Date.now() - enrichmentStart) / 1000).toFixed(2) });
+        // STRICT MODE BARRIER: Check for fatal errors after ENRICHMENT (REG-330)
+        if (this.strictMode) {
+            const enrichmentDiagnostics = this.diagnosticCollector.getByPhase('ENRICHMENT');
+            const strictErrors = enrichmentDiagnostics.filter(d => d.severity === 'fatal');
+            if (strictErrors.length > 0) {
+                this.logger.error(`Strict mode: ${strictErrors.length} unresolved reference(s) found`);
+                for (const err of strictErrors) {
+                    this.logger.error(`  [${err.code}] ${err.message}`, {
+                        file: err.file,
+                        line: err.line,
+                        plugin: err.plugin,
+                    });
+                }
+                throw new Error(`Strict mode: ${strictErrors.length} unresolved reference(s) found during ENRICHMENT. ` +
+                    `Run without --strict for graceful degradation, or fix the underlying issues.`);
+            }
+        }
         // PHASE 4: VALIDATION - проверка корректности графа (глобально)
         const validationStart = Date.now();
         this.profiler.start('VALIDATION');
         this.onProgress({ phase: 'validation', currentPlugin: 'Starting validation...', message: 'Validating graph structure...', totalFiles: 0, processedFiles: 0 });
         await this.runPhase('VALIDATION', { manifest, graph: this.graph, workerCount: this.workerCount });
         this.profiler.end('VALIDATION');
-        console.log(`[Orchestrator] ⏱️ VALIDATION phase: ${((Date.now() - validationStart) / 1000).toFixed(2)}s`);
+        this.logger.info('VALIDATION phase complete', { duration: ((Date.now() - validationStart) / 1000).toFixed(2) });
         // Flush graph to ensure all edges are persisted and queryable
         if (this.graph.flush) {
             await this.graph.flush();
         }
         const totalTime = ((Date.now() - totalStartTime) / 1000).toFixed(2);
-        console.log(`[Orchestrator] ⏱️ Total time: ${totalTime}s for ${unitsToProcess.length} units`);
+        this.logger.info('Analysis complete', { duration: totalTime, units: unitsToProcess.length });
         // Print profiling summary
         this.profiler.printSummary();
         return manifest;
@@ -262,14 +334,82 @@ export class Orchestrator {
         return units;
     }
     /**
-     * PHASE 0: Discovery - запуск плагинов DISCOVERY фазы
+     * PHASE 0: Discovery - запуск плагинов DISCOVERY фазы.
+     * If config services are provided, they take precedence and plugins are skipped.
      */
     async discover(projectPath) {
+        // REG-174: If config provided services, use them directly instead of running discovery plugins
+        if (this.configServices && this.configServices.length > 0) {
+            this.logger.info('Using config-provided services (skipping discovery plugins)', {
+                serviceCount: this.configServices.length
+            });
+            const services = [];
+            // For each config service:
+            // 1. Resolve path relative to project root (validation ensures paths are relative)
+            // 2. Auto-detect entrypoint from package.json if not specified
+            // 3. Fall back to 'index.js' if detection fails
+            for (const configSvc of this.configServices) {
+                // All paths are relative (absolute paths rejected by ConfigLoader validation)
+                const servicePath = join(projectPath, configSvc.path);
+                // Resolve entrypoint
+                let entrypoint;
+                if (configSvc.entryPoint) {
+                    entrypoint = configSvc.entryPoint;
+                }
+                else {
+                    // Auto-detect if not provided
+                    const packageJsonPath = join(servicePath, 'package.json');
+                    if (existsSync(packageJsonPath)) {
+                        try {
+                            const pkg = JSON.parse(readFileSync(packageJsonPath, 'utf-8'));
+                            entrypoint = resolveSourceEntrypoint(servicePath, pkg) ?? pkg.main ?? 'index.js';
+                        }
+                        catch (e) {
+                            this.logger.warn('Failed to read package.json for auto-detection', {
+                                service: configSvc.name,
+                                path: packageJsonPath,
+                                error: e.message
+                            });
+                            entrypoint = 'index.js';
+                        }
+                    }
+                    else {
+                        entrypoint = 'index.js';
+                    }
+                }
+                // Create SERVICE node
+                const serviceNode = NodeFactory.createService(configSvc.name, servicePath, {
+                    discoveryMethod: 'config',
+                    entrypoint: entrypoint,
+                });
+                await this.graph.addNode(serviceNode);
+                services.push({
+                    id: serviceNode.id,
+                    name: configSvc.name,
+                    path: servicePath,
+                    metadata: {
+                        entrypoint: join(servicePath, entrypoint),
+                    },
+                });
+                this.logger.info('Registered config service', {
+                    name: configSvc.name,
+                    path: servicePath,
+                    entrypoint: entrypoint
+                });
+            }
+            return {
+                services,
+                entrypoints: [], // Config services don't provide entrypoints
+                projectPath: projectPath
+            };
+        }
+        // ORIGINAL CODE: Run discovery plugins if no config services
         const context = {
             projectPath,
             graph: this.graph,
             config: this.config,
-            phase: 'DISCOVERY'
+            phase: 'DISCOVERY',
+            logger: this.logger,
         };
         // Фильтруем плагины для фазы DISCOVERY
         const discoveryPlugins = this.plugins.filter(p => p.metadata.phase === 'DISCOVERY');
@@ -325,9 +465,58 @@ export class Orchestrator {
             const pluginContext = {
                 ...context,
                 onProgress: this.onProgress,
-                forceAnalysis: this.forceAnalysis
+                forceAnalysis: this.forceAnalysis,
+                logger: this.logger,
+                strictMode: this.strictMode, // REG-330: Pass strict mode flag
             };
-            await plugin.execute(pluginContext);
+            // Add reportIssue for VALIDATION phase
+            if (phaseName === 'VALIDATION') {
+                pluginContext.reportIssue = async (issue) => {
+                    const node = NodeFactory.createIssue(issue.category, issue.severity, issue.message, plugin.metadata.name, issue.file, issue.line, issue.column || 0, { context: issue.context });
+                    await context.graph.addNode(node);
+                    if (issue.targetNodeId) {
+                        await context.graph.addEdge({
+                            src: node.id,
+                            dst: issue.targetNodeId,
+                            type: 'AFFECTS',
+                        });
+                    }
+                    return node.id;
+                };
+            }
+            try {
+                const result = await plugin.execute(pluginContext);
+                // Collect errors into diagnostics
+                this.diagnosticCollector.addFromPluginResult(phaseName, plugin.metadata.name, result);
+                // Log plugin completion with warning if errors occurred
+                if (!result.success) {
+                    console.warn(`[Orchestrator] Plugin ${plugin.metadata.name} reported failure`, {
+                        errors: result.errors.length,
+                        warnings: result.warnings.length,
+                    });
+                }
+                // Check for fatal errors - STOP immediately
+                if (this.diagnosticCollector.hasFatal()) {
+                    const allDiagnostics = this.diagnosticCollector.getAll();
+                    const fatal = allDiagnostics.find(d => d.severity === 'fatal');
+                    throw new Error(`Fatal error in ${plugin.metadata.name}: ${fatal?.message || 'Unknown fatal error'}`);
+                }
+            }
+            catch (e) {
+                // Plugin threw an exception (not just returned errors)
+                const error = e instanceof Error ? e : new Error(String(e));
+                // Don't re-add if this was already a fatal error we threw
+                if (!this.diagnosticCollector.hasFatal()) {
+                    this.diagnosticCollector.add({
+                        code: 'ERR_PLUGIN_THREW',
+                        severity: 'fatal',
+                        message: error.message,
+                        phase: phaseName,
+                        plugin: plugin.metadata.name,
+                    });
+                }
+                throw error; // Re-throw to stop analysis
+            }
             // Send completion for this plugin
             this.onProgress({
                 phase: phaseName.toLowerCase(),
@@ -336,6 +525,12 @@ export class Orchestrator {
             });
         }
     }
+    /**
+     * Get the diagnostic collector for retrieving all collected diagnostics
+     */
+    getDiagnostics() {
+        return this.diagnosticCollector;
+    }
     /**
      * Run queue-based parallel analysis using worker_threads and RFDB server
      *
@@ -429,13 +624,13 @@ export class Orchestrator {
         }
         // Check if server binary exists
         const projectRoot = join(dirname(fileURLToPath(import.meta.url)), '../..');
-        const serverBinary = join(projectRoot, 'rust-engine/target/release/rfdb-server');
-        const debugBinary = join(projectRoot, 'rust-engine/target/debug/rfdb-server');
+        const serverBinary = join(projectRoot, 'packages/rfdb-server/target/release/rfdb-server');
+        const debugBinary = join(projectRoot, 'packages/rfdb-server/target/debug/rfdb-server');
         let binaryPath = existsSync(serverBinary) ? serverBinary : debugBinary;
         if (!existsSync(binaryPath)) {
             console.log(`[Orchestrator] RFDB server binary not found at ${binaryPath}, building...`);
             execSync('cargo build --bin rfdb-server', {
-                cwd: join(projectRoot, 'rust-engine'),
+                cwd: join(projectRoot, 'packages/rfdb-server'),
                 stdio: 'inherit',
             });
             binaryPath = debugBinary;

package/dist/config/ConfigLoader.d.ts

@@ -0,0 +1,90 @@
+import type { ServiceDefinition } from '@grafema/types';
+/**
+ * Grafema configuration schema.
+ *
+ * YAML Location: .grafema/config.yaml (preferred) or .grafema/config.json (deprecated)
+ *
+ * Example config.yaml:
+ *
+ * ```yaml
+ * # Plugins for each analysis phase
+ * plugins:
+ *   indexing:
+ *     - JSModuleIndexer
+ *   analysis:
+ *     - JSASTAnalyzer
+ *     - ExpressRouteAnalyzer
+ *   enrichment:
+ *     - MethodCallResolver
+ *   validation:
+ *     - EvalBanValidator
+ *
+ * # Optional: Explicit service definitions (bypass auto-discovery)
+ * services:
+ *   - name: "backend"
+ *     path: "apps/backend"        # Relative to project root
+ *     entryPoint: "src/index.ts"  # Optional, auto-detected if omitted
+ *   - name: "frontend"
+ *     path: "apps/frontend"
+ * ```
+ *
+ * If 'services' is not specified or empty, auto-discovery is used (SimpleProjectDiscovery).
+ * If 'services' is specified and non-empty, auto-discovery plugins are skipped entirely.
+ */
+export interface GrafemaConfig {
+    plugins: {
+        discovery?: string[];
+        indexing: string[];
+        analysis: string[];
+        enrichment: string[];
+        validation: string[];
+    };
+    /**
+     * Optional explicit services for manual configuration.
+     * If provided and non-empty, auto-discovery is skipped.
+     */
+    services: ServiceDefinition[];
+    /**
+     * Glob patterns for files to include during indexing (optional).
+     * See OrchestratorConfig.include for documentation.
+     */
+    include?: string[];
+    /**
+     * Glob patterns for files to exclude during indexing (optional).
+     * See OrchestratorConfig.exclude for documentation.
+     */
+    exclude?: string[];
+    /**
+     * Enable strict mode for fail-fast debugging.
+     * When true, analysis fails if enrichers cannot resolve references.
+     * When false (default), graceful degradation with warnings.
+     *
+     * Can be overridden via CLI: --strict
+     */
+    strict?: boolean;
+}
+/**
+ * Default plugin configuration.
+ * Matches current DEFAULT_PLUGINS in analyze.ts and config.ts (MCP).
+ */
+export declare const DEFAULT_CONFIG: GrafemaConfig;
+/**
+ * Load Grafema config from project directory.
+ *
+ * Priority:
+ * 1. config.yaml (preferred)
+ * 2. config.json (deprecated, fallback)
+ * 3. DEFAULT_CONFIG (if neither exists)
+ *
+ * Warnings:
+ * - Logs deprecation warning if config.json is used
+ * - Logs parse errors but doesn't throw (returns defaults)
+ *
+ * @param projectPath - Absolute path to project root
+ * @param logger - Optional logger for warnings (defaults to console.warn)
+ * @returns Parsed config or defaults
+ */
+export declare function loadConfig(projectPath: string, logger?: {
+    warn: (msg: string) => void;
+}): GrafemaConfig;
+//# sourceMappingURL=ConfigLoader.d.ts.map

package/dist/config/ConfigLoader.d.ts.map

@@ -0,0 +1 @@
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