@documentation-robotics/cli 0.1.13 → 0.2.0

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/**\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          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 { getCodebasePath } from \"../utils/globals.js\";\nimport { getErrorMessage } from \"../utils/errors.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  codebaseRoot: string;\n  manifest: Manifest;\n  graph: GraphModel;\n  layers: Map<string, Layer>;\n  relationships: Relationships;\n  lazyLoad: boolean;\n  loadedLayerFilter?: string[];\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.codebaseRoot = options.codebaseRoot ?? 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.loadedLayerFilter = options.layers;\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      // Support both standard structure (rootPath/documentation-robotics/model) and non-standard (rootPath directly)\n      let 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 (err) {\n        // Only ignore ENOENT (directory not found) \u2014 re-throw permission/I/O errors\n        const isNotFoundError = (err as any)?.code === \"ENOENT\";\n        if (!isNotFoundError) {\n          throw err;\n        }\n        // Standard structure doesn't exist, try non-standard structure (rootPath directly)\n        try {\n          const entries = await fs.readdir(this.rootPath, { 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 = `${this.rootPath}/${layerDir.name}`;\n          }\n        } catch (err) {\n          // Only ignore ENOENT (directory not found) \u2014 re-throw permission/I/O errors\n          const isNotFoundError = (err as any)?.code === \"ENOENT\";\n          if (!isNotFoundError) {\n            throw err;\n          }\n          // Neither structure found\n        }\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 ${name} not found`);\n    }\n\n    const fs = await import(\"fs/promises\");\n    const yaml = await import(\"yaml\");\n\n    let layerPath: string | null = null;\n\n    // Discover by scanning directory (support both standard and non-standard structures)\n    const modelDir = `${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 (err) {\n      // Only ignore ENOENT (directory not found) \u2014 re-throw permission/I/O errors\n      const isNotFoundError = (err as any)?.code === \"ENOENT\";\n      if (!isNotFoundError) {\n        throw err;\n      }\n      // Standard structure doesn't exist, try non-standard structure (rootPath directly)\n      try {\n        const entries = await fs.readdir(this.rootPath, { 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 = `${this.rootPath}/${layerDir.name}`;\n        }\n      } catch (err) {\n        // Only ignore ENOENT (directory not found) \u2014 re-throw permission/I/O errors\n        const isNotFoundError = (err as any)?.code === \"ENOENT\";\n        if (!isNotFoundError) {\n          throw err;\n        }\n        // Neither structure found\n      }\n    }\n\n    // If still not found, create using default format\n    if (!layerPath) {\n      // Find the order number for this layer\n      // Handle layer names with or without numeric prefix (e.g., \"motivation\" or \"01-motivation\")\n      const layerNameWithoutPrefix = name.replace(/^\\d{2}-/, \"\");\n      const 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}_${layerName}/`,\n        enabled: true,\n        ...(layer && { elements: this.getLayerElementCounts(layer) }),\n      };\n    }\n\n    if (this.manifest.codebase_path) {\n      yamlData.codebase_path = this.manifest.codebase_path;\n    }\n\n    if (this.manifest.changeset_history && this.manifest.changeset_history.length > 0) {\n      yamlData.changeset_history = this.manifest.changeset_history;\n    }\n\n    if (this.manifest.models && Object.keys(this.manifest.models).length > 0) {\n      yamlData.models = this.manifest.models;\n    }\n\n    await ensureDir(`${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    // Treat null (from comment-only files) as an empty array\n    if (data === null) {\n      data = [];\n    }\n\n    if (!Array.isArray(data)) {\n      const typeLabel = 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   * Auto-resolve codebaseRoot from farm manifest if inside a farm\n   *\n   * @param modelRoot - The model's project root (documentation_robotics parent)\n   * @returns Resolved codebase root path, or null if not in farm or resolution fails\n   */\n  private static async resolveFarmCodebaseRoot(modelRoot: string): Promise<string | null> {\n    const { findFarmRoot } = await import(\"../utils/project-paths.js\");\n    const { FarmManifest } = await import(\"./farm-manifest.js\");\n\n    // Find farm root (may return null if not in a farm)\n    const farmRoot = await findFarmRoot(modelRoot);\n    if (!farmRoot) {\n      return null;\n    }\n\n    // Load farm manifest\n    const farmYamlPath = path.join(farmRoot, \"farm.yaml\");\n    let manifest: any;\n    try {\n      manifest = await FarmManifest.load(farmYamlPath);\n    } catch (error) {\n      // Re-throw meaningful errors (YAML parse, permission errors, etc.)\n      // Only return null if the farm setup is genuinely not present\n      const errorMsg = getErrorMessage(error);\n      if (errorMsg.includes(\"ENOENT\") || errorMsg.includes(\"not found\")) {\n        return null; // Farm not found - expected case, not an error\n      }\n      throw new Error(`Failed to load farm manifest at ${farmYamlPath}: ${errorMsg}`);\n    }\n\n    // Find the model folder name relative to farm root\n    const modelName = path.basename(modelRoot);\n\n    // Look for a project where model matches our model's basename\n    for (const project of manifest.getAllProjects()) {\n      if (path.basename(project.model) === modelName) {\n        // Found matching project, resolve codebase path\n        const codebaseFullPath = path.resolve(farmRoot, project.source);\n        return codebaseFullPath;\n      }\n    }\n\n    return null; // No matching project found in farm - not an error\n  }\n\n  /**\n   * Walk upward from startPath looking for documentation-robotics/model/manifest.yaml,\n   * stopping at the nearest .git directory (repo boundary) so this can never cross into\n   * an unrelated parent project or a sibling farm/detached model directory.\n   *\n   * @param startPath - Directory to start the walk from\n   * @returns Manifest path if found within the repo boundary, or null\n   */\n  private static async findManifestUpwardBounded(startPath: string): Promise<string | null> {\n    let currentPath = startPath;\n\n    while (true) {\n      const candidateManifestPath = path.join(currentPath, \"documentation-robotics\", \"model\", \"manifest.yaml\");\n      try {\n        await fs.access(candidateManifestPath);\n        return candidateManifestPath;\n      } catch {\n        // Not found at this level, keep looking\n      }\n\n      // Stop once we've checked the repo root (marked by .git) - never walk past it\n      try {\n        await fs.access(path.join(currentPath, \".git\"));\n        return null;\n      } catch {\n        // Not a repo boundary, continue upward\n      }\n\n      const parentPath = path.dirname(currentPath);\n      if (parentPath === currentPath) {\n        return null; // Reached filesystem root\n      }\n      currentPath = parentPath;\n    }\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    // Highest priority: explicit startPath parameter (used in concurrent contexts to avoid env var mutations)\n    if (startPath) {\n      const resolvedPath = path.resolve(startPath);\n      let manifestPath: string;\n\n      if (resolvedPath.endsWith(\"manifest.yaml\")) {\n        manifestPath = resolvedPath;\n      } else if (resolvedPath.endsWith(\"model\")) {\n        manifestPath = path.join(resolvedPath, \"manifest.yaml\");\n      } else {\n        manifestPath = path.join(resolvedPath, \"documentation-robotics\", \"model\", \"manifest.yaml\");\n      }\n\n      try {\n        await fs.access(manifestPath);\n\n        // Determine projectRoot: flexible approach for both standard and non-standard structures\n        let projectRoot: string;\n        const manifestParentDir = path.dirname(manifestPath);\n\n        // First, try assuming the standard structure (manifest 3 levels deep)\n        const standardProjectRoot = path.dirname(path.dirname(path.dirname(manifestPath)));\n        const standardDocRobotsPath = path.join(standardProjectRoot, \"documentation-robotics\", \"model\");\n\n        try {\n          await fs.access(standardDocRobotsPath);\n          projectRoot = standardProjectRoot;\n        } catch (err) {\n          // Only ignore ENOENT (path not found) \u2014 re-throw permission/I/O errors\n          const isNotFoundError = (err as any)?.code === \"ENOENT\";\n          if (!isNotFoundError) {\n            throw err;\n          }\n          // Not in standard structure, use manifest's parent directory as project root\n          projectRoot = manifestParentDir;\n        }\n\n        return { projectRoot, manifestPath: path.normalize(manifestPath) };\n      } catch (err) {\n        // Only wrap ENOENT errors as \"not found\" \u2014 re-throw permission/I/O errors\n        const isNotFoundError = (err as any)?.code === \"ENOENT\";\n        if (!isNotFoundError) {\n          throw err;\n        }\n\n        // startPath itself doesn't directly contain the manifest (e.g. it's a\n        // subdirectory of the repo, like cli/ within the repo root). Fall back to a\n        // bounded upward walk stopping at the nearest .git boundary. This never crosses\n        // into a sibling farm/detached model directory since those are siblings of the\n        // codebase, not ancestors, so they can't be reached by walking upward.\n        const fallbackManifestPath = await Model.findManifestUpwardBounded(resolvedPath);\n        if (fallbackManifestPath) {\n          const fallbackProjectRoot = path.dirname(path.dirname(path.dirname(fallbackManifestPath)));\n          return { projectRoot: fallbackProjectRoot, manifestPath: path.normalize(fallbackManifestPath) };\n        }\n\n        throw new Error(`Model not found at ${startPath}`);\n      }\n    }\n\n    // Secondary priority: optional override via env var\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\n        // Determine projectRoot: flexible approach for both standard and non-standard structures\n        let projectRoot: string;\n        const manifestParentDir = path.dirname(manifestPath);\n\n        // First, try assuming the standard structure (manifest 3 levels deep)\n        const standardProjectRoot = path.dirname(path.dirname(path.dirname(manifestPath)));\n        const standardDocRobotsPath = path.join(standardProjectRoot, \"documentation-robotics\", \"model\");\n\n        try {\n          await fs.access(standardDocRobotsPath);\n          projectRoot = standardProjectRoot;\n        } catch (err) {\n          // Only ignore ENOENT (path not found) \u2014 re-throw permission/I/O errors\n          const isNotFoundError = (err as any)?.code === \"ENOENT\";\n          if (!isNotFoundError) {\n            throw err;\n          }\n          // Not in standard structure, use manifest's parent directory as project root\n          projectRoot = manifestParentDir;\n        }\n\n        return { projectRoot, manifestPath: path.normalize(manifestPath) };\n      } catch (err) {\n        // Only wrap ENOENT errors as \"not found\" \u2014 re-throw permission/I/O errors\n        const isNotFoundError = (err as any)?.code === \"ENOENT\";\n        if (!isNotFoundError) {\n          throw err;\n        }\n        throw new Error(`Model not found at DR_MODEL_PATH: ${process.env.DR_MODEL_PATH}`);\n      }\n    }\n\n    // Fallback: use findProjectRoot to locate documentation_robotics/ folder\n    const searchPath = process.cwd();\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   * Validate that the manifest's models field is a plain object.\n   *\n   * @param models - The raw value from manifest YAML\n   * @returns Validation result with valid flag and error message if invalid\n   */\n  static validateModelsField(models: unknown): { valid: boolean; error?: string } {\n    // Check if models is null or undefined (this shouldn't happen since we check before calling)\n    if (models === null || models === undefined) {\n      return { valid: true };\n    }\n\n    // Check if models is a plain object (not an array, string, or other primitive)\n    if (typeof models !== \"object\" || Array.isArray(models)) {\n      return {\n        valid: false,\n        error:\n          `Invalid manifest 'models' field: expected an object with model names as keys ` +\n          `(e.g., { \"auth-service\": { } }), but got ${Array.isArray(models) ? \"an array\" : `a ${typeof models}`}. ` +\n          `This often happens when YAML syntax is incorrect, like writing 'models: auth-service' ` +\n          `instead of 'models: { auth-service: {} }' or 'models:\\\\n  auth-service: {}'.`,\n      };\n    }\n\n    // Validate that it's a plain object (not a class instance)\n    if (Object.getPrototypeOf(models) !== Object.prototype) {\n      return {\n        valid: false,\n        error:\n          `Invalid manifest 'models' field: expected a plain object, but got an instance of ${\n            (models as any).constructor?.name || \"unknown\"\n          }. ` +\n          `Please ensure 'models' is a simple YAML object mapping model names to declarations.`,\n      };\n    }\n\n    return { valid: true };\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        cliVersion: manifestYaml.cli_version,\n        specVersion: manifestYaml.spec_version || \"0.6.0\",\n        created: manifestYaml.created || new Date().toISOString(),\n        modified: manifestYaml.updated || new Date().toISOString(),\n      };\n\n      // Load external model declarations if present\n      if (manifestYaml.models) {\n        const modelsValidation = Model.validateModelsField(manifestYaml.models);\n        if (!modelsValidation.valid) {\n          throw new Error(modelsValidation.error);\n        }\n        manifestData.models = manifestYaml.models;\n      }\n\n      // Load codebase_path if present\n      if (manifestYaml.codebase_path) {\n        manifestData.codebase_path = manifestYaml.codebase_path;\n      }\n\n      const manifest = new Manifest(manifestData);\n\n      // Resolve codebaseRoot with priority: options > CLI flag > manifest > farm > default\n      let codebaseRoot = projectRoot;\n      if (options.codebaseRoot) {\n        codebaseRoot = options.codebaseRoot;\n      } else {\n        const globalCodebasePath = getCodebasePath();\n        if (globalCodebasePath) {\n          codebaseRoot = path.resolve(globalCodebasePath);\n        } else if (manifest.codebase_path) {\n          codebaseRoot = path.resolve(projectRoot, manifest.codebase_path);\n        } else {\n          // Try to auto-resolve from farm manifest if inside a farm\n          const farmCodebaseRoot = await Model.resolveFarmCodebaseRoot(projectRoot);\n          if (farmCodebaseRoot) {\n            codebaseRoot = farmCodebaseRoot;\n          }\n        }\n      }\n\n      const model = new Model(projectRoot, manifest, { ...options, codebaseRoot });\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    const yaml = await import(\"yaml\");\n\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}_${layerName}`);\n    }\n\n    const manifest = new Manifest(manifestData);\n\n    // Resolve codebaseRoot with priority: options > CLI flag > manifest > default\n    let codebaseRoot = rootPath;\n    if (options.codebaseRoot) {\n      codebaseRoot = options.codebaseRoot;\n    } else {\n      const globalCodebasePath = getCodebasePath();\n      if (globalCodebasePath) {\n        codebaseRoot = path.resolve(globalCodebasePath);\n      } else if (manifest.codebase_path) {\n        codebaseRoot = path.resolve(rootPath, manifest.codebase_path);\n      }\n    }\n\n    const model = new Model(rootPath, manifest, { ...options, codebaseRoot });\n\n    await model.saveManifest();\n\n    // Initialize relationships.yaml with empty array\n    const relationshipsPath = `${rootPath}/documentation-robotics/model/relationships.yaml`;\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([]);\n    await writeFile(relationshipsPath, yamlContent);\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 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+  "names": ["path", "fs", "err", "layerId", "manifestPath", "projectRoot"]
 }

package/dist/core/virtual-projection.js

@@ -208,6 +208,7 @@ class VirtualProjectionEngine {
       manifest: baseModel.manifest,
       layers: projectedLayers,
       relationships: baseModel.relationships,
+      loadedLayerFilter: baseModel.loadedLayerFilter,
       isProjection: !0
     };
   }

package/dist/core/virtual-projection.js.map

@@ -1,7 +1,7 @@
 {
   "version": 3,
   "sources": ["../../src/core/virtual-projection.ts"],
-  "sourcesContent": ["/**\n * VirtualProjectionEngine - Computes merged model views by applying staged changes.\n *\n * Creates virtual (temporary) projections of the base model with staged changes applied,\n * without modifying or persisting the base model. Enables safe preview and validation\n * of changes before commit. Includes projection caching with TTL-based expiration.\n *\n * Staging changes are applied in sequence order to compute accurate merged views.\n */\n\nimport type { Model } from \"./model.js\";\nimport type { Layer } from \"./layer.js\";\nimport type { Element } from \"./element.js\";\nimport type { SourceReference, ElementMetadata } from \"../types/index.js\";\nimport type { Manifest } from \"./manifest.js\";\nimport type { Relationships } from \"./relationships.js\";\nimport { Layer as LayerClass } from \"./layer.js\";\nimport { Element as ElementClass } from \"./element.js\";\nimport type { StagedChange, Change } from \"./changeset.js\";\nimport { StagedChangesetStorage } from \"./staged-changeset-storage.js\";\n\n/**\n * Projected model with isProjection flag to prevent accidental saves.\n * This marker interface ensures that projected models are recognized as temporary\n * and cannot be persisted to disk without explicit commit of the underlying changeset.\n */\nexport interface ProjectedModel {\n  manifest: Manifest;\n  layers: Map<string, Layer>;\n  relationships: Relationships;\n  isProjection: true; // Always true; marks this as a temporary virtual projection\n}\n\n/**\n * Model diff categorizing changeset changes by type.\n * Separates staged changes into additions (new elements), modifications (updated attributes),\n * and deletions (removed elements). Used for preview and diff display operations.\n */\nexport interface ModelDiff {\n  additions: Array<{\n    elementId: string;\n    layerName: string;\n    data: Record<string, unknown>; // Complete element state (from change.after)\n  }>;\n  modifications: Array<{\n    elementId: string;\n    layerName: string;\n    before: Record<string, unknown>; // Previous state (from change.before)\n    after: Record<string, unknown>; // New state (from change.after)\n  }>;\n  deletions: Array<{\n    elementId: string;\n    layerName: string;\n    data: Record<string, unknown>; // Element state before deletion (from change.before)\n  }>;\n}\n\n/**\n * Single cached layer projection.\n * Stores the computed projected layer and timestamp for cache expiration.\n */\ninterface CacheEntry {\n  layer: Layer;\n  computedAt: string; // ISO timestamp for age calculation\n}\n\n/**\n * Cache hit/miss metrics for monitoring cache performance.\n * Tracks successful cache hits, misses, and invalidations per changeset.\n */\ninterface CacheMetrics {\n  hits: number; // Number of successful cache hits\n  misses: number; // Number of cache misses (required computation)\n  invalidations: number; // Number of invalidation operations\n  lastInvalidation?: string; // ISO timestamp of last invalidation\n}\n\n/**\n * Projection cache for storing computed layer projections.\n * Uses TTL-based expiration to prevent stale projections.\n * Entries are lazily removed when expired on access or during periodic cleanup.\n */\ninterface ProjectionCache {\n  cache: Map<string, CacheEntry>; // Key format: `${changesetId}:${layerName}`\n  metrics: Map<string, CacheMetrics>; // Cache metrics keyed by changesetId\n  maxAge: number; // Cache entry TTL in milliseconds (5 minutes default)\n  lastCleanup: number; // Timestamp of last cleanup to limit cleanup frequency\n}\n\n/**\n * VirtualProjectionEngine - Computes merged model views without persisting.\n * Applies staged changes to a cloned base model to compute projections.\n * Uses caching with TTL-based expiration to optimize repeated projections.\n */\nexport class VirtualProjectionEngine {\n  private stagingAreaManager: StagedChangesetStorage;\n  private projectionCache: ProjectionCache;\n\n  /**\n   * Create a new projection engine.\n   *\n   * @param rootPath - Root path to the model (used by StagedChangesetStorage)\n   */\n  constructor(rootPath: string) {\n    this.stagingAreaManager = new StagedChangesetStorage(rootPath);\n    this.projectionCache = {\n      cache: new Map(),\n      metrics: new Map(),\n      maxAge: 5 * 60 * 1000, // 5-minute TTL for cached projections\n      lastCleanup: Date.now(),\n    };\n  }\n\n  /**\n   * Project a single element by applying staged changes to it.\n   * Merges the element's base state with staged changes to compute its projected state.\n   *\n   * @param baseModel - The base model to project from\n   * @param changesetId - ID of the changeset containing staged changes\n   * @param elementId - ID of the element to project\n   * @returns Projected element with staged changes applied, or null if element is deleted\n   * @throws Error if changeset not found\n   *\n   * @remarks\n   * If multiple changes exist for the element, the last change determines final state.\n   * For 'delete' operations, returns null.\n   * For 'add' operations without base element, creates new element from staged data.\n   * For 'update' operations, merges staged changes with base element attributes.\n   */\n  async projectElement(\n    baseModel: Model,\n    changesetId: string,\n    elementId: string\n  ): Promise<Element | null> {\n    const changeset = await this.stagingAreaManager.load(changesetId);\n    if (!changeset) {\n      throw new Error(`Changeset '${changesetId}' not found`);\n    }\n\n    // Find all changes for this element across all layers\n    const elementChanges = changeset.changes.filter(\n      (c: Change) => c.elementId === elementId\n    ) as StagedChange[];\n\n    if (elementChanges.length === 0) {\n      // No changes, return base element if it exists\n      return baseModel.getElementById(elementId) || null;\n    }\n\n    // Get the last change to determine the element's final state\n    const lastChange = elementChanges[elementChanges.length - 1];\n\n    if (lastChange.type === \"delete\") {\n      return null;\n    }\n\n    // For add or update, construct the projected element\n    const baseElement = baseModel.getElementById(elementId);\n    const projectedData = lastChange.after || {};\n\n    if (baseElement) {\n      // Create a new element with projected data merged with base\n      const projectedAttributes =\n        typeof projectedData.attributes === \"object\" ? projectedData.attributes : {};\n\n      const mergedData = {\n        id: baseElement.id,\n        path: baseElement.path,\n        spec_node_id: baseElement.spec_node_id,\n        type: typeof projectedData.type === \"string\" ? projectedData.type : baseElement.type,\n        layer_id: baseElement.layer_id,\n        name: typeof projectedData.name === \"string\" ? projectedData.name : baseElement.name,\n        description:\n          typeof projectedData.description === \"string\"\n            ? projectedData.description\n            : baseElement.description,\n        attributes: {\n          ...baseElement.attributes,\n          ...projectedAttributes,\n        },\n        references: Array.isArray(projectedData.references)\n          ? projectedData.references\n          : baseElement.references,\n        relationships: Array.isArray(projectedData.relationships)\n          ? projectedData.relationships\n          : baseElement.relationships,\n        source_reference: baseElement.source_reference,\n        metadata: baseElement.metadata,\n      };\n\n      return new ElementClass(mergedData);\n    } else if (lastChange.type === \"add\") {\n      // New element being added\n      return new ElementClass({\n        id: (lastChange.after?.id as string) || elementId,\n        path: (lastChange.after?.path as string) || elementId,\n        spec_node_id: (lastChange.after?.spec_node_id as string) || \"\",\n        type: (projectedData.type as string) || \"unknown\",\n        layer_id: lastChange.layerName,\n        name: (projectedData.name as string) || elementId,\n        description: (projectedData.description as string) || \"\",\n        attributes: (typeof projectedData.attributes === \"object\"\n          ? projectedData.attributes\n          : {}) as Record<string, unknown>,\n        references: Array.isArray(projectedData.references) ? projectedData.references : [],\n        relationships: Array.isArray(projectedData.relationships)\n          ? projectedData.relationships\n          : [],\n        source_reference: projectedData.source_reference as SourceReference | undefined,\n        metadata: projectedData.metadata as ElementMetadata | undefined,\n        layer: lastChange.layerName,\n      });\n    }\n\n    return null;\n  }\n\n  /**\n   * Project a layer by applying staged changes to a clone of the base layer.\n   * Checks cache first; computes and caches result if not found or expired.\n   *\n   * @param baseModel - The base model to project from\n   * @param changesetId - ID of the changeset containing staged changes\n   * @param layerName - Name of the layer to project\n   * @returns Projected layer with staged changes applied\n   * @throws Error if changeset or base layer not found\n   *\n   * @remarks\n   * Computation process:\n   * 1. Check projection cache (returns if found and not expired)\n   * 2. Clone base layer to avoid mutations\n   * 3. Load staged changes filtered to this layer\n   * 4. Apply changes in sequence number order (add/update/delete)\n   * 5. Cache result with timestamp for TTL tracking\n   * 6. Trigger periodic cache cleanup\n   */\n  async projectLayer(baseModel: Model, changesetId: string, layerName: string): Promise<Layer> {\n    // Check cache first\n    const cacheKey = `${changesetId}:${layerName}`;\n    const cached = this.projectionCache.cache.get(cacheKey);\n\n    if (cached) {\n      const age = Date.now() - new Date(cached.computedAt).getTime();\n      if (age < this.projectionCache.maxAge) {\n        // Record cache hit\n        this.recordCacheHit(changesetId);\n        return cached.layer;\n      } else {\n        // Invalidate expired entry\n        this.projectionCache.cache.delete(cacheKey);\n      }\n    }\n\n    // Record cache miss\n    this.recordCacheMiss(changesetId);\n\n    // Load the committed base layer \u2014 must use getBaseLayer() (not getLayer()) to avoid\n    // infinite recursion: getLayer() calls projectLayer(), which would call getLayer() again.\n    const baseLayer = await baseModel.getBaseLayer(layerName);\n    const projectedLayer = baseLayer\n      ? this.cloneLayer(baseLayer)\n      : new LayerClass(layerName);\n\n    // Load staged changes for this layer\n    const changeset = await this.stagingAreaManager.load(changesetId);\n    if (!changeset) {\n      throw new Error(`Changeset '${changesetId}' not found`);\n    }\n\n    const layerChanges = (changeset.changes as StagedChange[])\n      .filter((c: StagedChange) => c.layerName === layerName)\n      .sort((a: StagedChange, b: StagedChange) => a.sequenceNumber - b.sequenceNumber);\n\n    // Apply changes in sequence order\n    for (const change of layerChanges) {\n      switch (change.type) {\n        case \"add\":\n          if (change.after) {\n            const newElement = new ElementClass({\n              id: (change.after.id as string) || change.elementId,\n              path: (change.after.path as string) || change.elementId,\n              spec_node_id: (change.after.spec_node_id as string) || \"\",\n              type: (change.after.type as string) || \"unknown\",\n              layer_id: layerName,\n              name: (change.after.name as string) || change.elementId,\n              description: (change.after.description as string) || \"\",\n              attributes: (typeof change.after.attributes === \"object\"\n                ? change.after.attributes\n                : {}) as Record<string, unknown>,\n              references: Array.isArray(change.after.references) ? change.after.references : [],\n              relationships: Array.isArray(change.after.relationships)\n                ? change.after.relationships\n                : [],\n              source_reference: change.after.source_reference as SourceReference | undefined,\n              metadata: change.after.metadata as ElementMetadata | undefined,\n              layer: layerName,\n            });\n            projectedLayer.addElement(newElement);\n          }\n          break;\n\n        case \"update\":\n          if (change.after) {\n            // Get the existing element to preserve all state\n            const existing = projectedLayer.getElement(change.elementId);\n            if (existing) {\n              // Create updated element with merged attributes\n              const afterAttributes =\n                typeof change.after.attributes === \"object\" ? change.after.attributes : {};\n\n              const mergedAttributes: Record<string, unknown> = {\n                ...existing.attributes,\n                ...afterAttributes,\n              };\n\n              const updatedElement = new ElementClass({\n                id: existing.id,\n                path: existing.path,\n                spec_node_id: existing.spec_node_id,\n                layer_id: existing.layer_id,\n                type: typeof change.after.type === \"string\" ? change.after.type : existing.type,\n                name: typeof change.after.name === \"string\" ? change.after.name : existing.name,\n                description:\n                  typeof change.after.description === \"string\"\n                    ? change.after.description\n                    : existing.description,\n                attributes: mergedAttributes,\n                references: Array.isArray(change.after.references)\n                  ? change.after.references\n                  : existing.references,\n                relationships: Array.isArray(change.after.relationships)\n                  ? change.after.relationships\n                  : existing.relationships,\n                layer: layerName,\n                source_reference: existing.source_reference,\n                metadata: existing.metadata,\n              });\n\n              projectedLayer.updateElement(updatedElement);\n            }\n          }\n          break;\n\n        case \"delete\":\n          const existingForDelete = projectedLayer.getElement(change.elementId);\n          if (existingForDelete) {\n            projectedLayer.deleteElement(existingForDelete.path || existingForDelete.id);\n          }\n          break;\n\n        case \"relationship-add\":\n        case \"relationship-delete\":\n          // Relationship changes are handled at the model level (model.relationships),\n          // not the layer level. Skip here; no layer mutation needed.\n          break;\n      }\n    }\n\n    // Cache the result\n    const cacheEntry: CacheEntry = {\n      layer: projectedLayer,\n      computedAt: new Date().toISOString(),\n    };\n    this.projectionCache.cache.set(cacheKey, cacheEntry);\n\n    // Periodic cleanup of expired entries\n    this.cleanupExpiredCache();\n\n    return projectedLayer;\n  }\n\n  /**\n   * Project entire model by applying staged changes to all layers.\n   * Creates a complete projected model view that includes both changed and unchanged layers.\n   *\n   * @param baseModel - The base model to project from\n   * @param changesetId - ID of the changeset containing staged changes\n   * @returns ProjectedModel with isProjection=true flag (prevents accidental saves)\n   * @throws Error if changeset not found\n   *\n   * @remarks\n   * Projection includes:\n   * - All layers mentioned in changeset changes\n   * - All layers from base model (to have complete model state)\n   * - Base model's manifest (unchanged)\n   * Returned model has isProjection=true to prevent accidental persistence.\n   */\n  async projectModel(baseModel: Model, changesetId: string): Promise<ProjectedModel> {\n    const changeset = await this.stagingAreaManager.load(changesetId);\n    if (!changeset) {\n      throw new Error(`Changeset '${changesetId}' not found`);\n    }\n\n    const projectedLayers = new Map<string, Layer>();\n\n    // Project all layers mentioned in the changeset\n    const layerNames = new Set<string>();\n    for (const change of changeset.changes) {\n      layerNames.add(change.layerName);\n    }\n\n    // Also include all base layers to get complete model\n    for (const baseLayerName of baseModel.getLayerNames()) {\n      layerNames.add(baseLayerName);\n    }\n\n    // Project each layer\n    for (const layerName of layerNames) {\n      const projectedLayer = await this.projectLayer(baseModel, changesetId, layerName);\n      projectedLayers.set(layerName, projectedLayer);\n    }\n\n    // Create projected model with isProjection flag\n    const projectedModel: ProjectedModel = {\n      manifest: baseModel.manifest,\n      layers: projectedLayers,\n      relationships: baseModel.relationships,\n      isProjection: true,\n    };\n\n    return projectedModel;\n  }\n\n  /**\n   * Compute diff by categorizing changeset changes by type.\n   * Extracts the staged changes and organizes them into additions, modifications, and deletions.\n   *\n   * @param _baseModel - The base model (unused; included for interface compatibility)\n   * @param changesetId - ID of the changeset to compute diff for\n   * @returns ModelDiff with changes categorized by type\n   * @throws Error if changeset not found\n   *\n   * @remarks\n   * Diff is computed directly from changeset changes; does not perform deep comparison.\n   * Each change's before/after snapshots are included for detailed display.\n   */\n  async computeDiff(_baseModel: Model, changesetId: string): Promise<ModelDiff> {\n    const changeset = await this.stagingAreaManager.load(changesetId);\n    if (!changeset) {\n      throw new Error(`Changeset '${changesetId}' not found`);\n    }\n\n    const changes = changeset.changes as StagedChange[];\n\n    return {\n      additions: changes\n        .filter((c: StagedChange) => c.type === \"add\")\n        .map((c: StagedChange) => ({\n          elementId: c.elementId,\n          layerName: c.layerName,\n          data: c.after || {},\n        })),\n\n      modifications: changes\n        .filter((c: StagedChange) => c.type === \"update\")\n        .map((c: StagedChange) => ({\n          elementId: c.elementId,\n          layerName: c.layerName,\n          before: c.before || {},\n          after: c.after || {},\n        })),\n\n      deletions: changes\n        .filter((c: StagedChange) => c.type === \"delete\")\n        .map((c: StagedChange) => ({\n          elementId: c.elementId,\n          layerName: c.layerName,\n          data: c.before || {},\n        })),\n    };\n  }\n\n  /**\n   * Get affected layers for an element in a changeset.\n   * Returns all layers that have cached projections and contain changes for the element.\n   *\n   * @param changesetId - ID of the changeset\n   * @param elementId - ID of the element being unstaged\n   * @returns Set of affected layer names\n   *\n   * @remarks\n   * When unstaging an element, only the layers where that element was modified\n   * need cache invalidation. This enables granular invalidation instead of\n   * invalidating the entire changeset cache.\n   */\n  private async getAffectedLayers(changesetId: string, elementId: string): Promise<Set<string>> {\n    const affectedLayers = new Set<string>();\n\n    try {\n      const changeset = await this.stagingAreaManager.load(changesetId);\n      if (!changeset) {\n        return affectedLayers;\n      }\n\n      // Find all layers that have changes for this element\n      for (const change of changeset.changes) {\n        if (change.elementId === elementId) {\n          affectedLayers.add(change.layerName);\n        }\n      }\n    } catch {\n      // If changeset can't be loaded, return empty set (no invalidation needed)\n      // This handles the case where changeset is deleted or corrupted\n    }\n\n    return affectedLayers;\n  }\n\n  /**\n   * Record a cache hit for metrics tracking.\n   *\n   * @param changesetId - ID of the changeset\n   */\n  private recordCacheHit(changesetId: string): void {\n    const metrics = this.projectionCache.metrics.get(changesetId) || {\n      hits: 0,\n      misses: 0,\n      invalidations: 0,\n    };\n    metrics.hits++;\n    this.projectionCache.metrics.set(changesetId, metrics);\n  }\n\n  /**\n   * Record a cache miss for metrics tracking.\n   *\n   * @param changesetId - ID of the changeset\n   */\n  private recordCacheMiss(changesetId: string): void {\n    const metrics = this.projectionCache.metrics.get(changesetId) || {\n      hits: 0,\n      misses: 0,\n      invalidations: 0,\n    };\n    metrics.misses++;\n    this.projectionCache.metrics.set(changesetId, metrics);\n  }\n\n  /**\n   * Record a cache invalidation for metrics tracking.\n   *\n   * @param changesetId - ID of the changeset\n   */\n  private recordInvalidation(changesetId: string): void {\n    const metrics = this.projectionCache.metrics.get(changesetId) || {\n      hits: 0,\n      misses: 0,\n      invalidations: 0,\n    };\n    metrics.invalidations++;\n    metrics.lastInvalidation = new Date().toISOString();\n    this.projectionCache.metrics.set(changesetId, metrics);\n  }\n\n  /**\n   * Get cache metrics for a changeset (for monitoring and debugging).\n   *\n   * @param changesetId - ID of the changeset\n   * @returns Cache metrics or undefined if no metrics exist\n   */\n  getCacheMetrics(changesetId: string): CacheMetrics | undefined {\n    return this.projectionCache.metrics.get(changesetId);\n  }\n\n  /**\n   * Invalidate projection cache when changes are staged.\n   * Removes cached projections to ensure fresh computation next time.\n   *\n   * @param changesetId - ID of the changeset being modified\n   * @param layerName - Optional: specific layer to invalidate (all if omitted)\n   *\n   * @remarks\n   * If layerName is provided, only that layer's projection is invalidated.\n   * Otherwise, all projections for the changeset are invalidated.\n   */\n  invalidateOnStage(changesetId: string, layerName?: string): void {\n    if (layerName) {\n      // Invalidate specific layer projection\n      const cacheKey = `${changesetId}:${layerName}`;\n      this.projectionCache.cache.delete(cacheKey);\n      this.recordInvalidation(changesetId);\n    } else {\n      // Invalidate all projections for this changeset\n      for (const key of this.projectionCache.cache.keys()) {\n        if (key.startsWith(`${changesetId}:`)) {\n          this.projectionCache.cache.delete(key);\n        }\n      }\n      this.recordInvalidation(changesetId);\n    }\n  }\n\n  /**\n   * Invalidate projection cache when changes are unstaged.\n   * Uses layer-specific invalidation for the affected element's layers.\n   *\n   * @param changesetId - ID of the changeset being modified\n   * @param elementId - Optional: ID of element being unstaged (enables granular invalidation)\n   *\n   * @remarks\n   * If elementId is provided, only the layers containing that element are invalidated.\n   * This is more efficient than invalidating the entire changeset cache when\n   * unstaging elements from a multi-layer changeset.\n   * If elementId is omitted, invalidates all projections for the changeset.\n   */\n  async invalidateOnUnstage(changesetId: string, elementId?: string): Promise<void> {\n    if (elementId) {\n      // Layer-specific invalidation: only invalidate affected layers\n      const affectedLayers = await this.getAffectedLayers(changesetId, elementId);\n      for (const layerName of affectedLayers) {\n        const cacheKey = `${changesetId}:${layerName}`;\n        this.projectionCache.cache.delete(cacheKey);\n      }\n      if (affectedLayers.size > 0) {\n        this.recordInvalidation(changesetId);\n      }\n    } else {\n      // Full invalidation: clear all projections for this changeset\n      for (const key of this.projectionCache.cache.keys()) {\n        if (key.startsWith(`${changesetId}:`)) {\n          this.projectionCache.cache.delete(key);\n        }\n      }\n      this.recordInvalidation(changesetId);\n    }\n  }\n\n  /**\n   * Invalidate all projections for a changeset when it's discarded.\n   * Clears all cached projections for this changeset to free memory.\n   *\n   * @param changesetId - ID of the changeset being discarded\n   */\n  invalidateOnDiscard(changesetId: string): void {\n    for (const key of this.projectionCache.cache.keys()) {\n      if (key.startsWith(`${changesetId}:`)) {\n        this.projectionCache.cache.delete(key);\n      }\n    }\n  }\n\n  /**\n   * Clone a layer to create an independent copy.\n   * Shallow clones all elements and metadata to avoid mutations.\n   * Cloned layer is marked clean to prevent unintended saves.\n   *\n   * @param layer - The layer to clone\n   * @returns New layer with cloned elements and metadata\n   *\n   * @remarks\n   * Cloning strategy:\n   * 1. Create new Layer with same name\n   * 2. Clone each element: shallow copy attributes object and array references\n   * 3. Copy layer metadata if present\n   * 4. Mark cloned layer as clean to prevent automatic saves\n   * This ensures changes to projection don't affect base layer.\n   * Note: Shallow cloning is sufficient since attributes are read-only in projections.\n   */\n  private cloneLayer(layer: Layer): Layer {\n    const cloned = new LayerClass(layer.name);\n\n    // Clone all elements (shallow copy - read-only in projection)\n    for (const element of layer.listElements()) {\n      const elementClone = new ElementClass({\n        id: element.id,\n        path: element.path,\n        spec_node_id: element.spec_node_id,\n        type: element.type,\n        layer_id: element.layer_id,\n        name: element.name,\n        description: element.description,\n        attributes: { ...element.attributes },\n        references: [...(element.references || [])],\n        relationships: [...(element.relationships || [])],\n        layer: element.layer,\n        source_reference: element.source_reference,\n        metadata: element.metadata,\n      });\n      cloned.addElement(elementClone);\n    }\n\n    // Preserve layer metadata if present\n    if (layer.metadata) {\n      cloned.metadata = { ...layer.metadata };\n    }\n\n    // Mark as clean to prevent projection from being saved\n    cloned.markClean();\n    return cloned;\n  }\n\n  /**\n   * Clean up expired cache entries periodically (every 60 seconds).\n   * Removes entries that exceed the maxAge TTL.\n   * Runs at most once per minute to limit overhead.\n   *\n   * @remarks\n   * Cleanup is triggered after each projection computation.\n   * Early exit if last cleanup was less than 60 seconds ago.\n   * Entries are marked for deletion based on age calculation from computedAt timestamp.\n   */\n  private cleanupExpiredCache(): void {\n    const now = Date.now();\n\n    // Limit cleanup frequency to at most every 60 seconds\n    if (now - this.projectionCache.lastCleanup < 60 * 1000) {\n      return;\n    }\n\n    // Remove entries that have exceeded their TTL\n    for (const [key, entry] of this.projectionCache.cache.entries()) {\n      const age = now - new Date(entry.computedAt).getTime();\n      if (age >= this.projectionCache.maxAge) {\n        this.projectionCache.cache.delete(key);\n      }\n    }\n\n    this.projectionCache.lastCleanup = now;\n  }\n}\n"],
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+  "sourcesContent": ["/**\n * VirtualProjectionEngine - Computes merged model views by applying staged changes.\n *\n * Creates virtual (temporary) projections of the base model with staged changes applied,\n * without modifying or persisting the base model. Enables safe preview and validation\n * of changes before commit. Includes projection caching with TTL-based expiration.\n *\n * Staging changes are applied in sequence order to compute accurate merged views.\n */\n\nimport type { Model } from \"./model.js\";\nimport type { Layer } from \"./layer.js\";\nimport type { Element } from \"./element.js\";\nimport type { SourceReference, ElementMetadata } from \"../types/index.js\";\nimport type { Manifest } from \"./manifest.js\";\nimport type { Relationships } from \"./relationships.js\";\nimport { Layer as LayerClass } from \"./layer.js\";\nimport { Element as ElementClass } from \"./element.js\";\nimport type { StagedChange, Change } from \"./changeset.js\";\nimport { StagedChangesetStorage } from \"./staged-changeset-storage.js\";\n\n/**\n * Projected model with isProjection flag to prevent accidental saves.\n * This marker interface ensures that projected models are recognized as temporary\n * and cannot be persisted to disk without explicit commit of the underlying changeset.\n */\nexport interface ProjectedModel {\n  manifest: Manifest;\n  layers: Map<string, Layer>;\n  relationships: Relationships;\n  loadedLayerFilter?: string[];\n  isProjection: true; // Always true; marks this as a temporary virtual projection\n}\n\n/**\n * Model diff categorizing changeset changes by type.\n * Separates staged changes into additions (new elements), modifications (updated attributes),\n * and deletions (removed elements). Used for preview and diff display operations.\n */\nexport interface ModelDiff {\n  additions: Array<{\n    elementId: string;\n    layerName: string;\n    data: Record<string, unknown>; // Complete element state (from change.after)\n  }>;\n  modifications: Array<{\n    elementId: string;\n    layerName: string;\n    before: Record<string, unknown>; // Previous state (from change.before)\n    after: Record<string, unknown>; // New state (from change.after)\n  }>;\n  deletions: Array<{\n    elementId: string;\n    layerName: string;\n    data: Record<string, unknown>; // Element state before deletion (from change.before)\n  }>;\n}\n\n/**\n * Single cached layer projection.\n * Stores the computed projected layer and timestamp for cache expiration.\n */\ninterface CacheEntry {\n  layer: Layer;\n  computedAt: string; // ISO timestamp for age calculation\n}\n\n/**\n * Cache hit/miss metrics for monitoring cache performance.\n * Tracks successful cache hits, misses, and invalidations per changeset.\n */\ninterface CacheMetrics {\n  hits: number; // Number of successful cache hits\n  misses: number; // Number of cache misses (required computation)\n  invalidations: number; // Number of invalidation operations\n  lastInvalidation?: string; // ISO timestamp of last invalidation\n}\n\n/**\n * Projection cache for storing computed layer projections.\n * Uses TTL-based expiration to prevent stale projections.\n * Entries are lazily removed when expired on access or during periodic cleanup.\n */\ninterface ProjectionCache {\n  cache: Map<string, CacheEntry>; // Key format: `${changesetId}:${layerName}`\n  metrics: Map<string, CacheMetrics>; // Cache metrics keyed by changesetId\n  maxAge: number; // Cache entry TTL in milliseconds (5 minutes default)\n  lastCleanup: number; // Timestamp of last cleanup to limit cleanup frequency\n}\n\n/**\n * VirtualProjectionEngine - Computes merged model views without persisting.\n * Applies staged changes to a cloned base model to compute projections.\n * Uses caching with TTL-based expiration to optimize repeated projections.\n */\nexport class VirtualProjectionEngine {\n  private stagingAreaManager: StagedChangesetStorage;\n  private projectionCache: ProjectionCache;\n\n  /**\n   * Create a new projection engine.\n   *\n   * @param rootPath - Root path to the model (used by StagedChangesetStorage)\n   */\n  constructor(rootPath: string) {\n    this.stagingAreaManager = new StagedChangesetStorage(rootPath);\n    this.projectionCache = {\n      cache: new Map(),\n      metrics: new Map(),\n      maxAge: 5 * 60 * 1000, // 5-minute TTL for cached projections\n      lastCleanup: Date.now(),\n    };\n  }\n\n  /**\n   * Project a single element by applying staged changes to it.\n   * Merges the element's base state with staged changes to compute its projected state.\n   *\n   * @param baseModel - The base model to project from\n   * @param changesetId - ID of the changeset containing staged changes\n   * @param elementId - ID of the element to project\n   * @returns Projected element with staged changes applied, or null if element is deleted\n   * @throws Error if changeset not found\n   *\n   * @remarks\n   * If multiple changes exist for the element, the last change determines final state.\n   * For 'delete' operations, returns null.\n   * For 'add' operations without base element, creates new element from staged data.\n   * For 'update' operations, merges staged changes with base element attributes.\n   */\n  async projectElement(\n    baseModel: Model,\n    changesetId: string,\n    elementId: string\n  ): Promise<Element | null> {\n    const changeset = await this.stagingAreaManager.load(changesetId);\n    if (!changeset) {\n      throw new Error(`Changeset '${changesetId}' not found`);\n    }\n\n    // Find all changes for this element across all layers\n    const elementChanges = changeset.changes.filter(\n      (c: Change) => c.elementId === elementId\n    ) as StagedChange[];\n\n    if (elementChanges.length === 0) {\n      // No changes, return base element if it exists\n      return baseModel.getElementById(elementId) || null;\n    }\n\n    // Get the last change to determine the element's final state\n    const lastChange = elementChanges[elementChanges.length - 1];\n\n    if (lastChange.type === \"delete\") {\n      return null;\n    }\n\n    // For add or update, construct the projected element\n    const baseElement = baseModel.getElementById(elementId);\n    const projectedData = lastChange.after || {};\n\n    if (baseElement) {\n      // Create a new element with projected data merged with base\n      const projectedAttributes =\n        typeof projectedData.attributes === \"object\" ? projectedData.attributes : {};\n\n      const mergedData = {\n        id: baseElement.id,\n        path: baseElement.path,\n        spec_node_id: baseElement.spec_node_id,\n        type: typeof projectedData.type === \"string\" ? projectedData.type : baseElement.type,\n        layer_id: baseElement.layer_id,\n        name: typeof projectedData.name === \"string\" ? projectedData.name : baseElement.name,\n        description:\n          typeof projectedData.description === \"string\"\n            ? projectedData.description\n            : baseElement.description,\n        attributes: {\n          ...baseElement.attributes,\n          ...projectedAttributes,\n        },\n        references: Array.isArray(projectedData.references)\n          ? projectedData.references\n          : baseElement.references,\n        relationships: Array.isArray(projectedData.relationships)\n          ? projectedData.relationships\n          : baseElement.relationships,\n        source_reference: baseElement.source_reference,\n        metadata: baseElement.metadata,\n      };\n\n      return new ElementClass(mergedData);\n    } else if (lastChange.type === \"add\") {\n      // New element being added\n      return new ElementClass({\n        id: (lastChange.after?.id as string) || elementId,\n        path: (lastChange.after?.path as string) || elementId,\n        spec_node_id: (lastChange.after?.spec_node_id as string) || \"\",\n        type: (projectedData.type as string) || \"unknown\",\n        layer_id: lastChange.layerName,\n        name: (projectedData.name as string) || elementId,\n        description: (projectedData.description as string) || \"\",\n        attributes: (typeof projectedData.attributes === \"object\"\n          ? projectedData.attributes\n          : {}) as Record<string, unknown>,\n        references: Array.isArray(projectedData.references) ? projectedData.references : [],\n        relationships: Array.isArray(projectedData.relationships)\n          ? projectedData.relationships\n          : [],\n        source_reference: projectedData.source_reference as SourceReference | undefined,\n        metadata: projectedData.metadata as ElementMetadata | undefined,\n        layer: lastChange.layerName,\n      });\n    }\n\n    return null;\n  }\n\n  /**\n   * Project a layer by applying staged changes to a clone of the base layer.\n   * Checks cache first; computes and caches result if not found or expired.\n   *\n   * @param baseModel - The base model to project from\n   * @param changesetId - ID of the changeset containing staged changes\n   * @param layerName - Name of the layer to project\n   * @returns Projected layer with staged changes applied\n   * @throws Error if changeset or base layer not found\n   *\n   * @remarks\n   * Computation process:\n   * 1. Check projection cache (returns if found and not expired)\n   * 2. Clone base layer to avoid mutations\n   * 3. Load staged changes filtered to this layer\n   * 4. Apply changes in sequence number order (add/update/delete)\n   * 5. Cache result with timestamp for TTL tracking\n   * 6. Trigger periodic cache cleanup\n   */\n  async projectLayer(baseModel: Model, changesetId: string, layerName: string): Promise<Layer> {\n    // Check cache first\n    const cacheKey = `${changesetId}:${layerName}`;\n    const cached = this.projectionCache.cache.get(cacheKey);\n\n    if (cached) {\n      const age = Date.now() - new Date(cached.computedAt).getTime();\n      if (age < this.projectionCache.maxAge) {\n        // Record cache hit\n        this.recordCacheHit(changesetId);\n        return cached.layer;\n      } else {\n        // Invalidate expired entry\n        this.projectionCache.cache.delete(cacheKey);\n      }\n    }\n\n    // Record cache miss\n    this.recordCacheMiss(changesetId);\n\n    // Load the committed base layer \u2014 must use getBaseLayer() (not getLayer()) to avoid\n    // infinite recursion: getLayer() calls projectLayer(), which would call getLayer() again.\n    const baseLayer = await baseModel.getBaseLayer(layerName);\n    const projectedLayer = baseLayer\n      ? this.cloneLayer(baseLayer)\n      : new LayerClass(layerName);\n\n    // Load staged changes for this layer\n    const changeset = await this.stagingAreaManager.load(changesetId);\n    if (!changeset) {\n      throw new Error(`Changeset '${changesetId}' not found`);\n    }\n\n    const layerChanges = (changeset.changes as StagedChange[])\n      .filter((c: StagedChange) => c.layerName === layerName)\n      .sort((a: StagedChange, b: StagedChange) => a.sequenceNumber - b.sequenceNumber);\n\n    // Apply changes in sequence order\n    for (const change of layerChanges) {\n      switch (change.type) {\n        case \"add\":\n          if (change.after) {\n            const newElement = new ElementClass({\n              id: (change.after.id as string) || change.elementId,\n              path: (change.after.path as string) || change.elementId,\n              spec_node_id: (change.after.spec_node_id as string) || \"\",\n              type: (change.after.type as string) || \"unknown\",\n              layer_id: layerName,\n              name: (change.after.name as string) || change.elementId,\n              description: (change.after.description as string) || \"\",\n              attributes: (typeof change.after.attributes === \"object\"\n                ? change.after.attributes\n                : {}) as Record<string, unknown>,\n              references: Array.isArray(change.after.references) ? change.after.references : [],\n              relationships: Array.isArray(change.after.relationships)\n                ? change.after.relationships\n                : [],\n              source_reference: change.after.source_reference as SourceReference | undefined,\n              metadata: change.after.metadata as ElementMetadata | undefined,\n              layer: layerName,\n            });\n            projectedLayer.addElement(newElement);\n          }\n          break;\n\n        case \"update\":\n          if (change.after) {\n            // Get the existing element to preserve all state\n            const existing = projectedLayer.getElement(change.elementId);\n            if (existing) {\n              // Create updated element with merged attributes\n              const afterAttributes =\n                typeof change.after.attributes === \"object\" ? change.after.attributes : {};\n\n              const mergedAttributes: Record<string, unknown> = {\n                ...existing.attributes,\n                ...afterAttributes,\n              };\n\n              const updatedElement = new ElementClass({\n                id: existing.id,\n                path: existing.path,\n                spec_node_id: existing.spec_node_id,\n                layer_id: existing.layer_id,\n                type: typeof change.after.type === \"string\" ? change.after.type : existing.type,\n                name: typeof change.after.name === \"string\" ? change.after.name : existing.name,\n                description:\n                  typeof change.after.description === \"string\"\n                    ? change.after.description\n                    : existing.description,\n                attributes: mergedAttributes,\n                references: Array.isArray(change.after.references)\n                  ? change.after.references\n                  : existing.references,\n                relationships: Array.isArray(change.after.relationships)\n                  ? change.after.relationships\n                  : existing.relationships,\n                layer: layerName,\n                source_reference: existing.source_reference,\n                metadata: existing.metadata,\n              });\n\n              projectedLayer.updateElement(updatedElement);\n            }\n          }\n          break;\n\n        case \"delete\":\n          const existingForDelete = projectedLayer.getElement(change.elementId);\n          if (existingForDelete) {\n            projectedLayer.deleteElement(existingForDelete.path || existingForDelete.id);\n          }\n          break;\n\n        case \"relationship-add\":\n        case \"relationship-delete\":\n          // Relationship changes are handled at the model level (model.relationships),\n          // not the layer level. Skip here; no layer mutation needed.\n          break;\n      }\n    }\n\n    // Cache the result\n    const cacheEntry: CacheEntry = {\n      layer: projectedLayer,\n      computedAt: new Date().toISOString(),\n    };\n    this.projectionCache.cache.set(cacheKey, cacheEntry);\n\n    // Periodic cleanup of expired entries\n    this.cleanupExpiredCache();\n\n    return projectedLayer;\n  }\n\n  /**\n   * Project entire model by applying staged changes to all layers.\n   * Creates a complete projected model view that includes both changed and unchanged layers.\n   *\n   * @param baseModel - The base model to project from\n   * @param changesetId - ID of the changeset containing staged changes\n   * @returns ProjectedModel with isProjection=true flag (prevents accidental saves)\n   * @throws Error if changeset not found\n   *\n   * @remarks\n   * Projection includes:\n   * - All layers mentioned in changeset changes\n   * - All layers from base model (to have complete model state)\n   * - Base model's manifest (unchanged)\n   * Returned model has isProjection=true to prevent accidental persistence.\n   */\n  async projectModel(baseModel: Model, changesetId: string): Promise<ProjectedModel> {\n    const changeset = await this.stagingAreaManager.load(changesetId);\n    if (!changeset) {\n      throw new Error(`Changeset '${changesetId}' not found`);\n    }\n\n    const projectedLayers = new Map<string, Layer>();\n\n    // Project all layers mentioned in the changeset\n    const layerNames = new Set<string>();\n    for (const change of changeset.changes) {\n      layerNames.add(change.layerName);\n    }\n\n    // Also include all base layers to get complete model\n    for (const baseLayerName of baseModel.getLayerNames()) {\n      layerNames.add(baseLayerName);\n    }\n\n    // Project each layer\n    for (const layerName of layerNames) {\n      const projectedLayer = await this.projectLayer(baseModel, changesetId, layerName);\n      projectedLayers.set(layerName, projectedLayer);\n    }\n\n    // Create projected model with isProjection flag\n    const projectedModel: ProjectedModel = {\n      manifest: baseModel.manifest,\n      layers: projectedLayers,\n      relationships: baseModel.relationships,\n      loadedLayerFilter: baseModel.loadedLayerFilter,\n      isProjection: true,\n    };\n\n    return projectedModel;\n  }\n\n  /**\n   * Compute diff by categorizing changeset changes by type.\n   * Extracts the staged changes and organizes them into additions, modifications, and deletions.\n   *\n   * @param _baseModel - The base model (unused; included for interface compatibility)\n   * @param changesetId - ID of the changeset to compute diff for\n   * @returns ModelDiff with changes categorized by type\n   * @throws Error if changeset not found\n   *\n   * @remarks\n   * Diff is computed directly from changeset changes; does not perform deep comparison.\n   * Each change's before/after snapshots are included for detailed display.\n   */\n  async computeDiff(_baseModel: Model, changesetId: string): Promise<ModelDiff> {\n    const changeset = await this.stagingAreaManager.load(changesetId);\n    if (!changeset) {\n      throw new Error(`Changeset '${changesetId}' not found`);\n    }\n\n    const changes = changeset.changes as StagedChange[];\n\n    return {\n      additions: changes\n        .filter((c: StagedChange) => c.type === \"add\")\n        .map((c: StagedChange) => ({\n          elementId: c.elementId,\n          layerName: c.layerName,\n          data: c.after || {},\n        })),\n\n      modifications: changes\n        .filter((c: StagedChange) => c.type === \"update\")\n        .map((c: StagedChange) => ({\n          elementId: c.elementId,\n          layerName: c.layerName,\n          before: c.before || {},\n          after: c.after || {},\n        })),\n\n      deletions: changes\n        .filter((c: StagedChange) => c.type === \"delete\")\n        .map((c: StagedChange) => ({\n          elementId: c.elementId,\n          layerName: c.layerName,\n          data: c.before || {},\n        })),\n    };\n  }\n\n  /**\n   * Get affected layers for an element in a changeset.\n   * Returns all layers that have cached projections and contain changes for the element.\n   *\n   * @param changesetId - ID of the changeset\n   * @param elementId - ID of the element being unstaged\n   * @returns Set of affected layer names\n   *\n   * @remarks\n   * When unstaging an element, only the layers where that element was modified\n   * need cache invalidation. This enables granular invalidation instead of\n   * invalidating the entire changeset cache.\n   */\n  private async getAffectedLayers(changesetId: string, elementId: string): Promise<Set<string>> {\n    const affectedLayers = new Set<string>();\n\n    try {\n      const changeset = await this.stagingAreaManager.load(changesetId);\n      if (!changeset) {\n        return affectedLayers;\n      }\n\n      // Find all layers that have changes for this element\n      for (const change of changeset.changes) {\n        if (change.elementId === elementId) {\n          affectedLayers.add(change.layerName);\n        }\n      }\n    } catch {\n      // If changeset can't be loaded, return empty set (no invalidation needed)\n      // This handles the case where changeset is deleted or corrupted\n    }\n\n    return affectedLayers;\n  }\n\n  /**\n   * Record a cache hit for metrics tracking.\n   *\n   * @param changesetId - ID of the changeset\n   */\n  private recordCacheHit(changesetId: string): void {\n    const metrics = this.projectionCache.metrics.get(changesetId) || {\n      hits: 0,\n      misses: 0,\n      invalidations: 0,\n    };\n    metrics.hits++;\n    this.projectionCache.metrics.set(changesetId, metrics);\n  }\n\n  /**\n   * Record a cache miss for metrics tracking.\n   *\n   * @param changesetId - ID of the changeset\n   */\n  private recordCacheMiss(changesetId: string): void {\n    const metrics = this.projectionCache.metrics.get(changesetId) || {\n      hits: 0,\n      misses: 0,\n      invalidations: 0,\n    };\n    metrics.misses++;\n    this.projectionCache.metrics.set(changesetId, metrics);\n  }\n\n  /**\n   * Record a cache invalidation for metrics tracking.\n   *\n   * @param changesetId - ID of the changeset\n   */\n  private recordInvalidation(changesetId: string): void {\n    const metrics = this.projectionCache.metrics.get(changesetId) || {\n      hits: 0,\n      misses: 0,\n      invalidations: 0,\n    };\n    metrics.invalidations++;\n    metrics.lastInvalidation = new Date().toISOString();\n    this.projectionCache.metrics.set(changesetId, metrics);\n  }\n\n  /**\n   * Get cache metrics for a changeset (for monitoring and debugging).\n   *\n   * @param changesetId - ID of the changeset\n   * @returns Cache metrics or undefined if no metrics exist\n   */\n  getCacheMetrics(changesetId: string): CacheMetrics | undefined {\n    return this.projectionCache.metrics.get(changesetId);\n  }\n\n  /**\n   * Invalidate projection cache when changes are staged.\n   * Removes cached projections to ensure fresh computation next time.\n   *\n   * @param changesetId - ID of the changeset being modified\n   * @param layerName - Optional: specific layer to invalidate (all if omitted)\n   *\n   * @remarks\n   * If layerName is provided, only that layer's projection is invalidated.\n   * Otherwise, all projections for the changeset are invalidated.\n   */\n  invalidateOnStage(changesetId: string, layerName?: string): void {\n    if (layerName) {\n      // Invalidate specific layer projection\n      const cacheKey = `${changesetId}:${layerName}`;\n      this.projectionCache.cache.delete(cacheKey);\n      this.recordInvalidation(changesetId);\n    } else {\n      // Invalidate all projections for this changeset\n      for (const key of this.projectionCache.cache.keys()) {\n        if (key.startsWith(`${changesetId}:`)) {\n          this.projectionCache.cache.delete(key);\n        }\n      }\n      this.recordInvalidation(changesetId);\n    }\n  }\n\n  /**\n   * Invalidate projection cache when changes are unstaged.\n   * Uses layer-specific invalidation for the affected element's layers.\n   *\n   * @param changesetId - ID of the changeset being modified\n   * @param elementId - Optional: ID of element being unstaged (enables granular invalidation)\n   *\n   * @remarks\n   * If elementId is provided, only the layers containing that element are invalidated.\n   * This is more efficient than invalidating the entire changeset cache when\n   * unstaging elements from a multi-layer changeset.\n   * If elementId is omitted, invalidates all projections for the changeset.\n   */\n  async invalidateOnUnstage(changesetId: string, elementId?: string): Promise<void> {\n    if (elementId) {\n      // Layer-specific invalidation: only invalidate affected layers\n      const affectedLayers = await this.getAffectedLayers(changesetId, elementId);\n      for (const layerName of affectedLayers) {\n        const cacheKey = `${changesetId}:${layerName}`;\n        this.projectionCache.cache.delete(cacheKey);\n      }\n      if (affectedLayers.size > 0) {\n        this.recordInvalidation(changesetId);\n      }\n    } else {\n      // Full invalidation: clear all projections for this changeset\n      for (const key of this.projectionCache.cache.keys()) {\n        if (key.startsWith(`${changesetId}:`)) {\n          this.projectionCache.cache.delete(key);\n        }\n      }\n      this.recordInvalidation(changesetId);\n    }\n  }\n\n  /**\n   * Invalidate all projections for a changeset when it's discarded.\n   * Clears all cached projections for this changeset to free memory.\n   *\n   * @param changesetId - ID of the changeset being discarded\n   */\n  invalidateOnDiscard(changesetId: string): void {\n    for (const key of this.projectionCache.cache.keys()) {\n      if (key.startsWith(`${changesetId}:`)) {\n        this.projectionCache.cache.delete(key);\n      }\n    }\n  }\n\n  /**\n   * Clone a layer to create an independent copy.\n   * Shallow clones all elements and metadata to avoid mutations.\n   * Cloned layer is marked clean to prevent unintended saves.\n   *\n   * @param layer - The layer to clone\n   * @returns New layer with cloned elements and metadata\n   *\n   * @remarks\n   * Cloning strategy:\n   * 1. Create new Layer with same name\n   * 2. Clone each element: shallow copy attributes object and array references\n   * 3. Copy layer metadata if present\n   * 4. Mark cloned layer as clean to prevent automatic saves\n   * This ensures changes to projection don't affect base layer.\n   * Note: Shallow cloning is sufficient since attributes are read-only in projections.\n   */\n  private cloneLayer(layer: Layer): Layer {\n    const cloned = new LayerClass(layer.name);\n\n    // Clone all elements (shallow copy - read-only in projection)\n    for (const element of layer.listElements()) {\n      const elementClone = new ElementClass({\n        id: element.id,\n        path: element.path,\n        spec_node_id: element.spec_node_id,\n        type: element.type,\n        layer_id: element.layer_id,\n        name: element.name,\n        description: element.description,\n        attributes: { ...element.attributes },\n        references: [...(element.references || [])],\n        relationships: [...(element.relationships || [])],\n        layer: element.layer,\n        source_reference: element.source_reference,\n        metadata: element.metadata,\n      });\n      cloned.addElement(elementClone);\n    }\n\n    // Preserve layer metadata if present\n    if (layer.metadata) {\n      cloned.metadata = { ...layer.metadata };\n    }\n\n    // Mark as clean to prevent projection from being saved\n    cloned.markClean();\n    return cloned;\n  }\n\n  /**\n   * Clean up expired cache entries periodically (every 60 seconds).\n   * Removes entries that exceed the maxAge TTL.\n   * Runs at most once per minute to limit overhead.\n   *\n   * @remarks\n   * Cleanup is triggered after each projection computation.\n   * Early exit if last cleanup was less than 60 seconds ago.\n   * Entries are marked for deletion based on age calculation from computedAt timestamp.\n   */\n  private cleanupExpiredCache(): void {\n    const now = Date.now();\n\n    // Limit cleanup frequency to at most every 60 seconds\n    if (now - this.projectionCache.lastCleanup < 60 * 1000) {\n      return;\n    }\n\n    // Remove entries that have exceeded their TTL\n    for (const [key, entry] of this.projectionCache.cache.entries()) {\n      const age = now - new Date(entry.computedAt).getTime();\n      if (age >= this.projectionCache.maxAge) {\n        this.projectionCache.cache.delete(key);\n      }\n    }\n\n    this.projectionCache.lastCleanup = now;\n  }\n}\n"],
+  "mappings": 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 }

package/dist/generated/node-types.js

@@ -877,7 +877,7 @@ const NODE_TYPE_MOTIVATION_ASSESSMENT = {
   title: "ObjectSchema",
   requiredAttributes: ["type"],
   optionalAttributes: ["properties", "patternProperties", "propertyNames", "required", "additionalProperties", "minProperties", "maxProperties"],
-  attributeConstraints: { type: { type: "string" }, properties: { type: "object", description: "Named property definitions for the object schema (primary mechanism for defining object structure)" }, patternProperties: { type: "string", description: "Pattern-matched property definitions applied to properties whose names match the given regex" }, propertyNames: { type: "string", description: "Schema applied to all property names of the object instance for name validation" }, required: { type: "string" }, additionalProperties: { type: "string" }, minProperties: { type: "integer" }, maxProperties: { type: "integer" } }
+  attributeConstraints: { type: { type: "string" }, properties: { type: "object", description: "Named property definitions for the object schema (primary mechanism for defining object structure)" }, patternProperties: { type: "string", description: "Pattern-matched property definitions applied to properties whose names match the given regex" }, propertyNames: { type: "string", description: "Schema applied to all property names of the object instance for name validation" }, required: { type: "array", items: { type: "string" } }, additionalProperties: { type: "string" }, minProperties: { type: "integer" }, maxProperties: { type: "integer" } }
 }, NODE_TYPE_DATA_MODEL_REFERENCE = {
   specNodeId: "data-model.reference",
   layer: "data-model",