@documentation-robotics/cli 0.1.10 → 0.1.12

package/dist/core/graph-model.js.map

@@ -1,7 +1,7 @@
 {
   "version": 3,
   "sources": ["../../src/core/graph-model.ts"],
-  "sourcesContent": ["import { Element } from \"./element.js\";\nimport type { ElementMetadata, Relationship, SourceReference } from \"../types/index.js\";\n\n/**\n * Graph node representing a model element\n * Replaces Element class for graph-based storage\n */\nexport interface GraphNode {\n  id: string; // Path (slug) used as graph key: {layer}.{type}.{kebab-name}\n  uuid?: string; // UUIDv4 preserved for round-tripping (element.id)\n  layer: string; // Layer this node belongs to\n  type: string; // Element type\n  name: string; // Display name\n  description?: string; // Optional description\n  properties?: Record<string, unknown>; // Custom properties\n  // Spec-node aligned fields (preserved through graph round-trip)\n  spec_node_id?: string;\n  layer_id?: string;\n  attributes?: Record<string, unknown>;\n  source_reference?: SourceReference;\n  metadata?: ElementMetadata;\n}\n\n/**\n * Graph edge representing a relationship between nodes\n */\nexport interface GraphEdge {\n  id: string; // Unique identifier\n  source: string; // Source node ID\n  destination: string; // Destination node ID\n  predicate: string; // Relationship type\n  properties?: Record<string, unknown>; // Optional properties\n  category?: \"structural\" | \"behavioral\";\n}\n\n/**\n * Index structures for efficient querying\n */\ninterface GraphIndices {\n  nodesByLayer: Map<string, Set<string>>; // layer -> node IDs\n  nodesByType: Map<string, Set<string>>; // type -> node IDs\n  edgesBySource: Map<string, Set<string>>; // source node ID -> edge IDs\n  edgesByDestination: Map<string, Set<string>>; // destination node ID -> edge IDs\n  edgesByPredicate: Map<string, Set<string>>; // predicate -> edge IDs\n}\n\n/**\n * Graph model interface for node/edge storage with query capabilities\n */\nexport interface IGraphModel {\n  nodes: Map<string, GraphNode>;\n  edges: Map<string, GraphEdge>;\n\n  // Query methods\n  getNode(id: string): GraphNode | undefined;\n  getNodesByLayer(layer: string): GraphNode[];\n  getNodesByType(type: string): GraphNode[];\n  getEdgesFrom(nodeId: string, predicate?: string): GraphEdge[];\n  getEdgesTo(nodeId: string, predicate?: string): GraphEdge[];\n  getEdgesBetween(sourceId: string, destinationId: string, predicate?: string): GraphEdge[];\n  getAllEdges(): GraphEdge[];\n\n  // Mutation methods\n  addNode(node: GraphNode): void;\n  removeNode(nodeId: string): boolean;\n  updateNode(nodeId: string, updates: Partial<GraphNode>): boolean;\n\n  addEdge(edge: GraphEdge): void;\n  removeEdge(edgeId: string): boolean;\n  updateEdge(edgeId: string, updates: Partial<GraphEdge>): boolean;\n\n  // Traversal\n  traverse(startNodeId: string, predicate?: string, maxDepth?: number): GraphNode[];\n\n  // Utility\n  getNodeCount(): number;\n  getEdgeCount(): number;\n  clear(): void;\n}\n\n/**\n * Implementation of graph model with indices for efficient queries\n */\nexport class GraphModel implements IGraphModel {\n  nodes: Map<string, GraphNode>;\n  edges: Map<string, GraphEdge>;\n  private indices: GraphIndices;\n  private nodesVersion: number = 0;\n\n  constructor() {\n    this.nodes = new Map();\n    this.edges = new Map();\n    this.indices = {\n      nodesByLayer: new Map(),\n      nodesByType: new Map(),\n      edgesBySource: new Map(),\n      edgesByDestination: new Map(),\n      edgesByPredicate: new Map(),\n    };\n  }\n\n  /**\n   * Get the current version of the nodes (for cache invalidation)\n   */\n  getNodesVersion(): number {\n    return this.nodesVersion;\n  }\n\n  /**\n   * Add a node to the graph and update indices\n   * If a node with the same ID exists, its old index entries are cleaned up\n   */\n  addNode(node: GraphNode): void {\n    const existingNode = this.nodes.get(node.id);\n\n    // Clean up old index entries if node is being replaced\n    if (existingNode) {\n      // Remove from old layer index\n      const oldLayerSet = this.indices.nodesByLayer.get(existingNode.layer);\n      if (oldLayerSet) {\n        oldLayerSet.delete(node.id);\n        if (oldLayerSet.size === 0) {\n          this.indices.nodesByLayer.delete(existingNode.layer);\n        }\n      }\n\n      // Remove from old type index\n      const oldTypeSet = this.indices.nodesByType.get(existingNode.type);\n      if (oldTypeSet) {\n        oldTypeSet.delete(node.id);\n        if (oldTypeSet.size === 0) {\n          this.indices.nodesByType.delete(existingNode.type);\n        }\n      }\n    }\n\n    // Add new node\n    this.nodes.set(node.id, node);\n\n    // Update layer index\n    if (!this.indices.nodesByLayer.has(node.layer)) {\n      this.indices.nodesByLayer.set(node.layer, new Set());\n    }\n    const layerSet = this.indices.nodesByLayer.get(node.layer);\n    if (layerSet) {\n      layerSet.add(node.id);\n    }\n\n    // Update type index\n    if (!this.indices.nodesByType.has(node.type)) {\n      this.indices.nodesByType.set(node.type, new Set());\n    }\n    const typeSet = this.indices.nodesByType.get(node.type);\n    if (typeSet) {\n      typeSet.add(node.id);\n    }\n\n    // Increment version to invalidate caches\n    this.nodesVersion++;\n  }\n\n  /**\n   * Remove a node from the graph\n   * Also removes all associated edges\n   */\n  removeNode(nodeId: string): boolean {\n    const node = this.nodes.get(nodeId);\n    if (!node) {\n      return false;\n    }\n\n    // Remove from nodes map\n    this.nodes.delete(nodeId);\n\n    // Remove from layer index\n    const layerSet = this.indices.nodesByLayer.get(node.layer);\n    if (layerSet) {\n      layerSet.delete(nodeId);\n      if (layerSet.size === 0) {\n        this.indices.nodesByLayer.delete(node.layer);\n      }\n    }\n\n    // Remove from type index\n    const typeSet = this.indices.nodesByType.get(node.type);\n    if (typeSet) {\n      typeSet.delete(nodeId);\n      if (typeSet.size === 0) {\n        this.indices.nodesByType.delete(node.type);\n      }\n    }\n\n    // Remove all edges involving this node\n    const edgesInvolving: string[] = [];\n    for (const [edgeId, edge] of this.edges.entries()) {\n      if (edge.source === nodeId || edge.destination === nodeId) {\n        edgesInvolving.push(edgeId);\n      }\n    }\n    for (const edgeId of edgesInvolving) {\n      this.removeEdge(edgeId);\n    }\n\n    // Increment version to invalidate caches\n    this.nodesVersion++;\n    return true;\n  }\n\n  /**\n   * Update node properties\n   */\n  updateNode(nodeId: string, updates: Partial<GraphNode>): boolean {\n    const node = this.nodes.get(nodeId);\n    if (!node) {\n      return false;\n    }\n\n    // Handle layer change\n    if (updates.layer && updates.layer !== node.layer) {\n      const oldLayerSet = this.indices.nodesByLayer.get(node.layer);\n      if (oldLayerSet) {\n        oldLayerSet.delete(nodeId);\n        if (oldLayerSet.size === 0) {\n          this.indices.nodesByLayer.delete(node.layer);\n        }\n      }\n      if (!this.indices.nodesByLayer.has(updates.layer)) {\n        this.indices.nodesByLayer.set(updates.layer, new Set());\n      }\n      const newLayerSet = this.indices.nodesByLayer.get(updates.layer);\n      if (newLayerSet) {\n        newLayerSet.add(nodeId);\n      }\n    }\n\n    // Handle type change\n    if (updates.type && updates.type !== node.type) {\n      const oldTypeSet = this.indices.nodesByType.get(node.type);\n      if (oldTypeSet) {\n        oldTypeSet.delete(nodeId);\n        if (oldTypeSet.size === 0) {\n          this.indices.nodesByType.delete(node.type);\n        }\n      }\n      if (!this.indices.nodesByType.has(updates.type)) {\n        this.indices.nodesByType.set(updates.type, new Set());\n      }\n      const newTypeSet = this.indices.nodesByType.get(updates.type);\n      if (newTypeSet) {\n        newTypeSet.add(nodeId);\n      }\n    }\n\n    // Apply updates\n    Object.assign(node, updates);\n    // Increment version to invalidate caches\n    this.nodesVersion++;\n    return true;\n  }\n\n  /**\n   * Add an edge to the graph and update indices\n   * Validates that both source and destination nodes exist\n   * @throws Error if source or destination node does not exist\n   */\n  addEdge(edge: GraphEdge): void {\n    // Validate that source node exists\n    if (!this.nodes.has(edge.source)) {\n      throw new Error(`Cannot add edge: source node \"${edge.source}\" does not exist`);\n    }\n\n    // Validate that destination node exists\n    if (!this.nodes.has(edge.destination)) {\n      throw new Error(`Cannot add edge: destination node \"${edge.destination}\" does not exist`);\n    }\n\n    this.edges.set(edge.id, edge);\n\n    // Update source index\n    if (!this.indices.edgesBySource.has(edge.source)) {\n      this.indices.edgesBySource.set(edge.source, new Set());\n    }\n    const sourceSet = this.indices.edgesBySource.get(edge.source);\n    if (sourceSet) {\n      sourceSet.add(edge.id);\n    }\n\n    // Update destination index\n    if (!this.indices.edgesByDestination.has(edge.destination)) {\n      this.indices.edgesByDestination.set(edge.destination, new Set());\n    }\n    const destSet = this.indices.edgesByDestination.get(edge.destination);\n    if (destSet) {\n      destSet.add(edge.id);\n    }\n\n    // Update predicate index\n    if (!this.indices.edgesByPredicate.has(edge.predicate)) {\n      this.indices.edgesByPredicate.set(edge.predicate, new Set());\n    }\n    const predicateSet = this.indices.edgesByPredicate.get(edge.predicate);\n    if (predicateSet) {\n      predicateSet.add(edge.id);\n    }\n  }\n\n  /**\n   * Remove an edge from the graph\n   */\n  removeEdge(edgeId: string): boolean {\n    const edge = this.edges.get(edgeId);\n    if (!edge) {\n      return false;\n    }\n\n    // Remove from edges map\n    this.edges.delete(edgeId);\n\n    // Remove from source index\n    const sourceSet = this.indices.edgesBySource.get(edge.source);\n    if (sourceSet) {\n      sourceSet.delete(edgeId);\n      if (sourceSet.size === 0) {\n        this.indices.edgesBySource.delete(edge.source);\n      }\n    }\n\n    // Remove from destination index\n    const destSet = this.indices.edgesByDestination.get(edge.destination);\n    if (destSet) {\n      destSet.delete(edgeId);\n      if (destSet.size === 0) {\n        this.indices.edgesByDestination.delete(edge.destination);\n      }\n    }\n\n    // Remove from predicate index\n    const predicateSet = this.indices.edgesByPredicate.get(edge.predicate);\n    if (predicateSet) {\n      predicateSet.delete(edgeId);\n      if (predicateSet.size === 0) {\n        this.indices.edgesByPredicate.delete(edge.predicate);\n      }\n    }\n\n    return true;\n  }\n\n  /**\n   * Update edge properties\n   */\n  updateEdge(edgeId: string, updates: Partial<GraphEdge>): boolean {\n    const edge = this.edges.get(edgeId);\n    if (!edge) {\n      return false;\n    }\n\n    // Handle predicate change\n    if (updates.predicate && updates.predicate !== edge.predicate) {\n      const oldPredicateSet = this.indices.edgesByPredicate.get(edge.predicate);\n      if (oldPredicateSet) {\n        oldPredicateSet.delete(edgeId);\n        if (oldPredicateSet.size === 0) {\n          this.indices.edgesByPredicate.delete(edge.predicate);\n        }\n      }\n      if (!this.indices.edgesByPredicate.has(updates.predicate)) {\n        this.indices.edgesByPredicate.set(updates.predicate, new Set());\n      }\n      const newPredicateSet = this.indices.edgesByPredicate.get(updates.predicate);\n      if (newPredicateSet) {\n        newPredicateSet.add(edgeId);\n      }\n    }\n\n    // Note: Source and destination changes are not supported (use removeEdge + addEdge)\n    // Apply updates\n    Object.assign(edge, updates);\n    return true;\n  }\n\n  /**\n   * Get a node by its ID\n   */\n  getNode(id: string): GraphNode | undefined {\n    return this.nodes.get(id);\n  }\n\n  /**\n   * Get all nodes in a specific layer\n   */\n  getNodesByLayer(layer: string): GraphNode[] {\n    const nodeIds = this.indices.nodesByLayer.get(layer) ?? new Set();\n    const result: GraphNode[] = [];\n    for (const id of nodeIds) {\n      const node = this.nodes.get(id);\n      if (node) {\n        result.push(node);\n      }\n    }\n    return result;\n  }\n\n  /**\n   * Get all nodes of a specific type\n   */\n  getNodesByType(type: string): GraphNode[] {\n    const nodeIds = this.indices.nodesByType.get(type) ?? new Set();\n    const result: GraphNode[] = [];\n    for (const id of nodeIds) {\n      const node = this.nodes.get(id);\n      if (node) {\n        result.push(node);\n      }\n    }\n    return result;\n  }\n\n  /**\n   * Get outgoing edges from a node, optionally filtered by predicate\n   */\n  getEdgesFrom(nodeId: string, predicate?: string): GraphEdge[] {\n    const edgeIds = this.indices.edgesBySource.get(nodeId) ?? new Set();\n    const edges: GraphEdge[] = [];\n    for (const id of edgeIds) {\n      const edge = this.edges.get(id);\n      if (edge) {\n        edges.push(edge);\n      }\n    }\n\n    if (predicate) {\n      return edges.filter((e) => e.predicate === predicate);\n    }\n    return edges;\n  }\n\n  /**\n   * Get incoming edges to a node, optionally filtered by predicate\n   */\n  getEdgesTo(nodeId: string, predicate?: string): GraphEdge[] {\n    const edgeIds = this.indices.edgesByDestination.get(nodeId) ?? new Set();\n    const edges: GraphEdge[] = [];\n    for (const id of edgeIds) {\n      const edge = this.edges.get(id);\n      if (edge) {\n        edges.push(edge);\n      }\n    }\n\n    if (predicate) {\n      return edges.filter((e) => e.predicate === predicate);\n    }\n    return edges;\n  }\n\n  /**\n   * Get edges between two specific nodes\n   */\n  getEdgesBetween(sourceId: string, destinationId: string, predicate?: string): GraphEdge[] {\n    const outgoing = this.getEdgesFrom(sourceId, predicate);\n    return outgoing.filter((e) => e.destination === destinationId);\n  }\n\n  /**\n   * Get all edges in the graph\n   */\n  getAllEdges(): GraphEdge[] {\n    return Array.from(this.edges.values());\n  }\n\n  /**\n   * Traverse the graph starting from a node using breadth-first search\n   */\n  traverse(startNodeId: string, predicate?: string, maxDepth: number = Infinity): GraphNode[] {\n    const visited = new Set<string>();\n    const result: GraphNode[] = [];\n    const queue: { nodeId: string; depth: number }[] = [{ nodeId: startNodeId, depth: 0 }];\n\n    while (queue.length > 0) {\n      const { nodeId, depth } = queue.shift()!;\n\n      if (visited.has(nodeId) || depth > maxDepth) {\n        continue;\n      }\n\n      visited.add(nodeId);\n      const node = this.nodes.get(nodeId);\n      if (node) {\n        result.push(node);\n      }\n\n      // Find outgoing edges\n      const edges = this.getEdgesFrom(nodeId, predicate);\n      for (const edge of edges) {\n        if (!visited.has(edge.destination)) {\n          queue.push({ nodeId: edge.destination, depth: depth + 1 });\n        }\n      }\n    }\n\n    return result;\n  }\n\n  /**\n   * Get total number of nodes\n   */\n  getNodeCount(): number {\n    return this.nodes.size;\n  }\n\n  /**\n   * Get total number of edges\n   */\n  getEdgeCount(): number {\n    return this.edges.size;\n  }\n\n  /**\n   * Clear all data from the graph\n   */\n  clear(): void {\n    this.nodes.clear();\n    this.edges.clear();\n    this.indices.nodesByLayer.clear();\n    this.indices.nodesByType.clear();\n    this.indices.edgesBySource.clear();\n    this.indices.edgesByDestination.clear();\n    this.indices.edgesByPredicate.clear();\n  }\n\n  /**\n   * Convert Element to GraphNode\n   * Preserves spec-node fields so they survive graph round-trips\n   */\n  /** UUID pattern for detecting actual UUIDs vs slug IDs */\n  private static readonly UUID_PATTERN = /^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$/i;\n\n  static fromElement(element: Element): GraphNode {\n    // path is the graph key; fall back to id for elements without a path\n    const graphId = element.path || element.id;\n    // Only preserve UUID when the id is actually a UUID (not a slug)\n    const isUUID = GraphModel.UUID_PATTERN.test(element.id);\n    return {\n      id: graphId,\n      uuid: isUUID ? element.id : undefined,   // preserve UUID for round-tripping\n      layer: element.layer || \"unknown\",\n      type: element.type,\n      name: element.name,\n      description: element.description,\n      properties: element.attributes || {},\n      spec_node_id: element.spec_node_id || undefined,\n      layer_id: element.layer_id || undefined,\n      attributes: element.attributes && Object.keys(element.attributes).length > 0\n        ? element.attributes\n        : undefined,\n      source_reference: element.source_reference,\n      metadata: element.metadata,\n    };\n  }\n\n  /**\n   * Convert Relationship to GraphEdge\n   */\n  static relationshipToEdge(relationship: Relationship, edgeId: string): GraphEdge {\n    return {\n      id: edgeId,\n      source: relationship.source,\n      destination: relationship.target,\n      predicate: relationship.predicate,\n      properties: relationship.properties,\n    };\n  }\n}\n"],
-  "mappings": 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+  "sourcesContent": ["import { Element } from \"./element.js\";\nimport type { ElementMetadata, Relationship, SourceReference } from \"../types/index.js\";\n\n/**\n * Graph node representing a model element\n * Replaces Element class for graph-based storage\n */\nexport interface GraphNode {\n  id: string; // Path (slug) used as graph key: {layer}.{type}.{kebab-name}\n  uuid?: string; // UUIDv4 preserved for round-tripping (element.id)\n  layer: string; // Layer this node belongs to\n  type: string; // Element type\n  name: string; // Display name\n  description?: string; // Optional description\n  properties?: Record<string, unknown>; // Custom properties\n  // Spec-node aligned fields (preserved through graph round-trip)\n  spec_node_id?: string;\n  layer_id?: string;\n  attributes?: Record<string, unknown>;\n  source_reference?: SourceReference;\n  metadata?: ElementMetadata;\n}\n\n/**\n * Graph edge representing a relationship between nodes\n */\nexport interface GraphEdge {\n  id: string; // Unique identifier\n  source: string; // Source node ID\n  destination: string; // Destination node ID\n  predicate: string; // Relationship type\n  properties?: Record<string, unknown>; // Optional properties\n  category?: \"structural\" | \"behavioral\";\n}\n\n/**\n * Index structures for efficient querying\n */\ninterface GraphIndices {\n  nodesByLayer: Map<string, Set<string>>; // layer -> node IDs\n  nodesByType: Map<string, Set<string>>; // type -> node IDs\n  edgesBySource: Map<string, Set<string>>; // source node ID -> edge IDs\n  edgesByDestination: Map<string, Set<string>>; // destination node ID -> edge IDs\n  edgesByPredicate: Map<string, Set<string>>; // predicate -> edge IDs\n}\n\n/**\n * Graph model interface for node/edge storage with query capabilities\n */\nexport interface IGraphModel {\n  nodes: Map<string, GraphNode>;\n  edges: Map<string, GraphEdge>;\n\n  // Query methods\n  getNode(id: string): GraphNode | undefined;\n  getNodesByLayer(layer: string): GraphNode[];\n  getNodesByType(type: string): GraphNode[];\n  getEdgesFrom(nodeId: string, predicate?: string): GraphEdge[];\n  getEdgesTo(nodeId: string, predicate?: string): GraphEdge[];\n  getEdgesBetween(sourceId: string, destinationId: string, predicate?: string): GraphEdge[];\n  getAllEdges(): GraphEdge[];\n\n  // Mutation methods\n  addNode(node: GraphNode): void;\n  removeNode(nodeId: string): boolean;\n  updateNode(nodeId: string, updates: Partial<GraphNode>): boolean;\n\n  addEdge(edge: GraphEdge): void;\n  removeEdge(edgeId: string): boolean;\n  updateEdge(edgeId: string, updates: Partial<GraphEdge>): boolean;\n\n  // Traversal\n  traverse(startNodeId: string, predicate?: string, maxDepth?: number): GraphNode[];\n\n  // Utility\n  getNodeCount(): number;\n  getEdgeCount(): number;\n  clear(): void;\n}\n\n/**\n * Implementation of graph model with indices for efficient queries\n */\nexport class GraphModel implements IGraphModel {\n  nodes: Map<string, GraphNode>;\n  edges: Map<string, GraphEdge>;\n  private indices: GraphIndices;\n  private nodesVersion: number = 0;\n\n  constructor() {\n    this.nodes = new Map();\n    this.edges = new Map();\n    this.indices = {\n      nodesByLayer: new Map(),\n      nodesByType: new Map(),\n      edgesBySource: new Map(),\n      edgesByDestination: new Map(),\n      edgesByPredicate: new Map(),\n    };\n  }\n\n  /**\n   * Get the current version of the nodes (for cache invalidation)\n   */\n  getNodesVersion(): number {\n    return this.nodesVersion;\n  }\n\n  /**\n   * Add a node to the graph and update indices\n   * If a node with the same ID exists, its old index entries are cleaned up\n   */\n  addNode(node: GraphNode): void {\n    const existingNode = this.nodes.get(node.id);\n\n    // Clean up old index entries if node is being replaced\n    if (existingNode) {\n      // Remove from old layer index\n      const oldLayerSet = this.indices.nodesByLayer.get(existingNode.layer);\n      if (oldLayerSet) {\n        oldLayerSet.delete(node.id);\n        if (oldLayerSet.size === 0) {\n          this.indices.nodesByLayer.delete(existingNode.layer);\n        }\n      }\n\n      // Remove from old type index\n      const oldTypeSet = this.indices.nodesByType.get(existingNode.type);\n      if (oldTypeSet) {\n        oldTypeSet.delete(node.id);\n        if (oldTypeSet.size === 0) {\n          this.indices.nodesByType.delete(existingNode.type);\n        }\n      }\n    }\n\n    // Add new node\n    this.nodes.set(node.id, node);\n\n    // Update layer index\n    if (!this.indices.nodesByLayer.has(node.layer)) {\n      this.indices.nodesByLayer.set(node.layer, new Set());\n    }\n    const layerSet = this.indices.nodesByLayer.get(node.layer);\n    if (layerSet) {\n      layerSet.add(node.id);\n    }\n\n    // Update type index\n    if (!this.indices.nodesByType.has(node.type)) {\n      this.indices.nodesByType.set(node.type, new Set());\n    }\n    const typeSet = this.indices.nodesByType.get(node.type);\n    if (typeSet) {\n      typeSet.add(node.id);\n    }\n\n    // Increment version to invalidate caches\n    this.nodesVersion++;\n  }\n\n  /**\n   * Remove a node from the graph\n   * Also removes all associated edges\n   */\n  removeNode(nodeId: string): boolean {\n    const node = this.nodes.get(nodeId);\n    if (!node) {\n      return false;\n    }\n\n    // Remove from nodes map\n    this.nodes.delete(nodeId);\n\n    // Remove from layer index\n    const layerSet = this.indices.nodesByLayer.get(node.layer);\n    if (layerSet) {\n      layerSet.delete(nodeId);\n      if (layerSet.size === 0) {\n        this.indices.nodesByLayer.delete(node.layer);\n      }\n    }\n\n    // Remove from type index\n    const typeSet = this.indices.nodesByType.get(node.type);\n    if (typeSet) {\n      typeSet.delete(nodeId);\n      if (typeSet.size === 0) {\n        this.indices.nodesByType.delete(node.type);\n      }\n    }\n\n    // Remove all edges involving this node\n    const edgesInvolving: string[] = [];\n    for (const [edgeId, edge] of this.edges.entries()) {\n      if (edge.source === nodeId || edge.destination === nodeId) {\n        edgesInvolving.push(edgeId);\n      }\n    }\n    for (const edgeId of edgesInvolving) {\n      this.removeEdge(edgeId);\n    }\n\n    // Increment version to invalidate caches\n    this.nodesVersion++;\n    return true;\n  }\n\n  /**\n   * Update node properties\n   */\n  updateNode(nodeId: string, updates: Partial<GraphNode>): boolean {\n    const node = this.nodes.get(nodeId);\n    if (!node) {\n      return false;\n    }\n\n    // Handle layer change\n    if (updates.layer && updates.layer !== node.layer) {\n      const oldLayerSet = this.indices.nodesByLayer.get(node.layer);\n      if (oldLayerSet) {\n        oldLayerSet.delete(nodeId);\n        if (oldLayerSet.size === 0) {\n          this.indices.nodesByLayer.delete(node.layer);\n        }\n      }\n      if (!this.indices.nodesByLayer.has(updates.layer)) {\n        this.indices.nodesByLayer.set(updates.layer, new Set());\n      }\n      const newLayerSet = this.indices.nodesByLayer.get(updates.layer);\n      if (newLayerSet) {\n        newLayerSet.add(nodeId);\n      }\n    }\n\n    // Handle type change\n    if (updates.type && updates.type !== node.type) {\n      const oldTypeSet = this.indices.nodesByType.get(node.type);\n      if (oldTypeSet) {\n        oldTypeSet.delete(nodeId);\n        if (oldTypeSet.size === 0) {\n          this.indices.nodesByType.delete(node.type);\n        }\n      }\n      if (!this.indices.nodesByType.has(updates.type)) {\n        this.indices.nodesByType.set(updates.type, new Set());\n      }\n      const newTypeSet = this.indices.nodesByType.get(updates.type);\n      if (newTypeSet) {\n        newTypeSet.add(nodeId);\n      }\n    }\n\n    // Apply updates\n    Object.assign(node, updates);\n    // Increment version to invalidate caches\n    this.nodesVersion++;\n    return true;\n  }\n\n  /**\n   * Add an edge to the graph and update indices\n   * Validates that both source and destination nodes exist\n   * @throws Error if source or destination node does not exist\n   */\n  addEdge(edge: GraphEdge): void {\n    // Validate that source node exists\n    if (!this.nodes.has(edge.source)) {\n      throw new Error(`Cannot add edge: source node \"${edge.source}\" does not exist`);\n    }\n\n    // Validate that destination node exists\n    if (!this.nodes.has(edge.destination)) {\n      throw new Error(`Cannot add edge: destination node \"${edge.destination}\" does not exist`);\n    }\n\n    this.edges.set(edge.id, edge);\n\n    // Update source index\n    if (!this.indices.edgesBySource.has(edge.source)) {\n      this.indices.edgesBySource.set(edge.source, new Set());\n    }\n    const sourceSet = this.indices.edgesBySource.get(edge.source);\n    if (sourceSet) {\n      sourceSet.add(edge.id);\n    }\n\n    // Update destination index\n    if (!this.indices.edgesByDestination.has(edge.destination)) {\n      this.indices.edgesByDestination.set(edge.destination, new Set());\n    }\n    const destSet = this.indices.edgesByDestination.get(edge.destination);\n    if (destSet) {\n      destSet.add(edge.id);\n    }\n\n    // Update predicate index\n    if (!this.indices.edgesByPredicate.has(edge.predicate)) {\n      this.indices.edgesByPredicate.set(edge.predicate, new Set());\n    }\n    const predicateSet = this.indices.edgesByPredicate.get(edge.predicate);\n    if (predicateSet) {\n      predicateSet.add(edge.id);\n    }\n  }\n\n  /**\n   * Remove an edge from the graph\n   */\n  removeEdge(edgeId: string): boolean {\n    const edge = this.edges.get(edgeId);\n    if (!edge) {\n      return false;\n    }\n\n    // Remove from edges map\n    this.edges.delete(edgeId);\n\n    // Remove from source index\n    const sourceSet = this.indices.edgesBySource.get(edge.source);\n    if (sourceSet) {\n      sourceSet.delete(edgeId);\n      if (sourceSet.size === 0) {\n        this.indices.edgesBySource.delete(edge.source);\n      }\n    }\n\n    // Remove from destination index\n    const destSet = this.indices.edgesByDestination.get(edge.destination);\n    if (destSet) {\n      destSet.delete(edgeId);\n      if (destSet.size === 0) {\n        this.indices.edgesByDestination.delete(edge.destination);\n      }\n    }\n\n    // Remove from predicate index\n    const predicateSet = this.indices.edgesByPredicate.get(edge.predicate);\n    if (predicateSet) {\n      predicateSet.delete(edgeId);\n      if (predicateSet.size === 0) {\n        this.indices.edgesByPredicate.delete(edge.predicate);\n      }\n    }\n\n    return true;\n  }\n\n  /**\n   * Update edge properties\n   */\n  updateEdge(edgeId: string, updates: Partial<GraphEdge>): boolean {\n    const edge = this.edges.get(edgeId);\n    if (!edge) {\n      return false;\n    }\n\n    // Handle predicate change\n    if (updates.predicate 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const edge = this.edges.get(id);\n      if (edge) {\n        edges.push(edge);\n      }\n    }\n\n    if (predicate) {\n      return edges.filter((e) => e.predicate === predicate);\n    }\n    return edges;\n  }\n\n  /**\n   * Get incoming edges to a node, optionally filtered by predicate\n   */\n  getEdgesTo(nodeId: string, predicate?: string): GraphEdge[] {\n    const edgeIds = this.indices.edgesByDestination.get(nodeId) ?? new Set();\n    const edges: GraphEdge[] = [];\n    for (const id of edgeIds) {\n      const edge = this.edges.get(id);\n      if (edge) {\n        edges.push(edge);\n      }\n    }\n\n    if (predicate) {\n      return edges.filter((e) => e.predicate === predicate);\n    }\n    return edges;\n  }\n\n  /**\n   * Get edges between two specific nodes\n   */\n  getEdgesBetween(sourceId: string, destinationId: string, predicate?: string): GraphEdge[] {\n    const outgoing = this.getEdgesFrom(sourceId, predicate);\n    return outgoing.filter((e) => e.destination === destinationId);\n  }\n\n  /**\n   * Get all edges in the graph\n   */\n  getAllEdges(): GraphEdge[] {\n    return Array.from(this.edges.values());\n  }\n\n  /**\n   * Traverse the graph starting from a node using breadth-first search\n   */\n  traverse(startNodeId: string, predicate?: string, maxDepth: number = Infinity): GraphNode[] {\n    const visited = new Set<string>();\n    const result: GraphNode[] = [];\n    const queue: { nodeId: string; depth: number }[] = [{ nodeId: startNodeId, depth: 0 }];\n\n    while (queue.length > 0) {\n      const { nodeId, depth } = queue.shift()!;\n\n      if (visited.has(nodeId) || depth > maxDepth) {\n        continue;\n      }\n\n      visited.add(nodeId);\n      const node = this.nodes.get(nodeId);\n      if (node) {\n        result.push(node);\n      }\n\n      // Find outgoing edges\n      const edges = this.getEdgesFrom(nodeId, predicate);\n      for (const edge of edges) {\n        if (!visited.has(edge.destination)) {\n          queue.push({ nodeId: edge.destination, depth: depth + 1 });\n        }\n      }\n    }\n\n    return result;\n  }\n\n  /**\n   * Get total number of nodes\n   */\n  getNodeCount(): number {\n    return this.nodes.size;\n  }\n\n  /**\n   * Get total number of edges\n   */\n  getEdgeCount(): number {\n    return this.edges.size;\n  }\n\n  /**\n   * Clear all data from the graph\n   */\n  clear(): void {\n    this.nodes.clear();\n    this.edges.clear();\n    this.indices.nodesByLayer.clear();\n    this.indices.nodesByType.clear();\n    this.indices.edgesBySource.clear();\n    this.indices.edgesByDestination.clear();\n    this.indices.edgesByPredicate.clear();\n  }\n\n  /**\n   * Convert Element to GraphNode\n   * Preserves spec-node fields so they survive graph round-trips\n   */\n  /** UUID pattern for detecting actual UUIDs vs slug IDs */\n  private static readonly UUID_PATTERN = /^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$/i;\n\n  static fromElement(element: Element): GraphNode {\n    // path is the graph key; fall back to id for elements without a path\n    const graphId = element.path || element.id;\n    // Only preserve UUID when the id is actually a UUID (not a slug)\n    const isUUID = GraphModel.UUID_PATTERN.test(element.id);\n    return {\n      id: graphId,\n      uuid: isUUID ? element.id : undefined,   // preserve UUID for round-tripping\n      layer: element.layer || \"unknown\",\n      type: element.type,\n      name: element.name,\n      description: element.description,\n      // `properties` is a SEPARATE COPY of `attributes`, never the same object reference.\n      // `Layer`'s node<->Element conversion (layer.ts's constructor/addElement) mutates\n      // `node.properties` in place to stash graph-internal bookkeeping keys\n      // (__references__/__relationships__/__semanticId__) that have no separate channel\n      // on GraphNode. If `properties` and `attributes` aliased the same object (as they\n      // did before), those mutations leaked straight into `attributes` too \u2014 and\n      // `attributes` is exactly what `Model.saveLayer()` persists to YAML and what\n      // `Layer.elements`/`getElement()` read back as the element's real domain data.\n      // That aliasing is what let `__semanticId__` (added after __references__/\n      // __relationships__ were already accounted for elsewhere) slip past\n      // model.ts's internal-key filter and get written into persisted YAML. Copying\n      // here means a future bookkeeping key added to layer.ts's `nodeProperties` can\n      // never repeat that leak, regardless of whether model.ts's filter is kept in sync.\n      properties: element.attributes ? { ...element.attributes } : {},\n      spec_node_id: element.spec_node_id || undefined,\n      layer_id: element.layer_id || undefined,\n      attributes: element.attributes && Object.keys(element.attributes).length > 0\n        ? element.attributes\n        : undefined,\n      source_reference: element.source_reference,\n      metadata: element.metadata,\n    };\n  }\n\n  /**\n   * Convert Relationship to GraphEdge\n   */\n  static relationshipToEdge(relationship: Relationship, edgeId: string): GraphEdge {\n    return {\n      id: edgeId,\n      source: relationship.source,\n      destination: relationship.target,\n      predicate: relationship.predicate,\n      properties: relationship.properties,\n    };\n  }\n}\n"],
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   "names": []
 }

package/dist/core/model.js

@@ -37,6 +37,15 @@ function typeToSnakeStem(specNodeId, type) {
   }
   return type;
 }
+const ALWAYS_INTERNAL_ATTRIBUTE_KEYS = /* @__PURE__ */ new Set(["__references__", "__relationships__", "__semanticId__"]);
+function isPersistableAttribute(specNodeId, key) {
+  if (!ALWAYS_INTERNAL_ATTRIBUTE_KEYS.has(key))
+    return !0;
+  if (!specNodeId)
+    return !1;
+  const nodeType = getNodeType(specNodeId);
+  return nodeType ? nodeType.requiredAttributes.includes(key) || nodeType.optionalAttributes.includes(key) : !1;
+}
 const isTelemetryEnabled = !1;
 class Model {
   rootPath;
@@ -242,16 +251,10 @@ class Model {
       }
       elementsByType.get(typeKey).elements.push(element);
     }
-    const INTERNAL_FIELDS = /* @__PURE__ */ new Set([
-      "__references__",
-      "__relationships__",
-      "source",
-      "x-source-reference"
-    ]);
     for (const [, { stem, elements }] of elementsByType) {
       const filename = `${stem}.yaml`, filePath = `${layerPath}/${filename}`, yamlData = {};
       for (const element of elements) {
-        const json = element.toJSON(), cleanAttrs = json.attributes ? Object.fromEntries(Object.entries(json.attributes).filter(([k]) => !INTERNAL_FIELDS.has(k))) : void 0, key = element.path || element.id;
+        const json = element.toJSON(), cleanAttrs = json.attributes ? Object.fromEntries(Object.entries(json.attributes).filter(([k]) => isPersistableAttribute(json.spec_node_id, k))) : void 0, key = element.path || element.id;
         yamlData[key] = {
           id: json.id,
           path: json.path,

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 { 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 = `${this.rootPath}/documentation-robotics/model/manifest.yaml`;\n\n    // Convert to YAML format\n    const yamlData: any = {\n      version: this.manifest.version,\n      schema: \"documentation-robotics-v1\",\n      cli_version: getCliVersion(),\n      spec_version: this.manifest.specVersion,\n      created: this.manifest.created,\n      updated: this.manifest.modified,\n      project: {\n        name: this.manifest.name,\n        description: this.manifest.description,\n        version: this.manifest.version,\n      },\n      documentation: \".dr/README.md\",\n      layers: {},\n    };\n\n    // Generate layer structure from current model state\n    for (let i = 0; i < CANONICAL_LAYER_NAMES.length; i++) {\n      const layerName = CANONICAL_LAYER_NAMES[i];\n      const layer = this.layers.get(layerName);\n      const orderNum = String(i + 1).padStart(2, \"0\");\n\n      yamlData.layers[layerName] = {\n        order: i + 1,\n        name: layerName.charAt(0).toUpperCase() + layerName.slice(1).replace(\"-\", \" \"),\n        path: `documentation-robotics/model/${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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+  "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/**\n * Graph-internal bookkeeping keys that `layer.ts`'s node<->Element conversion stuffs into the\n * same flat `attributes`/`properties` bag the underlying graph structure uses for everything\n * (it has no separate channel for them) \u2014 `__references__`/`__relationships__`/`__semanticId__`\n * mirror `element.references`/`element.relationships`/`element.semanticId`, which are real,\n * separately-typed fields on `Element` and get serialized to their own place (references\n * inline, relationships to relationships.yaml, semanticId isn't persisted at all \u2014 it only\n * exists to resolve legacy-format elements during a single load). These must never reach the\n * persisted YAML's `attributes` object.\n *\n * Double-underscore-prefixed specifically so a schema author would have to go out of their way\n * to collide with one \u2014 confirmed zero of the 191 node schemas declare an attribute with any of\n * these names. Contrast with the *type-blind* set this replaced, which also unconditionally\n * stripped plain `\"source\"`/`\"x-source-reference\"` \u2014 both of which ARE legitimate, sometimes-\n * required domain attributes on 41 node schemas across 8 layers (e.g.\n * security.accesscondition.source), and neither of which is ever actually used as internal\n * bookkeeping anywhere in this codebase. That collision silently destroyed real data on every\n * save for any element of one of those 41 types, without ever failing validation (validation\n * runs on the in-memory element, before this stripping) \u2014 see CHANGELOG for the incident this\n * fixes.\n *\n * `__semanticId__` is listed here purely as defense-in-depth, not as the primary guard: it can\n * only ever reach `attributes` via `GraphModel.fromElement()` aliasing `properties` and\n * `attributes` to the same object, which `layer.ts`'s bookkeeping-key injection would then\n * mutate through. That aliasing is fixed at the source in graph-model.ts (`properties` is now\n * always an independent copy), so `__semanticId__` should never actually arrive here \u2014 but\n * listing it means a regression of that aliasing fix fails safe instead of silently reopening\n * the same leak `__semanticId__` briefly caused.\n */\nconst ALWAYS_INTERNAL_ATTRIBUTE_KEYS = new Set([\"__references__\", \"__relationships__\", \"__semanticId__\"]);\n\n/**\n * Whether `key` should survive persistence in `specNodeId`'s `attributes`.\n *\n * Only ever strips the two confirmed-always-internal keys above, and even then only when the\n * node type's OWN schema doesn't declare that name as a real attribute \u2014 so if some future\n * schema ever legitimately needs an attribute literally called `__references__` (unlikely, but\n * the whole point of this function is to not have to trust \"unlikely\" again), it still survives.\n * Nothing else is ever stripped: the class of bug this fixes was a hardcoded, type-blind\n * reserved-word blocklist making that same \"trust the list, not the schema\" mistake for\n * `source`/`x-source-reference`. Consulting the schema instead of a fixed string list is what\n * keeps this from silently recurring for some other attribute name in the future.\n */\nfunction isPersistableAttribute(specNodeId: string | undefined, key: string): boolean {\n  if (!ALWAYS_INTERNAL_ATTRIBUTE_KEYS.has(key)) return true;\n  if (!specNodeId) return false;\n  const nodeType = getNodeType(specNodeId as SpecNodeId);\n  if (!nodeType) return false;\n  return nodeType.requiredAttributes.includes(key) || nodeType.optionalAttributes.includes(key);\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: ${err instanceof Error ? err.message : String(err)}`\n        );\n      }\n    }\n\n    // Group elements by type, computing the snake_case file stem from the spec node title\n    const elementsByType = new Map<string, { stem: string; elements: Element[] }>();\n    for (const element of layer.elements.values()) {\n      const typeKey = element.type;\n      if (!elementsByType.has(typeKey)) {\n        const stem = typeToSnakeStem(element.spec_node_id, element.type);\n        elementsByType.set(typeKey, { stem, elements: [] });\n      }\n      elementsByType.get(typeKey)!.elements.push(element);\n    }\n\n    // Write each type to its own YAML file\n    for (const [, { stem, elements }] of elementsByType) {\n      const filename = `${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 \u2014 see\n        // isPersistableAttribute's own doc for why this checks the schema rather than a\n        // hardcoded name list.\n        const cleanAttrs = json.attributes\n          ? Object.fromEntries(\n              Object.entries(json.attributes).filter(([k]) =>\n                isPersistableAttribute(json.spec_node_id, k)\n              )\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 = `${this.rootPath}/documentation-robotics/model/manifest.yaml`;\n\n    // Convert to YAML format\n    const yamlData: any = {\n      version: this.manifest.version,\n      schema: \"documentation-robotics-v1\",\n      cli_version: getCliVersion(),\n      spec_version: this.manifest.specVersion,\n      created: this.manifest.created,\n      updated: this.manifest.modified,\n      project: {\n        name: this.manifest.name,\n        description: this.manifest.description,\n        version: this.manifest.version,\n      },\n      documentation: \".dr/README.md\",\n      layers: {},\n    };\n\n    // Generate layer structure from current model state\n    for (let i = 0; i < CANONICAL_LAYER_NAMES.length; i++) {\n      const layerName = CANONICAL_LAYER_NAMES[i];\n      const layer = this.layers.get(layerName);\n      const orderNum = String(i + 1).padStart(2, \"0\");\n\n      yamlData.layers[layerName] = {\n        order: i + 1,\n        name: layerName.charAt(0).toUpperCase() + layerName.slice(1).replace(\"-\", \" \"),\n        path: `documentation-robotics/model/${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     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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 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   "names": ["path", "fs", "layerId", "manifestPath"]
 }

package/dist/core/reference-registry.js

@@ -1,9 +1,15 @@
 import Graph from "graphology";
+import { looksLikeElementReference } from "../utils/element-reference-shape.js";
 class ReferenceRegistry {
   references;
   targetIndex;
   typeIndex;
-  // Known reference property names from Python CLI
+  // Known reference property names from Python CLI. NOTE: matching one of these names (or the
+  // *Ref/*Reference naming convention scanNestedReferences uses) is necessary but not
+  // sufficient — the attribute's VALUE also has to look like an element id
+  // (looksLikeElementReference) before we register it as a reference. Name alone isn't
+  // reliable: e.g. api.link.operationRef is a schema-declared OpenAPI URL fragment, not a DR
+  // element reference, and matches "*Ref" purely by naming coincidence.
   static KNOWN_REF_PROPERTIES = /* @__PURE__ */ new Set([
     "realizes",
     "realizedBy",
@@ -98,14 +104,14 @@ class ReferenceRegistry {
         for (const [propName, propValue] of Object.entries(element.attributes))
           if (ReferenceRegistry.KNOWN_REF_PROPERTIES.has(propName)) {
             if (typeof propValue == "string")
-              this.addReference({
+              looksLikeElementReference(propValue) && this.addReference({
                 source: elementId,
                 target: propValue,
                 type: propName
               });
             else if (Array.isArray(propValue))
               for (const target of propValue)
-                typeof target == "string" && this.addReference({
+                typeof target == "string" && looksLikeElementReference(target) && this.addReference({
                   source: elementId,
                   target,
                   type: propName
@@ -137,7 +143,7 @@ class ReferenceRegistry {
       if (!(!path && ReferenceRegistry.KNOWN_REF_PROPERTIES.has(key)))
         if (key.endsWith("Ref") || key.endsWith("Reference")) {
           if (typeof value == "string")
-            references.push({
+            looksLikeElementReference(value) && references.push({
               source: sourceId,
               target: value,
               type: key,
@@ -145,7 +151,7 @@ class ReferenceRegistry {
             });
           else if (Array.isArray(value))
             for (const target of value)
-              typeof target == "string" && references.push({
+              typeof target == "string" && looksLikeElementReference(target) && references.push({
                 source: sourceId,
                 target,
                 type: key,

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/**\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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+  "sourcesContent": ["import Graph from \"graphology\";\nimport type { Reference, Element } from \"../types/index.js\";\nimport { looksLikeElementReference } from \"../utils/element-reference-shape.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. NOTE: matching one of these names (or the\n  // *Ref/*Reference naming convention scanNestedReferences uses) is necessary but not\n  // sufficient \u2014 the attribute's VALUE also has to look like an element id\n  // (looksLikeElementReference) before we register it as a reference. Name alone isn't\n  // reliable: e.g. api.link.operationRef is a schema-declared OpenAPI URL fragment, not a DR\n  // element reference, and matches \"*Ref\" purely by naming coincidence.\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            if (looksLikeElementReference(propValue)) {\n              this.addReference({\n                source: elementId,\n                target: propValue,\n                type: propName,\n              });\n            }\n          }\n          // Handle array of strings\n          else if (Array.isArray(propValue)) {\n            for (const target of propValue) {\n              if (typeof target === \"string\" && looksLikeElementReference(target)) {\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 ? 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