@documentation-robotics/cli 0.1.0 → 0.1.5

package/dist/core/model.js.map

@@ -1,7 +1,7 @@
 {
   "version": 3,
   "sources": ["../../src/core/model.ts"],
-  "sourcesContent": ["import { Layer } from \"./layer.js\"\nimport { Manifest } from \"./manifest.js\"\nimport { Element } from \"./element.js\";\nimport { ProjectionEngine } from \"./projection-engine.js\";\nimport { Relationships } from \"./relationships.js\";\nimport { ActiveChangesetContext } from \"./active-changeset.js\";\nimport { ensureDir, writeFile } from \"../utils/file-io.js\";\nimport { startSpan, endSpan } from \"../telemetry/index.js\";\nimport { findProjectRoot } from \"../utils/project-paths.js\";\nimport type { ManifestData, ModelOptions } from \"../types/index.js\";\nimport path from 'node:path';\nimport fs from 'node:fs/promises';\n\n// Fallback for runtime environments where TELEMETRY_ENABLED is not defined by esbuild\ndeclare const TELEMETRY_ENABLED: boolean | undefined\nconst isTelemetryEnabled = typeof TELEMETRY_ENABLED !== 'undefined' ? TELEMETRY_ENABLED : false\n\n/**\n * Model class representing the complete architecture model\n */\nexport class Model {\n  rootPath: string\n  manifest: Manifest\n  layers: Map<string, Layer>\n  relationships: Relationships\n  lazyLoad: boolean\n  private loadedLayers: Set<string>\n  private projectionEngine?: ProjectionEngine\n  private activeChangesetContext?: ActiveChangesetContext\n\n  constructor(rootPath: string, manifest: Manifest, options: ModelOptions = {}) {\n    this.rootPath = rootPath\n    this.manifest = manifest\n    this.layers = new Map()\n    this.relationships = new Relationships()\n    this.lazyLoad = options.lazyLoad ?? false\n    this.loadedLayers = new Set()\n  }\n\n  /**\n   * Get a layer, loading it if lazy loading is enabled\n   */\n  async getLayer(name: string): Promise<Layer | undefined> {\n    if (this.lazyLoad && !this.loadedLayers.has(name)) {\n      await this.loadLayer(name)\n    }\n    return this.layers.get(name)\n  }\n\n  /**\n   * Get an element by ID across all layers\n   */\n  getElementById(id: string): Element | undefined {\n    for (const layer of this.layers.values()) {\n      const element = layer.elements.get(id);\n      if (element) {\n        return element;\n      }\n    }\n    return undefined;\n  }\n\n  /**\n   * Get projection engine (lazily initialized)\n   */\n  getProjectionEngine(): ProjectionEngine {\n    if (!this.projectionEngine) {\n      this.projectionEngine = new ProjectionEngine(this);\n    }\n    return this.projectionEngine;\n  }\n\n  /**\n   * Get active changeset context (lazily initialized)\n   */\n  getActiveChangesetContext(): ActiveChangesetContext {\n    if (!this.activeChangesetContext) {\n      this.activeChangesetContext = new ActiveChangesetContext(this.rootPath);\n    }\n    return this.activeChangesetContext;\n  }\n\n  /**\n   * Load a layer from disk (legacy format: model/XX_layername/*.yaml files)\n   * Supports reading layer paths from manifest for Python CLI compatibility\n   */\n  async loadLayer(name: string): Promise<void> {\n    const layerSpan = isTelemetryEnabled ? startSpan('layer.load', {\n      'layer.name': name,\n    }) : null\n\n    try {\n      const fs = await import('fs/promises')\n      const yaml = await import('yaml')\n\n      let layerPath: string | null = null\n\n      // PRIORITY 1: Read layer path from manifest (Python CLI compatibility)\n      if (this.manifest.layers && this.manifest.layers[name]) {\n        const layerConfig = this.manifest.layers[name]\n        if (layerConfig.path) {\n          // Path in manifest is relative to root\n          const fullPath = `${this.rootPath}/${layerConfig.path.replace(/\\/$/, '')}`\n          try {\n            await fs.access(fullPath)\n            layerPath = fullPath\n          } catch (err) {\n            // Path in manifest doesn't exist - this is an error\n            if (process.env.DEBUG) {\n              console.debug(`Manifest specifies path ${layerConfig.path} but it doesn't exist`)\n            }\n          }\n        }\n      }\n\n      // FALLBACK: Auto-discover by scanning directory with naming convention\n      if (!layerPath) {\n        const modelDir = `${this.rootPath}/documentation-robotics/model`\n\n        try {\n          const entries = await fs.readdir(modelDir, { withFileTypes: true })\n          const layerDir = entries.find(e =>\n            e.isDirectory() && e.name.match(/^\\d{2}_/) && e.name.replace(/^\\d{2}_/, '') === name\n          )\n\n          if (layerDir) {\n            layerPath = `${modelDir}/${layerDir.name}`\n          }\n        } catch {\n          // Model directory doesn't exist or can't be read\n        }\n      }\n\n      if (!layerPath) {\n        return // Layer directory not found\n      }\n\n      const layer = new Layer(name)\n\n      // Load all YAML files in the layer directory\n      const files = await fs.readdir(layerPath)\n      for (const file of files) {\n        if (file.endsWith('.yaml') || file.endsWith('.yml')) {\n          const filePath = `${layerPath}/${file}`\n          const yamlContent = await fs.readFile(filePath, 'utf-8')\n          const elements = yaml.parse(yamlContent)\n\n          // Add each element from the YAML file\n          if (elements && typeof elements === 'object') {\n            for (const [key, element] of Object.entries(elements)) {\n              if (element && typeof element === 'object') {\n                const el: any = element\n\n                // Auto-generate layer-prefixed ID if missing (Python CLI compatibility)\n                // Python: element_id = f\"{self.name}.{key}\" when no id field\n                const elementId = el.id || `${name}.${key}`\n\n                // Infer type from filename if not specified (Python CLI compatibility)\n                // Python: _infer_type_from_file removes trailing 's' from stem\n                let elementType = el.type\n                if (!elementType) {\n                  const stem = file.replace(/\\.ya?ml$/, '')\n                  elementType = stem.endsWith('s') ? stem.slice(0, -1) : stem\n                }\n\n                const newElement = new Element({\n                  id: elementId,\n                  name: el.name || key,\n                  type: elementType,\n                  description: el.description || el.documentation || '',\n                  properties: el.properties || {},\n                  relationships: el.relationships || [],\n                  references: el.references || [],\n                  layer: name,  // Track layer (Python CLI compatibility)\n                  filePath: filePath,  // Track source file (Python CLI compatibility)\n                  rawData: el  // Preserve raw YAML data (Python CLI compatibility)\n                });\n                layer.addElement(newElement);\n              }\n            }\n          }\n        }\n      }\n\n      this.layers.set(name, layer)\n      this.loadedLayers.add(name)\n\n      if (isTelemetryEnabled && layerSpan) {\n        layerSpan.setAttribute('layer.element_count', layer.elements.size)\n      }\n    } finally {\n      if (isTelemetryEnabled) {\n        endSpan(layerSpan)\n      }\n    }\n  }\n\n  /**\n   * Add a layer to the model\n   */\n  addLayer(layer: Layer): void {\n    this.layers.set(layer.name, layer)\n    this.loadedLayers.add(layer.name)\n  }\n\n  /**\n   * Get all loaded layer names\n   */\n  getLayerNames(): string[] {\n    return Array.from(this.layers.keys())\n  }\n\n  /**\n   * Save a layer to disk (legacy format: model/XX_layername/*.yaml)\n   */\n  async saveLayer(name: string): Promise<void> {\n    const layer = this.layers.get(name)\n    if (!layer) {\n      throw new Error(`Layer ${name} not found`)\n    }\n\n    const fs = await import('fs/promises')\n    const yaml = await import('yaml')\n\n    let layerPath: string | null = null\n\n    // Try to get layer path from manifest first (Python CLI compatibility)\n    if (this.manifest.layers && this.manifest.layers[name]) {\n      const layerConfig = this.manifest.layers[name]\n      if (layerConfig.path) {\n        const fullPath = `${this.rootPath}/${layerConfig.path.replace(/\\/$/, '')}`\n        try {\n          await fs.access(fullPath)\n          layerPath = fullPath\n        } catch {\n          // Path doesn't exist, create it\n          await ensureDir(fullPath)\n          layerPath = fullPath\n        }\n      }\n    }\n\n    // If manifest path not found, try discovery by scanning directory\n    if (!layerPath) {\n      const modelDir = `${this.rootPath}/documentation-robotics/model`\n\n      try {\n        const entries = await fs.readdir(modelDir, { withFileTypes: true })\n        const layerDir = entries.find(e =>\n          e.isDirectory() && e.name.match(/^\\d{2}_/) &&\n          e.name.replace(/^\\d{2}_/, '') === name\n        )\n\n        if (layerDir) {\n          layerPath = `${modelDir}/${layerDir.name}`\n        }\n      } catch {\n        // Model directory doesn't exist or can't be read\n      }\n    }\n\n    // If still not found, create using default format\n    if (!layerPath) {\n      // Find the order number for this layer\n      // Handle layer names with or without numeric prefix (e.g., \"motivation\" or \"01-motivation\")\n      const layerNameWithoutPrefix = name.replace(/^\\d{2}-/, '')\n      const layerOrder = [\n        'motivation', 'business', 'security', 'application', 'technology',\n        'api', 'data-model', 'datastore', 'ux', 'navigation', 'apm', 'testing'\n      ]\n      const index = layerOrder.indexOf(layerNameWithoutPrefix)\n      if (index >= 0) {\n        const orderNum = String(index + 1).padStart(2, '0')\n        // Use Python CLI structure\n        layerPath = `${this.rootPath}/documentation-robotics/model/${orderNum}_${layerNameWithoutPrefix}`\n        await ensureDir(layerPath)\n      } else {\n        throw new Error(`Unknown layer ${name} and no path configured in manifest`)\n      }\n    }\n\n    // Delete all existing YAML files in the layer directory to ensure\n    // we don't keep stale files after element deletion\n    try {\n      const existingFiles = await fs.readdir(layerPath)\n      for (const file of existingFiles) {\n        if (file.endsWith('.yaml') || file.endsWith('.yml')) {\n          await fs.unlink(`${layerPath}/${file}`)\n        }\n      }\n    } catch (err) {\n      // Directory might not exist yet, that's okay\n    }\n\n    // Group elements by type\n    const elementsByType = new Map<string, any[]>()\n    for (const element of layer.elements.values()) {\n      const type = element.type + 's' // pluralize (e.g., goal -> goals)\n      if (!elementsByType.has(type)) {\n        elementsByType.set(type, [])\n      }\n      elementsByType.get(type)!.push(element)\n    }\n\n    // Write each type to its own YAML file\n    for (const [type, elements] of elementsByType) {\n      const filename = `${type}.yaml`\n      const filePath = `${layerPath}/${filename}`\n\n      // Convert elements to YAML format\n      const yamlData: any = {}\n      for (const element of elements) {\n        const key = element.id.split('.').pop() || element.id\n        yamlData[key] = {\n          id: element.id,\n          name: element.name,\n          type: element.type,\n          ...(element.description && { documentation: element.description }),\n          ...(Object.keys(element.properties || {}).length > 0 && { properties: element.properties }),\n          ...(element.references && element.references.length > 0 && { references: element.references }),\n          // Relationships are now stored in centralized relationships.yaml, not inline\n        }\n      }\n\n      await writeFile(filePath, yaml.stringify(yamlData))\n    }\n\n    layer.markClean()\n  }\n\n  /**\n   * Save model (saves all dirty layers and manifest)\n   */\n  async save(): Promise<void> {\n    await this.saveDirtyLayers();\n    await this.saveManifest();\n  }\n\n  /**\n   * Save all dirty layers to disk\n   */\n  async saveDirtyLayers(): Promise<void> {\n    // Count dirty layers before operation\n    let dirtyLayerCount = 0\n    for (const layer of this.layers.values()) {\n      if (layer.isDirty()) {\n        dirtyLayerCount++\n      }\n    }\n\n    const span = isTelemetryEnabled ? startSpan('model.save', {\n      'model.path': this.rootPath,\n      'model.dirty_layer_count': dirtyLayerCount,\n    }) : null\n\n    try {\n      for (const layer of this.layers.values()) {\n        if (layer.isDirty()) {\n          await this.saveLayer(layer.name)\n        }\n      }\n    } finally {\n      if (isTelemetryEnabled) {\n        endSpan(span)\n      }\n    }\n  }\n\n  /**\n   * Save the manifest to disk (Python CLI format: documentation-robotics/model/manifest.yaml)\n   * Preserves Python CLI metadata fields for compatibility\n   */\n  async saveManifest(): Promise<void> {\n    this.manifest.updateModified()\n    const yaml = await import('yaml')\n    const manifestPath = `${this.rootPath}/documentation-robotics/model/manifest.yaml`\n\n    // Convert to legacy YAML format, preserving Python CLI fields\n    const yamlData: any = {\n      version: this.manifest.version,\n      schema: 'documentation-robotics-v1',\n      cli_version: this.manifest.version || '0.1.0',\n      spec_version: this.manifest.specVersion,\n      created: this.manifest.created,\n      updated: this.manifest.modified,\n      project: {\n        name: this.manifest.name,\n        description: this.manifest.description,\n        version: this.manifest.version,\n      },\n      documentation: '.dr/README.md',\n      layers: this.manifest.layers || {} as any,\n    }\n\n    // If layers not preserved from load, generate default structure\n    if (!this.manifest.layers || Object.keys(this.manifest.layers).length === 0) {\n      const layerOrder = [\n        'motivation', 'business', 'security', 'application', 'technology',\n        'api', 'data-model', 'datastore', 'ux', 'navigation', 'apm', 'testing'\n      ]\n\n      for (let i = 0; i < layerOrder.length; i++) {\n        const layerName = layerOrder[i]\n        const layer = this.layers.get(layerName)\n        const orderNum = String(i + 1).padStart(2, '0')\n\n        yamlData.layers[layerName] = {\n          order: i + 1,\n          name: layerName.charAt(0).toUpperCase() + layerName.slice(1).replace('-', ' '),\n          path: `documentation-robotics/model/${orderNum}_${layerName}/`,\n          schema: `.dr/schemas/${orderNum}-${layerName}-layer.schema.json`,\n          enabled: true,\n          ...(layer && { elements: this.getLayerElementCounts(layer) }),\n        }\n      }\n    } else {\n      // Update element counts in existing layer configs\n      for (const [layerName, layerConfig] of Object.entries(yamlData.layers)) {\n        const layer = this.layers.get(layerName)\n        if (layer) {\n          (layerConfig as any).elements = this.getLayerElementCounts(layer)\n        }\n      }\n    }\n\n    // Preserve Python CLI metadata fields\n    if (this.manifest.statistics) {\n      // Update statistics with current counts\n      const stats = { ...this.manifest.statistics }\n      stats.total_elements = Array.from(this.layers.values())\n        .reduce((sum, layer) => sum + layer.elements.size, 0)\n      yamlData.statistics = stats\n    }\n\n    if (this.manifest.cross_references) {\n      yamlData.cross_references = this.manifest.cross_references\n    }\n\n    if (this.manifest.conventions) {\n      yamlData.conventions = this.manifest.conventions\n    }\n\n    if (this.manifest.upgrade_history) {\n      yamlData.upgrade_history = this.manifest.upgrade_history\n    }\n\n    if (this.manifest.changeset_history && this.manifest.changeset_history.length > 0) {\n      yamlData.changeset_history = this.manifest.changeset_history\n    }\n\n    await ensureDir(`${this.rootPath}/documentation-robotics/model`)\n    await writeFile(manifestPath, yaml.stringify(yamlData))\n  }\n\n  private getLayerElementCounts(layer: Layer): Record<string, number> {\n    const counts: Record<string, number> = {}\n    for (const element of layer.elements.values()) {\n      counts[element.type] = (counts[element.type] || 0) + 1\n    }\n    return counts\n  }\n\n  /**\n   * Load relationships from relationships.yaml\n   */\n  async loadRelationships(): Promise<void> {\n    const fs = await import('fs/promises')\n    const yaml = await import('yaml')\n    const relationshipsPath = `${this.rootPath}/documentation-robotics/model/relationships.yaml`\n\n    try {\n      const yamlContent = await fs.readFile(relationshipsPath, 'utf-8')\n      const data = yaml.parse(yamlContent)\n\n      if (Array.isArray(data)) {\n        this.relationships = Relationships.fromArray(data)\n      }\n    } catch (err) {\n      // If file doesn't exist, that's okay - start with empty relationships\n      if ((err as any).code !== 'ENOENT') {\n        // But if it's a different error, we should know about it\n        if (process.env.DEBUG) {\n          console.debug(`Warning: Failed to load relationships.yaml: ${err}`)\n        }\n      }\n    }\n  }\n\n  /**\n   * Save relationships to relationships.yaml\n   */\n  async saveRelationships(): Promise<void> {\n    const fs = await import('fs/promises')\n    const yaml = await import('yaml')\n    const relationshipsPath = `${this.rootPath}/documentation-robotics/model/relationships.yaml`\n\n    await ensureDir(`${this.rootPath}/documentation-robotics/model`)\n\n    const data = this.relationships.toArray()\n\n    // Add header comment with timestamp to ensure file always changes\n    // This matches Python CLI behavior\n    const timestamp = new Date().toISOString()\n    const header = `# Intra-layer relationships\n# Format: source_id -> predicate -> target_id\n# Last updated: ${timestamp}\n\n`\n    const yamlContent = header + yaml.stringify(data)\n\n    await fs.writeFile(relationshipsPath, yamlContent, 'utf-8')\n    this.relationships.markClean()\n  }\n\n  /**\n   * Resolve model paths (private helper)\n   *\n   * @param startPath - Starting path for search\n   * @returns Project root and manifest path\n   */\n  private static async resolveModelPaths(startPath?: string): Promise<{\n    projectRoot: string;\n    manifestPath: string;\n  }> {\n    const searchPath = startPath || process.cwd();\n\n    // Optional override via env var (highest priority)\n    if (process.env.DR_MODEL_PATH) {\n      const envPath = path.resolve(process.env.DR_MODEL_PATH);\n      let manifestPath: string;\n\n      if (envPath.endsWith('manifest.yaml')) {\n        manifestPath = envPath;\n      } else if (envPath.endsWith('model')) {\n        manifestPath = path.join(envPath, 'manifest.yaml');\n      } else {\n        manifestPath = path.join(envPath, 'documentation-robotics', 'model', 'manifest.yaml');\n      }\n\n      try {\n        await fs.access(manifestPath);\n        const projectRoot = path.dirname(path.dirname(path.dirname(manifestPath)));\n        return { projectRoot, manifestPath: path.normalize(manifestPath) };\n      } catch {\n        throw new Error(`Model not found at DR_MODEL_PATH: ${process.env.DR_MODEL_PATH}`);\n      }\n    }\n\n    // Use findProjectRoot to locate documentation_robotics/ folder\n    const projectRoot = await findProjectRoot(searchPath);\n\n    if (!projectRoot) {\n      throw new Error(\n        'No DR project found. Could not find documentation_robotics/ folder.\\n' +\n        'Run \"dr init\" to create a new project, or navigate to a directory containing a DR project.'\n      );\n    }\n\n    const manifestPath = path.join(projectRoot, 'documentation-robotics', 'model', 'manifest.yaml');\n\n    try {\n      await fs.access(manifestPath);\n      return { projectRoot, manifestPath };\n    } catch {\n      throw new Error(\n        `Found documentation_robotics/ at ${projectRoot} but no model found. ` +\n        `Expected: ${manifestPath}\\n` +\n        `Run \"dr init\" to create a model.`\n      );\n    }\n  }\n\n  /**\n   * Load a model from disk\n   *\n   * Expected structure:\n   * <project-root>/\n   * \u2514\u2500\u2500 documentation_robotics/\n   *     \u2514\u2500\u2500 model/\n   *         \u2514\u2500\u2500 manifest.yaml\n   *\n   * @param startPath - Starting path for project search (defaults to process.cwd())\n   * @param options - Model loading options\n   * @returns Loaded Model instance\n   */\n  static async load(startPath?: string, options: ModelOptions = {}): Promise<Model> {\n    const span = isTelemetryEnabled ? startSpan('model.load', {\n      'model.path': startPath || process.cwd(),\n      'model.type': 'dr-legacy',\n    }) : null\n\n    try {\n      // Resolve project root and manifest path\n      const { projectRoot, manifestPath } = await Model.resolveModelPaths(startPath);\n\n      const yaml = await import('yaml')\n\n      // Load manifest from resolved path\n      const yamlContent = await fs.readFile(manifestPath, 'utf-8')\n      const legacyData = yaml.parse(yamlContent)\n\n      // Convert legacy format to internal format\n      const manifestData: any = {\n        name: legacyData.project?.name || 'Unnamed Model',\n        description: legacyData.project?.description || '',\n        version: legacyData.project?.version || legacyData.version || '0.1.0',\n        specVersion: legacyData.spec_version || '0.6.0',\n        created: legacyData.created || new Date().toISOString(),\n        modified: legacyData.updated || new Date().toISOString(),\n        // Preserve Python CLI metadata fields\n        layers: legacyData.layers,\n        statistics: legacyData.statistics || {\n          total_elements: 0,\n          total_relationships: 0,\n          completeness: 0.0,\n          last_validation: null,\n          validation_status: 'not_validated'\n        },\n        cross_references: legacyData.cross_references || {\n          total: 0,\n          by_type: {}\n        },\n        conventions: legacyData.conventions,\n        upgrade_history: legacyData.upgrade_history || []\n      }\n      const manifest = new Manifest(manifestData)\n      const model = new Model(projectRoot, manifest, options)\n\n      // Load all available layers if lazyLoad is false\n      if (!options.lazyLoad) {\n        try {\n          // If manifest has layer definitions, use those\n          if (legacyData.layers) {\n            for (const layerName of Object.keys(legacyData.layers)) {\n              const layerConfig = legacyData.layers[layerName]\n              if (layerConfig.enabled !== false) {\n                await model.loadLayer(layerName)\n              }\n            }\n          } else {\n            // Otherwise scan for layer directories\n            const modelDir = manifestPath.replace('/manifest.yaml', '')\n            const entries = await fs.readdir(modelDir, { withFileTypes: true })\n\n            for (const entry of entries) {\n              if (entry.isDirectory() && entry.name.match(/^\\d{2}_/)) {\n                const layerName = entry.name.replace(/^\\d{2}_/, '')\n                await model.loadLayer(layerName)\n              }\n            }\n          }\n        } catch (e) {\n          // If layers directory doesn't exist or can't be read, just continue\n          if (process.env.DEBUG) {\n            const error = e instanceof Error ? e.message : String(e)\n            if (!error.includes('ENOENT')) {\n              console.debug(`Warning: Failed to load layers directory: ${error}`)\n            }\n          }\n        }\n      }\n\n      // Load relationships from relationships.yaml\n      await model.loadRelationships()\n\n      // Count total entities across all layers\n      let entityCount = 0\n      for (const layer of model.layers.values()) {\n        entityCount += layer.elements.size\n      }\n\n      if (isTelemetryEnabled && span) {\n        span.setAttribute('model.entity_count', entityCount)\n        span.setAttribute('model.layer_count', model.layers.size)\n      }\n\n      return model\n    } finally {\n      if (isTelemetryEnabled) {\n        endSpan(span)\n      }\n    }\n  }\n\n  /**\n   * Initialize a new model in a directory (legacy format)\n   */\n  static async init(\n    rootPath: string,\n    manifestData: ManifestData,\n    options: ModelOptions = {}\n  ): Promise<Model> {\n    // Create model directory using Python CLI structure: documentation-robotics/model/\n    await ensureDir(`${rootPath}/documentation-robotics/model`);\n\n    const layerOrder = [\n      'motivation', 'business', 'security', 'application', 'technology',\n      'api', 'data-model', 'datastore', 'ux', 'navigation', 'apm', 'testing'\n    ];\n\n    for (let i = 0; i < layerOrder.length; i++) {\n      const orderNum = String(i + 1).padStart(2, '0');\n      const layerName = layerOrder[i];\n      await ensureDir(`${rootPath}/documentation-robotics/model/${orderNum}_${layerName}`);\n    }\n\n    const manifest = new Manifest(manifestData);\n    const model = new Model(rootPath, manifest, options);\n\n    await model.saveManifest();\n\n    return model;\n  }\n}\n"],
-  "mappings": 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-  "names": ["fs", "manifestPath"]
+  "sourcesContent": ["import { Layer } from \"./layer.js\";\nimport { Manifest } from \"./manifest.js\";\nimport { Element } from \"./element.js\";\nimport { GraphModel, type GraphEdge } from \"./graph-model.js\";\nimport { VirtualProjectionEngine } from \"./virtual-projection.js\";\nimport { StagedChangesetStorage } from \"./staged-changeset-storage.js\";\nimport { Relationships } from \"./relationships.js\";\nimport { CANONICAL_LAYER_NAMES } from \"./layers.js\";\nimport type { StagedChange } from \"./changeset.js\";\nimport { ensureDir, writeFile } from \"../utils/file-io.js\";\nimport { getCliVersion } from \"../utils/spec-version.js\";\nimport { startSpan, endSpan, startActiveSpan } from \"../telemetry/index.js\";\nimport { findProjectRoot } from \"../utils/project-paths.js\";\nimport { getNodeType } from \"../generated/node-types.js\";\nimport type { SpecNodeId } from \"../generated/node-types.js\";\nimport type { ManifestData, ModelOptions } from \"../types/index.js\";\nimport path from \"node:path\";\nimport fs from \"node:fs/promises\";\nimport crypto from \"node:crypto\";\n\n/**\n * Derive a deterministic UUID from a path string using SHA-256.\n * Produces a stable UUID4-like value so migration doesn't regenerate UUIDs on every load.\n */\nfunction deterministicUUID(path: string): string {\n  const hash = crypto.createHash(\"sha256\").update(path).digest(\"hex\");\n  return [\n    hash.slice(0, 8),\n    hash.slice(8, 12),\n    \"4\" + hash.slice(13, 16), // version 4 marker\n    ((parseInt(hash.slice(16, 18), 16) & 0x3f) | 0x80).toString(16) + hash.slice(18, 20), // variant\n    hash.slice(20, 32),\n  ].join(\"-\");\n}\n\n/**\n * Convert a PascalCase title to snake_case.\n * Handles acronyms correctly: \"UXApplication\" \u2192 \"ux_application\", \"OpenAPIDocument\" \u2192 \"open_api_document\".\n */\nfunction titleToSnakeCase(title: string): string {\n  return title\n    .replace(/([A-Z]+)([A-Z][a-z])/g, \"$1_$2\") // \"APIDoc\" \u2192 \"API_Doc\"\n    .replace(/([a-z\\d])([A-Z])/g, \"$1_$2\")       // \"appComponent\" \u2192 \"app_Component\"\n    .toLowerCase();\n}\n\n/**\n * Derive a snake_case file stem for a given element type.\n * Uses the spec node title for accurate word boundaries (e.g., \"InputSpacePartition\" \u2192 \"input_space_partition\").\n * Falls back to the raw type string when the title is unavailable.\n */\nfunction typeToSnakeStem(specNodeId: string | undefined, type: string): string {\n  if (specNodeId) {\n    const nodeType = getNodeType(specNodeId as SpecNodeId);\n    if (nodeType?.title) {\n      return titleToSnakeCase(nodeType.title);\n    }\n  }\n  return type;\n}\n\n// Fallback for runtime environments where TELEMETRY_ENABLED is not defined by esbuild\ndeclare const TELEMETRY_ENABLED: boolean | undefined;\nconst isTelemetryEnabled = typeof TELEMETRY_ENABLED !== \"undefined\" ? TELEMETRY_ENABLED : false;\n\n/**\n * Model class representing the complete architecture model\n * Uses GraphModel internally for graph-based storage\n */\nexport class Model {\n  rootPath: string;\n  manifest: Manifest;\n  graph: GraphModel;\n  layers: Map<string, Layer>;\n  relationships: Relationships;\n  lazyLoad: boolean;\n  private loadedLayers: Set<string>;\n  private virtualProjectionEngine?: VirtualProjectionEngine;\n  /** ID of the currently active changeset, or null if none is active. Set during load(). */\n  private _activeChangesetId: string | null = null;\n  /** Layer names that exist only in staged changes (not yet committed to base model). */\n  private _stagedLayerNames: Set<string> = new Set();\n\n  constructor(rootPath: string, manifest: Manifest, options: ModelOptions = {}) {\n    this.rootPath = rootPath;\n    this.manifest = manifest;\n    this.graph = new GraphModel();\n    this.layers = new Map();\n    this.relationships = new Relationships();\n    this.lazyLoad = options.lazyLoad ?? false;\n    this.loadedLayers = new Set();\n  }\n\n  /**\n   * Get the committed base layer (no staging projection).\n   * Used internally by VirtualProjectionEngine and commit() to access the raw base model\n   * without triggering infinite recursion or double-projection.\n   */\n  async getBaseLayer(name: string): Promise<Layer | undefined> {\n    if (this.lazyLoad && !this.loadedLayers.has(name)) {\n      await this.loadLayer(name);\n    }\n    return this.layers.get(name);\n  }\n\n  /**\n   * Get a layer, transparently merging staged changes when an active changeset exists.\n   * Falls back to the committed base layer if no changeset is active or projection fails.\n   */\n  async getLayer(name: string): Promise<Layer | undefined> {\n    if (this.lazyLoad && !this.loadedLayers.has(name)) {\n      await this.loadLayer(name);\n    }\n\n    // If an active changeset is present, return a projected (base + staged) layer\n    if (this._activeChangesetId) {\n      try {\n        return await this.getVirtualProjectionEngine().projectLayer(\n          this,\n          this._activeChangesetId,\n          name\n        );\n      } catch {\n        // Fall back to base layer on projection failure (e.g. corrupt changeset)\n        return this.layers.get(name);\n      }\n    }\n\n    return this.layers.get(name);\n  }\n\n  /**\n   * Get an element by ID across all layers\n   * Supports both UUID and semantic ID (layer.type.kebab-name) lookup\n   */\n  getElementById(id: string): Element | undefined {\n    for (const layer of this.layers.values()) {\n      const element = layer.getElement(id);\n      if (element) {\n        return element;\n      }\n    }\n    return undefined;\n  }\n\n  /**\n   * Get virtual projection engine (lazily initialized)\n   */\n  getVirtualProjectionEngine(): VirtualProjectionEngine {\n    if (!this.virtualProjectionEngine) {\n      this.virtualProjectionEngine = new VirtualProjectionEngine(this.rootPath);\n    }\n    return this.virtualProjectionEngine;\n  }\n\n  /**\n   * Returns the active changeset ID, or null if no changeset is active.\n   * Used by commands that need to project the full model (e.g. validate).\n   */\n  getActiveChangesetId(): string | null {\n    return this._activeChangesetId;\n  }\n\n  /**\n   * Load a layer from disk (model/XX_layername/*.yaml files)\n   */\n  async loadLayer(name: string): Promise<void> {\n    await startActiveSpan(\"layer.load\", async (layerSpan) => {\n      const fs = await import(\"fs/promises\");\n      const yaml = await import(\"yaml\");\n\n      let layerPath: string | null = null;\n\n      // Auto-discover by scanning directory with naming convention\n      const modelDir = `${this.rootPath}/documentation-robotics/model`;\n\n      try {\n        const entries = await fs.readdir(modelDir, { withFileTypes: true });\n        const layerDir = entries.find(\n          (e) =>\n            e.isDirectory() && e.name.match(/^\\d{2}_/) && e.name.replace(/^\\d{2}_/, \"\") === name\n        );\n\n        if (layerDir) {\n          layerPath = `${modelDir}/${layerDir.name}`;\n        }\n      } catch {\n        // Model directory doesn't exist or can't be read\n      }\n\n      if (!layerPath) {\n        return; // Layer directory not found\n      }\n\n      const layer = new Layer(name, this.graph);\n      let parseErrorCount = 0;\n\n      // Load all YAML files in the layer directory\n      const files = await fs.readdir(layerPath);\n      for (const file of files) {\n        if (file.endsWith(\".yaml\") || file.endsWith(\".yml\")) {\n          const filePath = `${layerPath}/${file}`;\n          try {\n            const yamlContent = await fs.readFile(filePath, \"utf-8\");\n            const elements = yaml.parse(yamlContent);\n\n            // Add each element from the YAML file\n            if (elements && typeof elements === \"object\") {\n              for (const [key, element] of Object.entries(elements)) {\n                if (element && typeof element === \"object\") {\n                  const el: any = element;\n\n                  // Derive id, path, and type using the 3-case migration logic:\n                  // Case 1: element already has both id (UUID) and path \u2192 use as-is\n                  // Case 2: element.id looks like a slug (layer.type.name) \u2192 move to path, generate UUID\n                  // Case 3: element has UUID id but no path \u2192 derive path from layer_id.type.kebab(name)\n                  const isSlugPattern = /^[a-z][a-z0-9-]*\\.[a-z][a-z0-9-]*\\.[a-z][a-z0-9-]*$/.test(el.id || \"\");\n                  const isUUIDPattern = /^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$/i.test(el.id || \"\");\n\n                  let elementId: string;\n                  let elementPath: string;\n                  let extractedType: string | undefined = undefined;\n\n                  if (el.path && isUUIDPattern) {\n                    // Case 1: already has both path and UUID id\n                    elementId = el.id;\n                    elementPath = el.path;\n                    const pathParts = el.path.split(\".\");\n                    if (pathParts.length >= 3) extractedType = pathParts[1];\n                  } else if (el.path && !isUUIDPattern) {\n                    // Has a path but id is not a UUID \u2014 migrate id to deterministic UUID\n                    elementPath = el.path;\n                    elementId = deterministicUUID(el.path);\n                    const pathParts = el.path.split(\".\");\n                    if (pathParts.length >= 3) extractedType = pathParts[1];\n                  } else if (isSlugPattern) {\n                    // Case 2: slug-looking id \u2192 move to path, generate deterministic UUID\n                    elementPath = el.id;\n                    elementId = deterministicUUID(el.id);\n                    const parts = el.id.split(\".\");\n                    if (parts.length >= 3) extractedType = parts[1];\n                  } else if (isUUIDPattern) {\n                    // Case 3: UUID id, no path \u2192 derive path\n                    elementId = el.id;\n                    const layerId = el.layer_id || name;\n                    const rawType = el.type || \"\";\n                    const rawName = el.name || key;\n                    const kebabName = rawName.toLowerCase().replace(/[\\s_]+/g, \"-\").replace(/[^a-z0-9-]/g, \"\").replace(/-+/g, \"-\").replace(/^-+|-+$/g, \"\");\n                    elementPath = `${layerId}.${rawType}.${kebabName}`;\n                    extractedType = rawType || undefined;\n                  } else {\n                    // Fallback: derive a path from available data, generate deterministic UUID\n                    const layerId = el.layer_id || name;\n                    const rawType = el.type || (typeof el.id === \"string\" && el.id.includes(\".\") ? el.id.split(\".\")[1] : \"\") || \"\";\n                    const rawName = el.name || key;\n                    const kebabName = rawName.toLowerCase().replace(/[\\s_]+/g, \"-\").replace(/[^a-z0-9-]/g, \"\").replace(/-+/g, \"-\").replace(/^-+|-+$/g, \"\") || \"unknown\";\n                    elementPath = `${layerId}.${rawType || \"element\"}.${kebabName}`;\n                    elementId = deterministicUUID(elementPath);\n                    if (rawType) extractedType = rawType;\n                    else if (typeof el.id === \"string\" && el.id.includes(\".\")) {\n                      const parts = el.id.split(\".\");\n                      if (parts.length >= 3) extractedType = parts[1];\n                    }\n                  }\n\n                  const elementName = el.name || key;\n                  const elementType = el.type || extractedType;\n                  const layerId = el.layer_id || name;\n\n                  const newElement = new Element({\n                    id: elementId,\n                    path: elementPath,\n                    spec_node_id: el.spec_node_id,\n                    layer_id: layerId,\n                    attributes: el.attributes,\n                    source_reference: el.source_reference,\n                    metadata: el.metadata,\n                    name: elementName,\n                    type: elementType,\n                    description: el.description || \"\",\n                    relationships: el.relationships || [],\n                    references: el.references || [],\n                    layer: layerId,\n                  } as any);\n                  layer.addElement(newElement);\n                }\n              }\n            }\n          } catch (fileError) {\n            // Log YAML parsing errors but continue loading other files\n            const errorMsg = fileError instanceof Error ? fileError.message : String(fileError);\n            console.error(`Warning: Failed to parse ${filePath}: ${errorMsg}`);\n            parseErrorCount++;\n            // Continue with next file\n          }\n        }\n      }\n\n      // If we had parse errors, add a note to the layer\n      if (parseErrorCount > 0) {\n        console.error(\n          `Warning: Layer '${name}' loaded with ${parseErrorCount} YAML parse error(s)`\n        );\n      }\n\n      this.layers.set(name, layer);\n      this.loadedLayers.add(name);\n\n      layerSpan.setAttribute(\"layer.element_count\", layer.elements.size);\n    }, { \"layer.name\": name });\n  }\n\n  /**\n   * Add a layer to the model\n   */\n  addLayer(layer: Layer): void {\n    // If the layer has elements in its isolated graph, migrate them to the model's graph\n    if (layer.graph.getNodeCount() > 0) {\n      for (const node of layer.graph.nodes.values()) {\n        this.graph.addNode(node);\n      }\n      for (const edge of layer.graph.edges.values()) {\n        this.graph.addEdge(edge);\n      }\n    }\n    // Ensure layer uses the model's graph for future operations\n    layer.graph = this.graph;\n    this.layers.set(layer.name, layer);\n    this.loadedLayers.add(layer.name);\n  }\n\n  /**\n   * Get all layer names, including layers that exist only in staged changes.\n   * When an active changeset introduces elements for a layer with no committed data,\n   * that layer name is included so findElementLayer() and other callers can discover it.\n   */\n  getLayerNames(): string[] {\n    const base = Array.from(this.layers.keys());\n    if (this._stagedLayerNames.size === 0) {\n      return base;\n    }\n    // Include staged-only layers (layers that have staged elements but no committed elements)\n    const staged = Array.from(this._stagedLayerNames).filter((l) => !this.layers.has(l));\n    return [...base, ...staged];\n  }\n\n  /**\n   * Save a layer to disk (model/XX_layername/*.yaml)\n   */\n  async saveLayer(name: string): Promise<void> {\n    const layer = this.layers.get(name);\n    if (!layer) {\n      throw new Error(`Layer ${name} not found`);\n    }\n\n    const fs = await import(\"fs/promises\");\n    const yaml = await import(\"yaml\");\n\n    let layerPath: string | null = null;\n\n    // Discover by scanning directory\n    const modelDir = `${this.rootPath}/documentation-robotics/model`;\n\n    try {\n      const entries = await fs.readdir(modelDir, { withFileTypes: true });\n      const layerDir = entries.find(\n        (e) =>\n          e.isDirectory() && e.name.match(/^\\d{2}_/) && e.name.replace(/^\\d{2}_/, \"\") === name\n      );\n\n      if (layerDir) {\n        layerPath = `${modelDir}/${layerDir.name}`;\n      }\n    } catch {\n      // Model directory doesn't exist or can't be read\n    }\n\n    // If still not found, create using default format\n    if (!layerPath) {\n      // Find the order number for this layer\n      // Handle layer names with or without numeric prefix (e.g., \"motivation\" or \"01-motivation\")\n      const layerNameWithoutPrefix = name.replace(/^\\d{2}-/, \"\");\n      const index = CANONICAL_LAYER_NAMES.indexOf(layerNameWithoutPrefix as typeof CANONICAL_LAYER_NAMES[number]);\n      if (index >= 0) {\n        const orderNum = String(index + 1).padStart(2, \"0\");\n        layerPath = `${this.rootPath}/documentation-robotics/model/${orderNum}_${layerNameWithoutPrefix}`;\n        await ensureDir(layerPath);\n      } else {\n        throw new Error(`Unknown layer ${name} and no path configured in manifest`);\n      }\n    }\n\n    // Delete all existing YAML files in the layer directory to ensure\n    // we don't keep stale files after element deletion\n    try {\n      const existingFiles = await fs.readdir(layerPath);\n      for (const file of existingFiles) {\n        if (file.endsWith(\".yaml\") || file.endsWith(\".yml\")) {\n          await fs.unlink(`${layerPath}/${file}`);\n        }\n      }\n    } catch (err) {\n      // Only ignore \"directory not found\" errors \u2014 re-throw permission/I/O errors\n      const isNotFoundError = (err as any)?.code === \"ENOENT\";\n      if (!isNotFoundError) {\n        throw new Error(\n          `Failed to clean existing YAML files: ${err instanceof Error ? err.message : String(err)}`\n        );\n      }\n    }\n\n    // Group elements by type, computing the snake_case file stem from the spec node title\n    const elementsByType = new Map<string, { stem: string; elements: Element[] }>();\n    for (const element of layer.elements.values()) {\n      const typeKey = element.type;\n      if (!elementsByType.has(typeKey)) {\n        const stem = typeToSnakeStem(element.spec_node_id, element.type);\n        elementsByType.set(typeKey, { stem, elements: [] });\n      }\n      elementsByType.get(typeKey)!.elements.push(element);\n    }\n\n    // Internal graph fields \u2014 never written to YAML\n    const INTERNAL_FIELDS = new Set([\n      \"__references__\", \"__relationships__\",\n      \"source\", \"x-source-reference\",\n    ]);\n\n    // Write each type to its own YAML file\n    for (const [, { stem, elements }] of elementsByType) {\n      const filename = `${stem}.yaml`;\n      const filePath = `${layerPath}/${filename}`;\n\n      // Convert elements to spec-node format YAML\n      const yamlData: any = {};\n      for (const element of elements) {\n        const json = element.toJSON();\n\n        // Clean attributes: remove graph-internal keys that should not be persisted\n        const cleanAttrs = json.attributes\n          ? Object.fromEntries(\n              Object.entries(json.attributes).filter(([k]) => !INTERNAL_FIELDS.has(k))\n            )\n          : undefined;\n\n        // Use path as YAML key (human-readable); fall back to id for elements without path\n        const key = element.path || element.id;\n        yamlData[key] = {\n          id: json.id,\n          path: json.path,\n          spec_node_id: json.spec_node_id,\n          type: json.type,\n          layer_id: json.layer_id,\n          name: json.name,\n          ...(json.description && { description: json.description }),\n          ...(cleanAttrs && Object.keys(cleanAttrs).length > 0 && { attributes: cleanAttrs }),\n          ...(json.source_reference && { source_reference: json.source_reference }),\n          ...(json.metadata && { metadata: json.metadata }),\n          ...(json.references && json.references.length > 0 && { references: json.references }),\n          // Relationships are now stored in centralized relationships.yaml, not inline\n        };\n      }\n\n      await writeFile(filePath, yaml.stringify(yamlData));\n    }\n\n    layer.markClean();\n  }\n\n  /**\n   * Save model (saves all dirty layers and manifest)\n   */\n  async save(): Promise<void> {\n    await this.saveDirtyLayers();\n    await this.saveManifest();\n  }\n\n  /**\n   * Save all dirty layers to disk\n   */\n  async saveDirtyLayers(): Promise<void> {\n    // Count dirty layers before operation\n    let dirtyLayerCount = 0;\n    for (const layer of this.layers.values()) {\n      if (layer.isDirty()) {\n        dirtyLayerCount++;\n      }\n    }\n\n    const span = isTelemetryEnabled\n      ? startSpan(\"model.save\", {\n          \"model.path\": this.rootPath,\n          \"model.dirty_layer_count\": dirtyLayerCount,\n        })\n      : null;\n\n    try {\n      for (const layer of this.layers.values()) {\n        if (layer.isDirty()) {\n          await this.saveLayer(layer.name);\n        }\n      }\n    } finally {\n      if (isTelemetryEnabled) {\n        endSpan(span);\n      }\n    }\n  }\n\n  /**\n   * Save the manifest to disk (documentation-robotics/model/manifest.yaml)\n   */\n  async saveManifest(): Promise<void> {\n    this.manifest.updateModified();\n    const yaml = await import(\"yaml\");\n    const manifestPath = `${this.rootPath}/documentation-robotics/model/manifest.yaml`;\n\n    // Convert to YAML format\n    const yamlData: any = {\n      version: this.manifest.version,\n      schema: \"documentation-robotics-v1\",\n      cli_version: getCliVersion(),\n      spec_version: this.manifest.specVersion,\n      created: this.manifest.created,\n      updated: this.manifest.modified,\n      project: {\n        name: this.manifest.name,\n        description: this.manifest.description,\n        version: this.manifest.version,\n      },\n      documentation: \".dr/README.md\",\n      layers: {},\n    };\n\n    // Generate layer structure from current model state\n    const layerOrder = [\n      \"motivation\",\n      \"business\",\n      \"security\",\n      \"application\",\n      \"technology\",\n      \"api\",\n      \"data-model\",\n      \"data-store\",\n      \"ux\",\n      \"navigation\",\n      \"apm\",\n      \"testing\",\n    ];\n\n    for (let i = 0; i < layerOrder.length; i++) {\n      const layerName = layerOrder[i];\n      const layer = this.layers.get(layerName);\n      const orderNum = String(i + 1).padStart(2, \"0\");\n\n      yamlData.layers[layerName] = {\n        order: i + 1,\n        name: layerName.charAt(0).toUpperCase() + layerName.slice(1).replace(\"-\", \" \"),\n        path: `documentation-robotics/model/${orderNum}_${layerName}/`,\n        enabled: true,\n        ...(layer && { elements: this.getLayerElementCounts(layer) }),\n      };\n    }\n\n    if (this.manifest.changeset_history && this.manifest.changeset_history.length > 0) {\n      yamlData.changeset_history = this.manifest.changeset_history;\n    }\n\n    await ensureDir(`${this.rootPath}/documentation-robotics/model`);\n    await writeFile(manifestPath, yaml.stringify(yamlData));\n  }\n\n  private getLayerElementCounts(layer: Layer): Record<string, number> {\n    const counts: Record<string, number> = {};\n    for (const element of layer.elements.values()) {\n      counts[element.type] = (counts[element.type] || 0) + 1;\n    }\n    return counts;\n  }\n\n  /**\n   * Load relationships from relationships.yaml\n   */\n  async loadRelationships(): Promise<void> {\n    const fs = await import(\"fs/promises\");\n    const yaml = await import(\"yaml\");\n    const relationshipsPath = `${this.rootPath}/documentation-robotics/model/relationships.yaml`;\n\n    let data: any;\n    try {\n      const yamlContent = await fs.readFile(relationshipsPath, \"utf-8\");\n      data = yaml.parse(yamlContent);\n    } catch (err) {\n      // If file doesn't exist, that's okay - start with empty relationships\n      if ((err as any).code !== \"ENOENT\") {\n        // But if it's a different error (YAML parse, permission denied, etc), throw it\n        // so the caller knows about the issue\n        throw new Error(\n          `Failed to load relationships.yaml: ${err instanceof Error ? err.message : String(err)}`\n        );\n      }\n      // ENOENT: file doesn't exist, return with empty relationships\n      return;\n    }\n\n    // Validate that parsed content is an array\n    if (!Array.isArray(data)) {\n      const typeLabel = data === null ? \"null\" : typeof data;\n      console.warn(\n        `Warning: relationships.yaml contains non-array content (received ${typeLabel}). Expected an array of relationships. Skipping relationship loading.`\n      );\n      return;\n    }\n\n    this.relationships = Relationships.fromArray(data);\n    // Sync relationships to graph as a secondary in-memory index.\n    // addEdge() may throw if nodes from other layers haven't been loaded yet;\n    // failures are silently skipped \u2014 this.relationships holds the primary data.\n    for (let i = 0; i < data.length; i++) {\n      const rel = data[i];\n      const edge: GraphEdge = {\n        id: `rel-${i}-${crypto.randomBytes(4).toString(\"hex\")}`,\n        source: rel.source,\n        destination: rel.target,\n        predicate: rel.predicate,\n        properties: rel.properties,\n        category: rel.category,\n      };\n      try {\n        this.graph.addEdge(edge);\n      } catch {\n        // Silently skip edges whose nodes haven't been loaded yet.\n        // The primary relationship data lives in this.relationships; the graph\n        // is a secondary index. Cross-layer relationships referencing nodes from\n        // unloaded layers are expected during partial model construction.\n      }\n    }\n  }\n\n  /**\n   * Save relationships to relationships.yaml\n   */\n  async saveRelationships(): Promise<void> {\n    const fs = await import(\"fs/promises\");\n    const yaml = await import(\"yaml\");\n    const relationshipsPath = `${this.rootPath}/documentation-robotics/model/relationships.yaml`;\n\n    await ensureDir(`${this.rootPath}/documentation-robotics/model`);\n\n    const data = this.relationships.toArray();\n\n    // Add header comment with timestamp to ensure file always changes\n    const timestamp = new Date().toISOString();\n    const header = `# Intra-layer relationships\n# Format: source_id -> predicate -> target_id\n# Last updated: ${timestamp}\n\n`;\n    const yamlContent = header + yaml.stringify(data);\n\n    await fs.writeFile(relationshipsPath, yamlContent, \"utf-8\");\n    this.relationships.markClean();\n  }\n\n  /**\n   * Resolve model paths (private helper)\n   *\n   * @param startPath - Starting path for search\n   * @returns Project root and manifest path\n   */\n  private static async resolveModelPaths(startPath?: string): Promise<{\n    projectRoot: string;\n    manifestPath: string;\n  }> {\n    const searchPath = startPath || process.cwd();\n\n    // Optional override via env var (highest priority)\n    if (process.env.DR_MODEL_PATH) {\n      const envPath = path.resolve(process.env.DR_MODEL_PATH);\n      let manifestPath: string;\n\n      if (envPath.endsWith(\"manifest.yaml\")) {\n        manifestPath = envPath;\n      } else if (envPath.endsWith(\"model\")) {\n        manifestPath = path.join(envPath, \"manifest.yaml\");\n      } else {\n        manifestPath = path.join(envPath, \"documentation-robotics\", \"model\", \"manifest.yaml\");\n      }\n\n      try {\n        await fs.access(manifestPath);\n        const projectRoot = path.dirname(path.dirname(path.dirname(manifestPath)));\n        return { projectRoot, manifestPath: path.normalize(manifestPath) };\n      } catch {\n        throw new Error(`Model not found at DR_MODEL_PATH: ${process.env.DR_MODEL_PATH}`);\n      }\n    }\n\n    // Use findProjectRoot to locate documentation_robotics/ folder\n    const projectRoot = await findProjectRoot(searchPath);\n\n    if (!projectRoot) {\n      throw new Error(\n        \"No DR project found. Could not find documentation_robotics/ folder.\\n\" +\n          'Run \"dr init\" to create a new project, or navigate to a directory containing a DR project.'\n      );\n    }\n\n    const manifestPath = path.join(projectRoot, \"documentation-robotics\", \"model\", \"manifest.yaml\");\n\n    try {\n      await fs.access(manifestPath);\n      return { projectRoot, manifestPath };\n    } catch {\n      throw new Error(\n        `Found documentation_robotics/ at ${projectRoot} but no model found. ` +\n          `Expected: ${manifestPath}\\n` +\n          `Run \"dr init\" to create a model.`\n      );\n    }\n  }\n\n  /**\n   * Load a model from disk\n   *\n   * Expected structure:\n   * <project-root>/\n   * \u2514\u2500\u2500 documentation_robotics/\n   *     \u2514\u2500\u2500 model/\n   *         \u2514\u2500\u2500 manifest.yaml\n   *\n   * @param startPath - Starting path for project search (defaults to process.cwd())\n   * @param options - Model loading options\n   * @returns Loaded Model instance\n   */\n  static async load(startPath?: string, options: ModelOptions = {}): Promise<Model> {\n    return startActiveSpan(\"model.load\", async (span) => {\n      // Resolve project root and manifest path\n      const { projectRoot, manifestPath } = await Model.resolveModelPaths(startPath);\n\n      const yaml = await import(\"yaml\");\n\n      // Load manifest from resolved path\n      const yamlContent = await fs.readFile(manifestPath, \"utf-8\");\n      const manifestYaml = yaml.parse(yamlContent);\n\n      // Convert manifest to internal format\n      const manifestData: any = {\n        name: manifestYaml.project?.name || \"Unnamed Model\",\n        description: manifestYaml.project?.description || \"\",\n        version: manifestYaml.project?.version || manifestYaml.version || \"0.1.0\",\n        specVersion: manifestYaml.spec_version || \"0.6.0\",\n        created: manifestYaml.created || new Date().toISOString(),\n        modified: manifestYaml.updated || new Date().toISOString(),\n      };\n      const manifest = new Manifest(manifestData);\n      const model = new Model(projectRoot, manifest, options);\n\n      // Load all available layers if lazyLoad is false\n      if (!options.lazyLoad) {\n        try {\n          // If manifest has layer definitions, use those\n          if (manifestYaml.layers) {\n            for (const layerName of Object.keys(manifestYaml.layers)) {\n              const layerConfig = manifestYaml.layers[layerName];\n              if (layerConfig.enabled !== false) {\n                if (!options.layers || options.layers.includes(layerName)) {\n                  await model.loadLayer(layerName);\n                }\n              }\n            }\n          } else {\n            // Otherwise scan for layer directories\n            const modelDir = manifestPath.replace(\"/manifest.yaml\", \"\");\n            const entries = await fs.readdir(modelDir, { withFileTypes: true });\n\n            for (const entry of entries) {\n              if (entry.isDirectory() && entry.name.match(/^\\d{2}_/)) {\n                const layerName = entry.name.replace(/^\\d{2}_/, \"\");\n                if (!options.layers || options.layers.includes(layerName)) {\n                  await model.loadLayer(layerName);\n                }\n              }\n            }\n          }\n        } catch (e) {\n          // Check if this is a \"directory not found\" error (expected case)\n          const isNotFoundError = (e as any)?.code === \"ENOENT\";\n          if (!isNotFoundError) {\n            // Re-throw non-ENOENT errors: permission errors, YAML parsing failures, I/O errors, etc.\n            throw new Error(\n              `Failed to load layers: ${e instanceof Error ? e.message : String(e)}`\n            );\n          }\n          // ENOENT is expected if layer directory doesn't exist yet, so just continue\n        }\n      }\n\n      // Load relationships from relationships.yaml\n      await model.loadRelationships();\n\n      // Check for active changeset and pre-load staged metadata for transparent projection.\n      // This enables getLayer() to return projected views and getLayerNames() to include\n      // layers that exist only in staged changes.\n      const activePath = path.join(\n        projectRoot,\n        \"documentation-robotics\",\n        \"changesets\",\n        \".active\"\n      );\n      try {\n        const activeContent = await fs.readFile(activePath, \"utf-8\");\n        const activeId = activeContent.trim();\n        if (activeId) {\n          model._activeChangesetId = activeId;\n          const storage = new StagedChangesetStorage(projectRoot);\n          const changeset = await storage.load(activeId);\n          if (changeset) {\n            for (const change of changeset.changes as StagedChange[]) {\n              // Track layer names for getLayerNames()\n              if (\n                change.type === \"add\" ||\n                change.type === \"update\" ||\n                change.type === \"delete\"\n              ) {\n                model._stagedLayerNames.add(change.layerName);\n              }\n\n              // Inject staged relationship-adds into model.relationships so that\n              // read commands (list, show, export) transparently see staged relationships.\n              if (change.type === \"relationship-add\" && change.after) {\n                const rel = change.after as {\n                  source: string;\n                  target: string;\n                  predicate: string;\n                  layer: string;\n                  targetLayer?: string;\n                  category?: \"structural\" | \"behavioral\";\n                  properties?: Record<string, unknown>;\n                };\n                // Only inject if not already in relationships.yaml (prevents duplicates\n                // if .active file is stale after a partial commit or manual edit).\n                const alreadyPresent = model.relationships.find(\n                  rel.source,\n                  rel.target,\n                  rel.predicate\n                );\n                if (alreadyPresent.length === 0) {\n                  model.relationships.add({\n                    source: rel.source,\n                    target: rel.target,\n                    predicate: rel.predicate,\n                    layer: rel.layer,\n                    ...(rel.targetLayer ? { targetLayer: rel.targetLayer } : {}),\n                    category: rel.category ?? \"structural\",\n                    ...(rel.properties ? { properties: rel.properties } : {}),\n                  });\n                }\n              }\n\n              // Remove staged relationship-deletes from model.relationships so that\n              // read commands see the relationship as already deleted.\n              if (change.type === \"relationship-delete\" && change.before) {\n                const rel = change.before as {\n                  source: string;\n                  target: string;\n                  predicate?: string;\n                };\n                model.relationships.delete(rel.source, rel.target, rel.predicate);\n              }\n            }\n          }\n        }\n      } catch {\n        // No active changeset or unreadable \u2014 proceed with base model only\n        model._activeChangesetId = null;\n      }\n\n      // Count total entities across all layers\n      let entityCount = 0;\n      for (const layer of model.layers.values()) {\n        entityCount += layer.elements.size;\n      }\n\n      span.setAttribute(\"model.entity_count\", entityCount);\n      span.setAttribute(\"model.layer_count\", model.layers.size);\n\n      return model;\n    }, {\n      \"model.path\": startPath || process.cwd(),\n      \"model.type\": \"dr\",\n    });\n  }\n\n  /**\n   * Initialize a new model in a directory\n   */\n  static async init(\n    rootPath: string,\n    manifestData: ManifestData,\n    options: ModelOptions = {}\n  ): Promise<Model> {\n    // Create model directory structure\n    await ensureDir(`${rootPath}/documentation-robotics/model`);\n\n    for (let i = 0; i < CANONICAL_LAYER_NAMES.length; i++) {\n      const orderNum = String(i + 1).padStart(2, \"0\");\n      const layerName = CANONICAL_LAYER_NAMES[i];\n      await ensureDir(`${rootPath}/documentation-robotics/model/${orderNum}_${layerName}`);\n    }\n\n    const manifest = new Manifest(manifestData);\n    const model = new Model(rootPath, manifest, options);\n\n    await model.saveManifest();\n\n    return model;\n  }\n\n  /**\n   * Graph-based API methods for querying the model\n   * These methods delegate to the underlying GraphModel for efficient queries\n   */\n\n  /**\n   * Get a node by its UUID\n   */\n  getNode(id: string) {\n    return this.graph.getNode(id);\n  }\n\n  /**\n   * Get all nodes in a specific layer\n   */\n  getNodesByLayer(layerId: string) {\n    return this.graph.getNodesByLayer(layerId);\n  }\n\n  /**\n   * Get all nodes of a specific type\n   */\n  getNodesByType(type: string) {\n    return this.graph.getNodesByType(type);\n  }\n\n  /**\n   * Get all edges (relationships) in the model\n   */\n  getAllEdges() {\n    return this.graph.getAllEdges();\n  }\n\n  /**\n   * Get edges originating from a specific node\n   */\n  getEdgesFrom(nodeId: string, predicate?: string) {\n    return this.graph.getEdgesFrom(nodeId, predicate);\n  }\n\n  /**\n   * Get edges terminating at a specific node\n   */\n  getEdgesTo(nodeId: string, predicate?: string) {\n    return this.graph.getEdgesTo(nodeId, predicate);\n  }\n\n  /**\n   * Get edges between two specific nodes\n   */\n  getEdgesBetween(sourceId: string, destinationId: string, predicate?: string) {\n    return this.graph.getEdgesBetween(sourceId, destinationId, predicate);\n  }\n\n  /**\n   * Traverse the graph starting from a node, following a specific predicate\n   */\n  async traverse(startNodeId: string, predicate: string, maxDepth: number = 10) {\n    return this.graph.traverse(startNodeId, predicate, maxDepth);\n  }\n\n  /**\n   * Create a backup of the current model state\n   * Used for rollback support in migration operations\n   *\n   * @param label Descriptive label for the backup (e.g., \"pre-migration\")\n   * @returns Path to the backup directory\n   */\n  async createBackup(label: string): Promise<string> {\n    const timestamp = new Date().toISOString().replace(/[:.]/g, \"-\");\n    const backupDir = path.join(this.rootPath, \".dr-backups\", `${label}-${timestamp}`);\n\n    // Create backup directory\n    await ensureDir(backupDir);\n\n    // Backup layers directory\n    const layersSource = path.join(this.rootPath, \"documentation-robotics\", \"model\");\n    const layersBackup = path.join(backupDir, \"layers\");\n    if (await this.directoryExists(layersSource)) {\n      await this.copyDirectory(layersSource, layersBackup);\n    }\n\n    // Backup manifest\n    const manifestSource = path.join(this.rootPath, \"documentation-robotics\", \"model\", \"manifest.yaml\");\n    const manifestBackup = path.join(backupDir, \"manifest.yaml\");\n    if (await this.fileExists(manifestSource)) {\n      await fs.copyFile(manifestSource, manifestBackup);\n    }\n\n    return backupDir;\n  }\n\n  /**\n   * Restore model from a backup directory\n   * Used for rollback after failed migrations\n   *\n   * @param backupPath Path to the backup directory\n   */\n  async restoreFromBackup(backupPath: string): Promise<void> {\n    // Restore layers\n    const layersBackup = path.join(backupPath, \"layers\");\n    const layersTarget = path.join(this.rootPath, \"documentation-robotics\", \"model\");\n    if (await this.directoryExists(layersBackup)) {\n      await this.copyDirectory(layersBackup, layersTarget);\n    }\n\n    // Restore manifest\n    const manifestBackup = path.join(backupPath, \"manifest.yaml\");\n    const manifestTarget = path.join(this.rootPath, \"documentation-robotics\", \"model\", \"manifest.yaml\");\n    if (await this.fileExists(manifestBackup)) {\n      await fs.copyFile(manifestBackup, manifestTarget);\n    }\n\n    // Reload model to refresh in-memory state\n    const reloadedModel = await Model.load(this.rootPath, { lazyLoad: this.lazyLoad });\n    this.layers = reloadedModel.layers;\n    this.manifest = reloadedModel.manifest;\n    this.graph = reloadedModel.graph;\n    this.relationships = reloadedModel.relationships;\n  }\n\n  /**\n   * Save dirty layers with atomic write semantics\n   * Writes to temporary file first, then renames on success to ensure data safety\n   *\n   * @throws Error if atomic write fails\n   */\n  async saveDirtyLayersAtomic(): Promise<void> {\n    // First, save all layers to temporary files\n    const tempLayerWrites: Array<{ layer: Layer; tempPath: string }> = [];\n\n    try {\n      for (const layer of this.layers.values()) {\n        if (layer.isDirty()) {\n          const layerPath = path.join(\n            this.rootPath,\n            \"documentation-robotics\",\n            \"model\",\n            `${layer.name}_layer`\n          );\n\n          const tempPath = `${layerPath}.tmp`;\n          await ensureDir(tempPath);\n\n          // Write layer elements to temp directory\n          for (const element of layer.elements.values()) {\n            const elementPath = path.join(tempPath, `${element.path || element.id}.json`);\n            const content = JSON.stringify(element.toJSON(), null, 2);\n            await writeFile(elementPath, content);\n          }\n\n          tempLayerWrites.push({ layer, tempPath });\n        }\n      }\n\n      // All temp writes succeeded, now commit by renaming\n      for (const { layer, tempPath } of tempLayerWrites) {\n        const layerPath = path.join(\n          this.rootPath,\n          \"documentation-robotics\",\n          \"model\",\n          `${layer.name}_layer`\n        );\n\n        // Remove old directory and rename temp to actual\n        if (await this.directoryExists(layerPath)) {\n          await fs.rm(layerPath, { recursive: true, force: true });\n        }\n        await fs.rename(tempPath, layerPath);\n      }\n    } catch (error) {\n      // Cleanup any temp directories on failure\n      for (const { tempPath } of tempLayerWrites) {\n        if (await this.directoryExists(tempPath)) {\n          await fs.rm(tempPath, { recursive: true, force: true });\n        }\n      }\n      throw error;\n    }\n  }\n\n  /**\n   * Helper: Check if file exists\n   */\n  private async fileExists(filePath: string): Promise<boolean> {\n    try {\n      await fs.access(filePath);\n      return true;\n    } catch {\n      return false;\n    }\n  }\n\n  /**\n   * Helper: Check if directory exists\n   */\n  private async directoryExists(dirPath: string): Promise<boolean> {\n    try {\n      const stat = await fs.stat(dirPath);\n      return stat.isDirectory();\n    } catch {\n      return false;\n    }\n  }\n\n  /**\n   * Helper: Recursively copy directory\n   */\n  private async copyDirectory(src: string, dest: string): Promise<void> {\n    await ensureDir(dest);\n    const entries = await fs.readdir(src, { withFileTypes: true });\n\n    for (const entry of entries) {\n      const srcPath = path.join(src, entry.name);\n      const destPath = path.join(dest, entry.name);\n\n      if (entry.isDirectory()) {\n        await this.copyDirectory(srcPath, destPath);\n      } else {\n        await fs.copyFile(srcPath, destPath);\n      }\n    }\n  }\n}\n"],
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+  "names": ["path", "fs", "layerId", "manifestPath"]
 }

package/dist/core/mutation-handler.js

@@ -0,0 +1,179 @@
+import { StagingAreaManager } from "./staging-area.js";
+import { isValidLayerName } from "./layers.js";
+import { CLIError } from "../utils/errors.js";
+import { getErrorMessage } from "../utils/errors.js";
+import { ModelReportOrchestrator } from "../reports/model-report-orchestrator.js";
+import { emitLog, SeverityNumber } from "../telemetry/index.js";
+class MutationHandler {
+  context;
+  steps = [];
+  stagingManager;
+  constructor(model, elementId, layerName) {
+    this.context = { model, elementId, layerName }, this.stagingManager = new StagingAreaManager(model.rootPath, model);
+  }
+  /**
+   * Set the element being mutated
+   */
+  setElement(element) {
+    return this.context.element = element, this;
+  }
+  /**
+   * Add a mutation step
+   */
+  addStep(step) {
+    return this.steps.push(step), this;
+  }
+  /**
+   * Get before state (snapshot before mutations)
+   */
+  getBeforeState() {
+    return this.context.before;
+  }
+  /**
+   * Get after state (result of mutations)
+   */
+  getAfterState() {
+    return this.context.after;
+  }
+  /**
+   * Get staging manager for accessing changeset information
+   */
+  getStagingManager() {
+    return this.stagingManager;
+  }
+  /**
+   * Compute before and after states
+   *
+   * For add: before is undefined, after is the new element state
+   * For update: before is original state, after is modified state
+   * For delete: before is original state, after is undefined
+   */
+  async computeStates(element) {
+    this.context.element = element, this.context.before = element.toJSON(), this.context.after = { ...this.context.before };
+  }
+  /**
+   * Execute mutation for add operation
+   */
+  async executeAdd(element, mutator) {
+    this.context.element = element, this.context.before = void 0;
+    const activeChangeset = await this.stagingManager.getActive();
+    if (activeChangeset && activeChangeset.status === "staged") {
+      this.context.after = element.toJSON(), await this.stagingManager.stage(activeChangeset.id, {
+        type: "add",
+        elementId: this.context.elementId,
+        layerName: this.context.layerName,
+        after: this.context.after,
+        timestamp: (/* @__PURE__ */ new Date()).toISOString()
+      });
+      return;
+    }
+    await mutator(element), this.context.after = element.toJSON(), await this._persistChanges("add");
+  }
+  /**
+   * Execute mutation for update operation
+   */
+  async executeUpdate(element, mutator) {
+    this.context.element = element, this.context.before = element.toJSON(), this.context.after = { ...this.context.before };
+    const activeChangeset = await this.stagingManager.getActive();
+    if (activeChangeset && activeChangeset.status === "staged") {
+      await mutator(element, this.context.after), await this.stagingManager.stage(activeChangeset.id, {
+        type: "update",
+        elementId: this.context.elementId,
+        layerName: this.context.layerName,
+        before: this.context.before,
+        after: this.context.after,
+        timestamp: (/* @__PURE__ */ new Date()).toISOString()
+      });
+      return;
+    }
+    await this._executeBasePath(mutator);
+  }
+  /**
+   * Execute mutation for delete operation
+   */
+  async executeDelete(element) {
+    this.context.element = element, this.context.before = element.toJSON(), this.context.after = void 0;
+    const activeChangeset = await this.stagingManager.getActive();
+    if (activeChangeset && activeChangeset.status === "staged") {
+      await this.stagingManager.stage(activeChangeset.id, {
+        type: "delete",
+        elementId: this.context.elementId,
+        layerName: this.context.layerName,
+        before: this.context.before,
+        timestamp: (/* @__PURE__ */ new Date()).toISOString()
+      });
+      return;
+    }
+    if (!(await this.context.model.getLayer(this.context.layerName)).deleteElement(element.path || element.id))
+      throw new CLIError(`Failed to delete element ${this.context.elementId}`, 1, [
+        "Element may have already been deleted"
+      ]);
+    this.context.model.relationships.deleteForElement(this.context.elementId), await this._persistChanges("delete");
+  }
+  /**
+   * Execute all registered steps and persist
+   */
+  async execute(mutator, type) {
+    if (!this.context.element)
+      throw new CLIError("Element not set on MutationHandler", 1);
+    const activeChangeset = await this.stagingManager.getActive();
+    if (activeChangeset && activeChangeset.status === "staged") {
+      this.context.before === void 0 && type !== "add" && (this.context.before = this.context.element.toJSON()), this.context.after = type === "delete" ? void 0 : {
+        ...this.context.before || this.context.element.toJSON()
+      }, type !== "delete" && this.context.after && await mutator(this.context.element, this.context.after), await this.stagingManager.stage(activeChangeset.id, {
+        type,
+        elementId: this.context.elementId,
+        layerName: this.context.layerName,
+        ...this.context.before !== void 0 && { before: this.context.before },
+        ...this.context.after !== void 0 && { after: this.context.after },
+        timestamp: (/* @__PURE__ */ new Date()).toISOString()
+      });
+      return;
+    }
+    await this._executeBasePath(mutator, type);
+  }
+  /**
+   * Base model path: execute mutations and persist atomically
+   */
+  async _executeBasePath(mutator, type) {
+    if (!this.context.element)
+      throw new CLIError("Element not set", 1);
+    this.context.before === void 0 && (this.context.before = this.context.element.toJSON()), this.context.after === void 0 && (this.context.after = { ...this.context.before }), await mutator(this.context.element, this.context.after), await this._persistChanges(type);
+  }
+  /**
+   * Persist changes to disk
+   *
+   * Performs sequential writes to layer, relationships, and manifest files.
+   * If any write fails, subsequent writes are skipped via error propagation.
+   * Note: Not truly atomic—if a write succeeds then a later write fails,
+   * earlier writes remain on disk. Use within transaction-like contexts only.
+   */
+  async _persistChanges(type) {
+    try {
+      await this.context.model.saveLayer(this.context.layerName), type === "delete" && this.context.model.relationships.isDirty() && await this.context.model.saveRelationships(), await this.context.model.saveManifest();
+    } catch (error) {
+      throw new CLIError(`Failed to persist changes: ${getErrorMessage(error)}`, 1, ["Check that the model directory is writable", "Verify the model is not corrupted"]);
+    }
+    try {
+      const orchestrator = new ModelReportOrchestrator(this.context.model, this.context.model.rootPath);
+      if (isValidLayerName(this.context.layerName)) {
+        const affected = orchestrator.computeAffectedLayers(this.context.layerName);
+        await orchestrator.regenerate(affected);
+      } else
+        emitLog(SeverityNumber.WARN, "Report regeneration skipped: invalid layer name", {
+          "layer.name": this.context.layerName,
+          elementId: this.context.elementId
+        });
+    } catch (error) {
+      emitLog(SeverityNumber.WARN, "Failed to update layer reports after mutation", {
+        error: getErrorMessage(error),
+        "layer.name": this.context.layerName,
+        elementId: this.context.elementId
+      });
+    }
+  }
+}
+export {
+  MutationHandler
+};
+//# sourceMappingURL=mutation-handler.js.map

package/dist/core/mutation-handler.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../src/core/mutation-handler.ts"],
+  "sourcesContent": ["/**\n * MutationHandler - Unified mutation execution strategy\n *\n * Eliminates duplicate code paths by centralizing all element mutations.\n * Ensures consistency between staging and base model operations through\n * a single execution path that supports both.\n *\n * This fixes data corruption risk from divergent code paths in add/update/delete commands.\n */\n\nimport { Model } from \"./model.js\";\nimport { Element } from \"./element.js\";\nimport { StagingAreaManager } from \"./staging-area.js\";\nimport { isValidLayerName } from \"./layers.js\";\nimport { CLIError } from \"../utils/errors.js\";\nimport { getErrorMessage } from \"../utils/errors.js\";\nimport { ModelReportOrchestrator } from \"../reports/model-report-orchestrator.js\";\nimport { emitLog, SeverityNumber } from \"../telemetry/index.js\";\n\nexport type MutationType = \"add\" | \"update\" | \"delete\";\n\nexport interface MutationContext {\n  model: Model;\n  elementId: string;\n  layerName: string;\n  element?: Element;\n  before?: Record<string, unknown>;\n  after?: Record<string, unknown>;\n}\n\nexport interface MutationStep {\n  execute: (context: MutationContext) => void | Promise<void>;\n  stageable: boolean; // Can this step be executed in staging?\n  description: string;\n}\n\n/**\n * Unified mutation executor\n *\n * Single point of mutation execution that:\n * 1. Builds complete before/after states\n * 2. Validates mutations\n * 3. Executes consistently for both staging and base model\n * 4. Handles all persistence atomically\n * 5. Tracks changes in legacy changeset context\n */\nexport class MutationHandler {\n  private context: MutationContext;\n  private steps: MutationStep[] = [];\n  private stagingManager: StagingAreaManager;\n\n  constructor(model: Model, elementId: string, layerName: string) {\n    this.context = { model, elementId, layerName };\n    this.stagingManager = new StagingAreaManager(model.rootPath, model);\n  }\n\n  /**\n   * Set the element being mutated\n   */\n  setElement(element: Element): this {\n    this.context.element = element;\n    return this;\n  }\n\n  /**\n   * Add a mutation step\n   */\n  addStep(step: MutationStep): this {\n    this.steps.push(step);\n    return this;\n  }\n\n  /**\n   * Get before state (snapshot before mutations)\n   */\n  getBeforeState(): Record<string, unknown> | undefined {\n    return this.context.before;\n  }\n\n  /**\n   * Get after state (result of mutations)\n   */\n  getAfterState(): Record<string, unknown> | undefined {\n    return this.context.after;\n  }\n\n  /**\n   * Get staging manager for accessing changeset information\n   */\n  getStagingManager(): StagingAreaManager {\n    return this.stagingManager;\n  }\n\n  /**\n   * Compute before and after states\n   *\n   * For add: before is undefined, after is the new element state\n   * For update: before is original state, after is modified state\n   * For delete: before is original state, after is undefined\n   */\n  async computeStates(element: Element): Promise<void> {\n    this.context.element = element;\n    this.context.before = element.toJSON() as unknown as Record<string, unknown>;\n    this.context.after = { ...this.context.before };\n  }\n\n  /**\n   * Execute mutation for add operation\n   */\n  async executeAdd(\n    element: Element,\n    mutator: (elem: Element) => void | Promise<void>\n  ): Promise<void> {\n    // For add, before is undefined, after is the new element\n    this.context.element = element;\n    this.context.before = undefined;\n\n    // Check if we're in staging mode\n    const activeChangeset = await this.stagingManager.getActive();\n    if (activeChangeset && activeChangeset.status === \"staged\") {\n      // Staging path: capture after state and stage\n      this.context.after = element.toJSON() as unknown as Record<string, unknown>;\n\n      await this.stagingManager.stage(activeChangeset.id, {\n        type: \"add\",\n        elementId: this.context.elementId,\n        layerName: this.context.layerName,\n        after: this.context.after,\n        timestamp: new Date().toISOString(),\n      });\n      return;\n    }\n\n    // Base model path: add element and persist\n    await mutator(element);\n    this.context.after = element.toJSON() as unknown as Record<string, unknown>;\n\n    // Persist to base model\n    await this._persistChanges(\"add\");\n  }\n\n  /**\n   * Execute mutation for update operation\n   */\n  async executeUpdate(\n    element: Element,\n    mutator: (elem: Element, after: Record<string, unknown>) => Promise<void>\n  ): Promise<void> {\n    // Compute before and after states\n    this.context.element = element;\n    this.context.before = element.toJSON() as unknown as Record<string, unknown>;\n    this.context.after = { ...this.context.before };\n\n    // Check if we're in staging mode\n    const activeChangeset = await this.stagingManager.getActive();\n    if (activeChangeset && activeChangeset.status === \"staged\") {\n      // Staging path: apply mutations to after state, then stage\n      await mutator(element, this.context.after);\n\n      await this.stagingManager.stage(activeChangeset.id, {\n        type: \"update\",\n        elementId: this.context.elementId,\n        layerName: this.context.layerName,\n        before: this.context.before,\n        after: this.context.after,\n        timestamp: new Date().toISOString(),\n      });\n      return;\n    }\n\n    // Base model path: apply mutations atomically\n    await this._executeBasePath(mutator);\n  }\n\n  /**\n   * Execute mutation for delete operation\n   */\n  async executeDelete(element: Element): Promise<void> {\n    // For delete, before is the current state, after is undefined\n    this.context.element = element;\n    this.context.before = element.toJSON() as unknown as Record<string, unknown>;\n    this.context.after = undefined;\n\n    // Check if we're in staging mode\n    const activeChangeset = await this.stagingManager.getActive();\n    if (activeChangeset && activeChangeset.status === \"staged\") {\n      // Staging path: stage the deletion only\n      await this.stagingManager.stage(activeChangeset.id, {\n        type: \"delete\",\n        elementId: this.context.elementId,\n        layerName: this.context.layerName,\n        before: this.context.before,\n        timestamp: new Date().toISOString(),\n      });\n      return;\n    }\n\n    // Base model path: delete from model\n    const layer = (await this.context.model.getLayer(this.context.layerName))!;\n    const deleted = layer.deleteElement(element.path || element.id);\n\n    if (!deleted) {\n      throw new CLIError(`Failed to delete element ${this.context.elementId}`, 1, [\n        \"Element may have already been deleted\",\n      ]);\n    }\n\n    // Delete relationships\n    this.context.model.relationships.deleteForElement(this.context.elementId);\n\n    // Track and save atomically\n    await this._persistChanges(\"delete\");\n  }\n\n  /**\n   * Execute all registered steps and persist\n   */\n  async execute(\n    mutator: (elem: Element, after: Record<string, unknown>) => Promise<void>,\n    type: \"add\" | \"update\" | \"delete\"\n  ): Promise<void> {\n    if (!this.context.element) {\n      throw new CLIError(\"Element not set on MutationHandler\", 1);\n    }\n\n    // Check if we're in staging mode\n    const activeChangeset = await this.stagingManager.getActive();\n    if (activeChangeset && activeChangeset.status === \"staged\") {\n      // Staging path: build after state and stage\n      if (this.context.before === undefined && type !== \"add\") {\n        this.context.before = this.context.element.toJSON() as unknown as Record<string, unknown>;\n      }\n\n      this.context.after =\n        type === \"delete\"\n          ? undefined\n          : {\n              ...(this.context.before ||\n                (this.context.element.toJSON() as unknown as Record<string, unknown>)),\n            };\n\n      if (type !== \"delete\" && this.context.after) {\n        await mutator(this.context.element, this.context.after);\n      }\n\n      await this.stagingManager.stage(activeChangeset.id, {\n        type,\n        elementId: this.context.elementId,\n        layerName: this.context.layerName,\n        ...(this.context.before !== undefined && { before: this.context.before }),\n        ...(this.context.after !== undefined && { after: this.context.after }),\n        timestamp: new Date().toISOString(),\n      });\n      return;\n    }\n\n    // Base model path: execute and persist atomically\n    await this._executeBasePath(mutator, type);\n  }\n\n  /**\n   * Base model path: execute mutations and persist atomically\n   */\n  private async _executeBasePath(\n    mutator: (elem: Element, after: Record<string, unknown>) => Promise<void>,\n    type?: string\n  ): Promise<void> {\n    if (!this.context.element) {\n      throw new CLIError(\"Element not set\", 1);\n    }\n\n    // Initialize before state if not already set\n    if (this.context.before === undefined) {\n      this.context.before = this.context.element.toJSON() as unknown as Record<string, unknown>;\n    }\n\n    // Initialize after state if not already set\n    if (this.context.after === undefined) {\n      this.context.after = { ...this.context.before };\n    }\n\n    // Apply mutations to element AND after state together\n    // This ensures they stay in sync\n    await mutator(this.context.element, this.context.after);\n\n    // Persist changes to disk\n    await this._persistChanges(type);\n  }\n\n  /**\n   * Persist changes to disk\n   *\n   * Performs sequential writes to layer, relationships, and manifest files.\n   * If any write fails, subsequent writes are skipped via error propagation.\n   * Note: Not truly atomic\u2014if a write succeeds then a later write fails,\n   * earlier writes remain on disk. Use within transaction-like contexts only.\n   */\n  private async _persistChanges(type?: string): Promise<void> {\n    try {\n      // Save layer\n      await this.context.model.saveLayer(this.context.layerName);\n\n      // Save relationships if modified (for deletes)\n      if (type === \"delete\" && this.context.model.relationships.isDirty()) {\n        await this.context.model.saveRelationships();\n      }\n\n      // Save manifest\n      await this.context.model.saveManifest();\n    } catch (error) {\n      throw new CLIError(\n        `Failed to persist changes: ${getErrorMessage(error)}`,\n        1,\n        [\"Check that the model directory is writable\", \"Verify the model is not corrupted\"]\n      );\n    }\n\n    // Post-persist: regenerate affected layer reports (non-blocking, FR-4)\n    // This is a separate try/catch from the above to ensure report failures never cause mutations to fail\n    try {\n      const orchestrator = new ModelReportOrchestrator(\n        this.context.model,\n        this.context.model.rootPath\n      );\n      if (isValidLayerName(this.context.layerName)) {\n        const affected = orchestrator.computeAffectedLayers(this.context.layerName);\n        await orchestrator.regenerate(affected);\n      } else {\n        emitLog(SeverityNumber.WARN, \"Report regeneration skipped: invalid layer name\", {\n          \"layer.name\": this.context.layerName,\n          \"elementId\": this.context.elementId,\n        });\n      }\n    } catch (error) {\n      emitLog(SeverityNumber.WARN, \"Failed to update layer reports after mutation\", {\n        \"error\": getErrorMessage(error),\n        \"layer.name\": this.context.layerName,\n        \"elementId\": this.context.elementId,\n      });\n    }\n  }\n}\n"],
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+  "names": []
+}

package/dist/core/reference-registry.js

@@ -84,29 +84,37 @@ class ReferenceRegistry {
    * Scans element properties for known reference names
    */
   registerElement(element) {
-    if (element.references)
-      for (const ref of element.references)
-        this.addReference(ref);
-    if (element.properties) {
-      for (const [propName, propValue] of Object.entries(element.properties))
-        if (ReferenceRegistry.KNOWN_REF_PROPERTIES.has(propName)) {
-          if (typeof propValue == "string")
-            this.addReference({
-              source: element.id,
-              target: propValue,
-              type: propName
-            });
-          else if (Array.isArray(propValue))
-            for (const target of propValue)
-              typeof target == "string" && this.addReference({
-                source: element.id,
-                target,
+    if (!element)
+      return;
+    const elementId = element.path || element.id;
+    if (elementId) {
+      if (element.references)
+        for (const ref of element.references)
+          this.addReference({
+            ...ref,
+            source: elementId
+          });
+      if (element.attributes) {
+        for (const [propName, propValue] of Object.entries(element.attributes))
+          if (ReferenceRegistry.KNOWN_REF_PROPERTIES.has(propName)) {
+            if (typeof propValue == "string")
+              this.addReference({
+                source: elementId,
+                target: propValue,
                 type: propName
               });
-        }
-      const nestedRefs = this.scanNestedReferences(element.id, element.properties);
-      for (const ref of nestedRefs)
-        this.addReference(ref);
+            else if (Array.isArray(propValue))
+              for (const target of propValue)
+                typeof target == "string" && this.addReference({
+                  source: elementId,
+                  target,
+                  type: propName
+                });
+          }
+        const nestedRefs = this.scanNestedReferences(elementId, element.attributes);
+        for (const ref of nestedRefs)
+          this.addReference(ref);
+      }
     }
   }
   /**

package/dist/core/reference-registry.js.map

@@ -1,7 +1,7 @@
 {
   "version": 3,
   "sources": ["../../src/core/reference-registry.ts"],
-  "sourcesContent": ["import Graph from 'graphology';\nimport type { Reference, Element } from \"../types/index.js\";\n\n/**\n * Reference registry - tracks and validates cross-layer references\n */\nexport class ReferenceRegistry {\n  private references: Map<string, Reference[]>;\n  private targetIndex: Map<string, Reference[]>;\n  private typeIndex: Map<string, Reference[]>;\n\n  // Known reference property names from Python CLI\n  private static readonly KNOWN_REF_PROPERTIES = new Set([\n    'realizes', 'realizedBy',\n    'serves', 'servedBy',\n    'accesses', 'accessedBy',\n    'uses', 'usedBy',\n    'composedOf', 'partOf',\n    'flows', 'triggers',\n    'archimateRef', 'businessActorRef', 'stakeholderRef',\n    'motivationGoalRef', 'dataObjectRef', 'apiOperationRef',\n    'applicationServiceRef', 'schemaRef'\n  ]);\n\n  constructor() {\n    this.references = new Map();\n    this.targetIndex = new Map();\n    this.typeIndex = new Map();\n  }\n\n  /**\n   * Add a reference to the registry\n   */\n  addReference(reference: Reference): void {\n    // Add to source index\n    const sourceKey = reference.source;\n    if (!this.references.has(sourceKey)) {\n      this.references.set(sourceKey, []);\n    }\n    this.references.get(sourceKey)!.push(reference);\n\n    // Add to target index\n    const targetKey = reference.target;\n    if (!this.targetIndex.has(targetKey)) {\n      this.targetIndex.set(targetKey, []);\n    }\n    this.targetIndex.get(targetKey)!.push(reference);\n\n    // Add to type index\n    const typeKey = reference.type;\n    if (!this.typeIndex.has(typeKey)) {\n      this.typeIndex.set(typeKey, []);\n    }\n    this.typeIndex.get(typeKey)!.push(reference);\n  }\n\n  /**\n   * Get all references from a source element\n   */\n  getReferencesFrom(sourceId: string): Reference[] {\n    return this.references.get(sourceId) ?? [];\n  }\n\n  /**\n   * Get all references to a target element\n   */\n  getReferencesTo(targetId: string): Reference[] {\n    return this.targetIndex.get(targetId) ?? [];\n  }\n\n  /**\n   * Get all references of a specific type\n   */\n  getReferencesByType(type: string): Reference[] {\n    return this.typeIndex.get(type) ?? [];\n  }\n\n  /**\n   * Check if a reference exists\n   */\n  hasReference(sourceId: string, targetId: string): boolean {\n    const refs = this.references.get(sourceId) ?? [];\n    return refs.some(ref => ref.target === targetId);\n  }\n\n  /**\n   * Get all references\n   */\n  getAllReferences(): Reference[] {\n    const allRefs: Reference[] = [];\n    for (const refs of this.references.values()) {\n      allRefs.push(...refs);\n    }\n    return allRefs;\n  }\n\n  /**\n   * Clear all references\n   */\n  clear(): void {\n    this.references.clear();\n    this.targetIndex.clear();\n    this.typeIndex.clear();\n  }\n\n  /**\n   * Register an element and all its references\n   * Scans element properties for known reference names\n   */\n  registerElement(element: Element): void {\n    // Extract references from explicit references array\n    if (element.references) {\n      for (const ref of element.references) {\n        this.addReference(ref);\n      }\n    }\n\n    // Scan properties for known reference properties\n    if (element.properties) {\n      for (const [propName, propValue] of Object.entries(element.properties)) {\n        if (ReferenceRegistry.KNOWN_REF_PROPERTIES.has(propName)) {\n          // Handle string value\n          if (typeof propValue === 'string') {\n            this.addReference({\n              source: element.id,\n              target: propValue,\n              type: propName\n            });\n          }\n          // Handle array of strings\n          else if (Array.isArray(propValue)) {\n            for (const target of propValue) {\n              if (typeof target === 'string') {\n                this.addReference({\n                  source: element.id,\n                  target: target,\n                  type: propName\n                });\n              }\n            }\n          }\n        }\n      }\n\n      // Scan nested properties for *Ref/*Reference properties\n      const nestedRefs = this.scanNestedReferences(element.id, element.properties);\n      for (const ref of nestedRefs) {\n        this.addReference(ref);\n      }\n    }\n  }\n\n  /**\n   * Recursively scan nested structures for reference properties\n   * Matches Python CLI behavior: looks for properties ending in \"Ref\" or \"Reference\"\n   */\n  private scanNestedReferences(\n    sourceId: string,\n    data: any,\n    path: string = ''\n  ): Reference[] {\n    const references: Reference[] = [];\n\n    if (!data || typeof data !== 'object') {\n      return references;\n    }\n\n    // Handle arrays\n    if (Array.isArray(data)) {\n      for (let i = 0; i < data.length; i++) {\n        const itemPath = path ? `${path}[${i}]` : `[${i}]`;\n        references.push(...this.scanNestedReferences(sourceId, data[i], itemPath));\n      }\n      return references;\n    }\n\n    // Scan object properties\n    for (const [key, value] of Object.entries(data)) {\n      const currentPath = path ? `${path}.${key}` : key;\n\n      // Skip if this is a top-level known reference property (already handled)\n      if (!path && ReferenceRegistry.KNOWN_REF_PROPERTIES.has(key)) {\n        continue;\n      }\n\n      // Check if property name ends with \"Ref\" or \"Reference\"\n      if (key.endsWith('Ref') || key.endsWith('Reference')) {\n        // Handle string value\n        if (typeof value === 'string') {\n          references.push({\n            source: sourceId,\n            target: value,\n            type: key,\n            description: `Nested reference at ${currentPath}`,\n          });\n        }\n        // Handle array of strings\n        else if (Array.isArray(value)) {\n          for (const target of value) {\n            if (typeof target === 'string') {\n              references.push({\n                source: sourceId,\n                target: target,\n                type: key,\n                description: `Nested reference at ${currentPath}`,\n              });\n            }\n          }\n        }\n      }\n      // Recurse into nested objects\n      else if (value && typeof value === 'object' && !Array.isArray(value)) {\n        references.push(...this.scanNestedReferences(sourceId, value, currentPath));\n      }\n      // Recurse into arrays\n      else if (Array.isArray(value)) {\n        references.push(...this.scanNestedReferences(sourceId, value, currentPath));\n      }\n    }\n\n    return references;\n  }\n\n  /**\n   * Find broken references (references to non-existent elements)\n   */\n  findBrokenReferences(validIds: Set<string>): Reference[] {\n    return this.getAllReferences().filter(ref => !validIds.has(ref.target));\n  }\n\n  /**\n   * Get dependency graph as a directed graph using graphology\n   * Nodes are element IDs, edges represent references\n   */\n  getDependencyGraph(): Graph {\n    const graph = new Graph({ type: 'directed' });\n\n    // Add all unique nodes\n    const nodes = new Set<string>();\n    for (const ref of this.getAllReferences()) {\n      nodes.add(ref.source);\n      nodes.add(ref.target);\n    }\n\n    for (const node of nodes) {\n      graph.addNode(node);\n    }\n\n    // Add edges for all references\n    for (const ref of this.getAllReferences()) {\n      // Use reference type as edge data\n      graph.addEdge(ref.source, ref.target, {\n        type: ref.type,\n        description: ref.description,\n      });\n    }\n\n    return graph;\n  }\n\n  /**\n   * Get statistics about registered references\n   */\n  getStats(): {\n    totalReferences: number;\n    uniqueSources: number;\n    uniqueTargets: number;\n    referenceTypes: string[];\n  } {\n    return {\n      totalReferences: this.getAllReferences().length,\n      uniqueSources: this.references.size,\n      uniqueTargets: this.targetIndex.size,\n      referenceTypes: Array.from(this.typeIndex.keys()),\n    };\n  }\n}\n"],
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+  "sourcesContent": ["import Graph from \"graphology\";\nimport type { Reference, Element } from \"../types/index.js\";\n\n\n/**\n * Reference registry - tracks and validates cross-layer references\n *\n * NOTE: Phase 3 Deferred - Registry Consolidation\n * This registry will be consolidated into the GraphModel query API in a future phase.\n * The graph model provides the foundation with graph-based reference tracking.\n * Current approach maintains backward compatibility while the transition occurs.\n *\n * Future: Use GraphModel.getEdgesFrom/To/Between with predicate filtering\n * instead of maintaining separate reference registry.\n *\n * See: https://github.com/tinkermonkey/documentation_robotics/discussions/317\n */\nexport class ReferenceRegistry {\n  private references: Map<string, Reference[]>;\n  private targetIndex: Map<string, Reference[]>;\n  private typeIndex: Map<string, Reference[]>;\n\n  // Known reference property names from Python CLI\n  private static readonly KNOWN_REF_PROPERTIES = new Set([\n    \"realizes\",\n    \"realizedBy\",\n    \"serves\",\n    \"servedBy\",\n    \"accesses\",\n    \"accessedBy\",\n    \"uses\",\n    \"usedBy\",\n    \"composedOf\",\n    \"partOf\",\n    \"flows\",\n    \"triggers\",\n    \"archimateRef\",\n    \"businessActorRef\",\n    \"stakeholderRef\",\n    \"motivationGoalRef\",\n    \"dataObjectRef\",\n    \"apiOperationRef\",\n    \"applicationServiceRef\",\n    \"schemaRef\",\n  ]);\n\n  constructor() {\n    this.references = new Map();\n    this.targetIndex = new Map();\n    this.typeIndex = new Map();\n  }\n\n  /**\n   * Add a reference to the registry\n   */\n  addReference(reference: Reference): void {\n    // Add to source index\n    const sourceKey = reference.source;\n    if (!this.references.has(sourceKey)) {\n      this.references.set(sourceKey, []);\n    }\n    this.references.get(sourceKey)!.push(reference);\n\n    // Add to target index\n    const targetKey = reference.target;\n    if (!this.targetIndex.has(targetKey)) {\n      this.targetIndex.set(targetKey, []);\n    }\n    this.targetIndex.get(targetKey)!.push(reference);\n\n    // Add to type index\n    const typeKey = reference.type;\n    if (!this.typeIndex.has(typeKey)) {\n      this.typeIndex.set(typeKey, []);\n    }\n    this.typeIndex.get(typeKey)!.push(reference);\n  }\n\n  /**\n   * Get all references from a source element\n   */\n  getReferencesFrom(sourceId: string): Reference[] {\n    return this.references.get(sourceId) ?? [];\n  }\n\n  /**\n   * Get all references to a target element\n   */\n  getReferencesTo(targetId: string): Reference[] {\n    return this.targetIndex.get(targetId) ?? [];\n  }\n\n  /**\n   * Get all references of a specific type\n   */\n  getReferencesByType(type: string): Reference[] {\n    return this.typeIndex.get(type) ?? [];\n  }\n\n  /**\n   * Check if a reference exists\n   */\n  hasReference(sourceId: string, targetId: string): boolean {\n    const refs = this.references.get(sourceId) ?? [];\n    return refs.some((ref) => ref.target === targetId);\n  }\n\n  /**\n   * Get all references\n   */\n  getAllReferences(): Reference[] {\n    const allRefs: Reference[] = [];\n    for (const refs of this.references.values()) {\n      allRefs.push(...refs);\n    }\n    return allRefs;\n  }\n\n  /**\n   * Clear all references\n   */\n  clear(): void {\n    this.references.clear();\n    this.targetIndex.clear();\n    this.typeIndex.clear();\n  }\n\n  /**\n   * Register an element and all its references\n   * Scans element properties for known reference names\n   */\n  registerElement(element: Element): void {\n    // Validate required element properties\n    if (!element) {\n      return;\n    }\n\n    // Use element's path (slug) as the registry key; fall back to id for legacy elements\n    const elementId = element.path || element.id;\n\n    // Skip if element has no ID\n    if (!elementId) {\n      return;\n    }\n\n    // Extract references from explicit references array\n    if (element.references) {\n      for (const ref of element.references) {\n        // Rewrite source to use consistent ID\n        this.addReference({\n          ...ref,\n          source: elementId,\n        });\n      }\n    }\n\n    // Scan attributes for known reference properties\n    if (element.attributes) {\n      for (const [propName, propValue] of Object.entries(element.attributes)) {\n        if (ReferenceRegistry.KNOWN_REF_PROPERTIES.has(propName)) {\n          // Handle string value\n          if (typeof propValue === \"string\") {\n            this.addReference({\n              source: elementId,\n              target: propValue,\n              type: propName,\n            });\n          }\n          // Handle array of strings\n          else if (Array.isArray(propValue)) {\n            for (const target of propValue) {\n              if (typeof target === \"string\") {\n                this.addReference({\n                  source: elementId,\n                  target: target,\n                  type: propName,\n                });\n              }\n            }\n          }\n        }\n      }\n\n      // Scan nested attributes for *Ref/*Reference properties\n      const nestedRefs = this.scanNestedReferences(elementId, element.attributes);\n      for (const ref of nestedRefs) {\n        this.addReference(ref);\n      }\n    }\n  }\n\n  /**\n   * Recursively scan nested structures for reference properties\n   * Matches Python CLI behavior: looks for properties ending in \"Ref\" or \"Reference\"\n   */\n  private scanNestedReferences(sourceId: string, data: any, path: string = \"\"): Reference[] {\n    const references: Reference[] = [];\n\n    if (!data || typeof data !== \"object\") {\n      return references;\n    }\n\n    // Handle arrays\n    if (Array.isArray(data)) {\n      for (let i = 0; i < data.length; i++) {\n        const itemPath = path ? `${path}[${i}]` : `[${i}]`;\n        references.push(...this.scanNestedReferences(sourceId, data[i], itemPath));\n      }\n      return references;\n    }\n\n    // Scan object properties\n    for (const [key, value] of Object.entries(data)) {\n      const currentPath = path ? `${path}.${key}` : key;\n\n      // Skip if this is a top-level known reference property (already handled)\n      if (!path && ReferenceRegistry.KNOWN_REF_PROPERTIES.has(key)) {\n        continue;\n      }\n\n      // Check if property name ends with \"Ref\" or \"Reference\"\n      if (key.endsWith(\"Ref\") || key.endsWith(\"Reference\")) {\n        // Handle string value\n        if (typeof value === \"string\") {\n          references.push({\n            source: sourceId,\n            target: value,\n            type: key,\n            description: `Nested reference at ${currentPath}`,\n          });\n        }\n        // Handle array of strings\n        else if (Array.isArray(value)) {\n          for (const target of value) {\n            if (typeof target === \"string\") {\n              references.push({\n                source: sourceId,\n                target: target,\n                type: key,\n                description: `Nested reference at ${currentPath}`,\n              });\n            }\n          }\n        }\n      }\n      // Recurse into nested objects\n      else if (value && typeof value === \"object\" && !Array.isArray(value)) {\n        references.push(...this.scanNestedReferences(sourceId, value, currentPath));\n      }\n      // Recurse into arrays\n      else if (Array.isArray(value)) {\n        references.push(...this.scanNestedReferences(sourceId, value, currentPath));\n      }\n    }\n\n    return references;\n  }\n\n  /**\n   * Find broken references (references to non-existent elements)\n   */\n  findBrokenReferences(validIds: Set<string>): Reference[] {\n    return this.getAllReferences().filter((ref) => !validIds.has(ref.target));\n  }\n\n  /**\n   * Get dependency graph as a directed graph using graphology\n   * Nodes are element IDs, edges represent references\n   */\n  getDependencyGraph(): Graph {\n    const graph = new Graph({ type: \"directed\" });\n\n    // Add all unique nodes\n    const nodes = new Set<string>();\n    for (const ref of this.getAllReferences()) {\n      nodes.add(ref.source);\n      nodes.add(ref.target);\n    }\n\n    for (const node of nodes) {\n      graph.addNode(node);\n    }\n\n    // Add edges for all references\n    for (const ref of this.getAllReferences()) {\n      // Use reference type as edge data\n      graph.addEdge(ref.source, ref.target, {\n        type: ref.type,\n        description: ref.description,\n      });\n    }\n\n    return graph;\n  }\n\n  /**\n   * Get statistics about registered references\n   */\n  getStats(): {\n    totalReferences: number;\n    uniqueSources: number;\n    uniqueTargets: number;\n    referenceTypes: string[];\n  } {\n    return {\n      totalReferences: this.getAllReferences().length,\n      uniqueSources: this.references.size,\n      uniqueTargets: this.targetIndex.size,\n      referenceTypes: Array.from(this.typeIndex.keys()),\n    };\n  }\n}\n"],
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