@documentation-robotics/cli 0.2.0 → 0.4.0

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 { 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 directory and rename temp to actual\n        if (await this.directoryExists(layerPath)) {\n          await fs.rm(layerPath, { recursive: true, force: true });\n        }\n        await fs.rename(tempPath, layerPath);\n      }\n    } catch (error) {\n      // Cleanup any temp directories on failure\n      for (const { tempPath } of tempLayerWrites) {\n        if (await this.directoryExists(tempPath)) {\n          await fs.rm(tempPath, { recursive: true, force: true });\n        }\n      }\n      throw error;\n    }\n  }\n\n  /**\n   * Helper: Check if file exists\n   */\n  private async fileExists(filePath: string): Promise<boolean> {\n    try {\n      await fs.access(filePath);\n      return true;\n    } catch {\n      return false;\n    }\n  }\n\n  /**\n   * Helper: Check if directory exists\n   */\n  private async directoryExists(dirPath: string): Promise<boolean> {\n    try {\n      const stat = await fs.stat(dirPath);\n      return stat.isDirectory();\n    } catch {\n      return 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+  "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, type Relationship } 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 { assertBaseModelWritable } from \"./changeset-only-guard.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   * relationships.yaml as committed, captured at load time before the active changeset's staged\n   * relationship changes are merged into `relationships`. Null when no changeset was active.\n   */\n  private _baseRelationships: Relationship[] | null = null;\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 (err) {\n        // Only fall back to base layer if the changeset is missing/corrupted\n        const errorMessage = err instanceof Error ? err.message : String(err);\n        const isChangesetNotFound =\n          errorMessage.includes(\"Changeset\") && errorMessage.includes(\"not found\");\n        const isCorrupted = errorMessage.includes(\"corrupted\");\n\n        if (isChangesetNotFound || isCorrupted) {\n          // Expected case: changeset missing or corrupted, safe to fall back to base\n          return this.layers.get(name);\n        }\n\n        // Unexpected error: projection engine bug (TypeError, ReferenceError, etc.)\n        // Re-throw so caller sees the actual problem\n        throw err;\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   * The committed relationships, without the active changeset's staged additions and removals\n   * that load() merges into `relationships` for read commands. Equal to `relationships.getAll()`\n   * when no changeset was active at load time.\n   */\n  getBaseRelationships(): Relationship[] {\n    return this._baseRelationships ? [...this._baseRelationships] : this.relationships.getAll();\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   * Records that the active changeset now stages an element change in `layerName`, so\n   * getLayerNames() (and findElementLayer()) discover a layer the base model does not have without\n   * a reload. StagingAreaManager calls this when it stages into this model's active changeset.\n   */\n  noteStagedLayer(changesetId: string, layerName: string): void {\n    if (this._activeChangesetId && this._activeChangesetId === changesetId && layerName) {\n      this._stagedLayerNames.add(layerName);\n    }\n  }\n\n  /**\n   * Save a layer to disk (model/XX_layername/*.yaml)\n   */\n  async saveLayer(name: string): Promise<void> {\n    assertBaseModelWritable();\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    assertBaseModelWritable();\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}-${crypto.randomBytes(4).toString(\"hex\")}`,\n        source: rel.source,\n        destination: rel.target,\n        predicate: rel.predicate,\n        properties: rel.properties,\n        category: rel.category,\n      };\n      try {\n        this.graph.addEdge(edge);\n      } catch {\n        // Silently skip edges whose nodes haven't been loaded yet.\n        // The primary relationship data lives in this.relationships; the graph\n        // is a secondary index. Cross-layer relationships referencing nodes from\n        // unloaded layers are expected during partial model construction.\n      }\n    }\n  }\n\n  /**\n   * Save relationships to relationships.yaml\n   *\n   * @param options.preserveHeader - Keep the file's existing leading comment block\n   *   (refreshing its `# Last updated:` line) instead of writing the standard header.\n   */\n  async saveRelationships(options: { preserveHeader?: boolean } = {}): Promise<void> {\n    assertBaseModelWritable();\n    const fs = await import(\"fs/promises\");\n    const yaml = await import(\"yaml\");\n    const relationshipsPath = `${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    let header = `# Intra-layer relationships\n# Format: source_id -> predicate -> target_id\n# Last updated: ${timestamp}\n\n`;\n    if (options.preserveHeader) {\n      try {\n        const { extractRelationshipsHeader } = await import(\"./relationship-prune.js\");\n        const existing = extractRelationshipsHeader(await fs.readFile(relationshipsPath, \"utf-8\"));\n        if (existing) {\n          header =\n            existing.replace(/^(# Last updated:).*$/m, `$1 ${timestamp}`) + \"\\n\";\n        }\n      } catch {\n        // Missing or unreadable file: fall back to the standard header\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 (err) {\n        // Only ignore ENOENT (file 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 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 (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        // 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          // Keep the committed relationships before the active changeset's are merged in below,\n          // for views that apply a changeset themselves (ChangesetGraph).\n          model._baseRelationships = model.relationships.getAll();\n          const storage = new StagedChangesetStorage(projectRoot);\n          try {\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          } catch (err) {\n            // Changeset loading or processing failed \u2014 re-throw with context\n            const errorMessage = err instanceof Error ? err.message : String(err);\n            throw new Error(\n              `Failed to load active changeset '${activeId}': ${errorMessage}`,\n              { cause: err }\n            );\n          }\n        }\n      } catch (err) {\n        // Only ignore ENOENT (.active file doesn't exist - expected for no active changeset)\n        const isNotFoundError = (err as any)?.code === \"ENOENT\";\n        if (!isNotFoundError) {\n          // Re-throw permission/I/O errors and changeset loading errors\n          throw err;\n        }\n        // No active changeset file \u2014 proceed with base model only\n        model._activeChangesetId = null;\n      }\n\n      // Count total entities across all layers\n      let entityCount = 0;\n      for (const layer of model.layers.values()) {\n        entityCount += layer.elements.size;\n      }\n\n      span.setAttribute(\"model.entity_count\", entityCount);\n      span.setAttribute(\"model.layer_count\", model.layers.size);\n\n      return model;\n    }, {\n      \"model.path\": startPath || process.cwd(),\n      \"model.type\": \"dr\",\n    });\n  }\n\n  /**\n   * Initialize a new model in a directory\n   */\n  static async init(\n    rootPath: string,\n    manifestData: ManifestData,\n    options: ModelOptions = {}\n  ): Promise<Model> {\n    const yaml = await import(\"yaml\");\n\n    // Create model directory structure\n    await ensureDir(`${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    assertBaseModelWritable();\n    // First, save all layers to temporary files\n    const tempLayerWrites: Array<{ layer: Layer; tempPath: string }> = [];\n\n    try {\n      for (const layer of this.layers.values()) {\n        if (layer.isDirty()) {\n          const layerPath = path.join(\n            this.rootPath,\n            \"documentation-robotics\",\n            \"model\",\n            `${layer.name}_layer`\n          );\n\n          const tempPath = `${layerPath}.tmp`;\n          await ensureDir(tempPath);\n\n          // Write layer elements to temp directory\n          for (const element of layer.elements.values()) {\n            const elementPath = path.join(tempPath, `${element.path || element.id}.json`);\n            const content = JSON.stringify(element.toJSON(), null, 2);\n            await writeFile(elementPath, content);\n          }\n\n          tempLayerWrites.push({ layer, tempPath });\n        }\n      }\n\n      // All temp writes succeeded, now commit by renaming\n      for (const { layer, tempPath } of tempLayerWrites) {\n        const layerPath = path.join(\n          this.rootPath,\n          \"documentation-robotics\",\n          \"model\",\n          `${layer.name}_layer`\n        );\n\n        // Remove old directory and rename temp to actual\n        if (await this.directoryExists(layerPath)) {\n          await fs.rm(layerPath, { recursive: true, force: true });\n        }\n        await fs.rename(tempPath, layerPath);\n      }\n    } catch (error) {\n      // Cleanup any temp directories on failure\n      for (const { tempPath } of tempLayerWrites) {\n        if (await this.directoryExists(tempPath)) {\n          await fs.rm(tempPath, { recursive: true, force: true });\n        }\n      }\n      throw error;\n    }\n  }\n\n  /**\n   * Helper: Check if file exists\n   */\n  private async fileExists(filePath: string): Promise<boolean> {\n    try {\n      await fs.access(filePath);\n      return true;\n    } catch {\n      return false;\n    }\n  }\n\n  /**\n   * Helper: Check if directory exists\n   */\n  private async directoryExists(dirPath: string): Promise<boolean> {\n    try {\n      const stat = await fs.stat(dirPath);\n      return stat.isDirectory();\n    } catch {\n      return false;\n    }\n  }\n\n  /**\n   * Helper: Recursively copy directory\n   */\n  private async copyDirectory(src: string, dest: string): Promise<void> {\n    await ensureDir(dest);\n    const entries = await fs.readdir(src, { withFileTypes: true });\n\n    for (const entry of entries) {\n      const srcPath = path.join(src, entry.name);\n      const destPath = path.join(dest, entry.name);\n\n      if (entry.isDirectory()) {\n        await this.copyDirectory(srcPath, destPath);\n      } else {\n        await fs.copyFile(srcPath, destPath);\n      }\n    }\n  }\n}\n"],
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   "names": ["path", "fs", "err", "layerId", "manifestPath", "projectRoot"]
 }

package/dist/core/mutation-handler.js

@@ -1,13 +1,24 @@
+import { elementIdentifiers } from "./relationships.js";
 import { StagingAreaManager } from "./staging-area.js";
 import { isValidLayerName } from "./layers.js";
 import { CLIError } from "../utils/errors.js";
+import { ChangesetOnlyError } from "./changeset-only-guard.js";
 import { getErrorMessage } from "../utils/errors.js";
 import { ModelReportOrchestrator } from "../reports/model-report-orchestrator.js";
 import { emitLog, SeverityNumber } from "../telemetry/index.js";
+import { changedFields } from "./changeset-summary.js";
+function foldIntoSnapshot(addAfter, before, after) {
+  const folded = { ...addAfter }, b = before ?? {}, a = after ?? {};
+  for (const key of /* @__PURE__ */ new Set([...Object.keys(b), ...Object.keys(a)]))
+    JSON.stringify(b[key]) !== JSON.stringify(a[key]) && (a[key] === void 0 ? delete folded[key] : folded[key] = a[key]);
+  return "source_reference" in a && JSON.stringify(b.source_reference) !== JSON.stringify(a.source_reference) && delete folded.sourceReference, folded;
+}
 class MutationHandler {
   context;
   steps = [];
   stagingManager;
+  changedFields = [];
+  foldedIntoAdd = !1;
   constructor(model, elementId, layerName) {
     this.context = { model, elementId, layerName }, this.stagingManager = new StagingAreaManager(model.rootPath, model);
   }
@@ -41,6 +52,30 @@ class MutationHandler {
   getStagingManager() {
     return this.stagingManager;
   }
+  /**
+   * The fields the last executeUpdate changed (`attributes.x` for attribute keys), sorted.
+   * Empty before an update runs or when it changed nothing.
+   */
+  getChangedFields() {
+    return this.changedFields;
+  }
+  /** Whether the last executeUpdate rewrote the changeset's staged add of the element in place. */
+  wasFoldedIntoAdd() {
+    return this.foldedIntoAdd;
+  }
+  /**
+   * The active changeset's add of this element, when an update should be folded into it: the
+   * add is the element's only staged element change (an update staged after it by an earlier
+   * build keeps the old append behaviour, so it is not overridden), and the base model does not
+   * already hold the element (commit skips such an add; a staged update still applies).
+   */
+  async stagedAddToFoldInto(changeset, element) {
+    const ids = new Set(elementIdentifiers(element, this.context.elementId)), own = changeset.changes.filter((c) => !c.type.startsWith("relationship-") && ids.has(c.elementId));
+    if (own.length !== 1 || own[0].type !== "add" || !own[0].after)
+      return null;
+    const baseLayer = await this.context.model.getBaseLayer(this.context.layerName);
+    return [...ids].some((id) => baseLayer?.getElement(id)) ? null : own[0];
+  }
   /**
    * Compute before and after states
    *
@@ -76,7 +111,20 @@ class MutationHandler {
     this.context.element = element, this.context.before = element.toJSON(), this.context.after = { ...this.context.before };
     const activeChangeset = await this.stagingManager.getActive();
     if (activeChangeset && activeChangeset.status === "staged") {
-      await mutator(element, this.context.after), await this.stagingManager.stage(activeChangeset.id, {
+      await mutator(element, this.context.after), this.changedFields = changedFields(this.context.before, this.context.after);
+      const add = await this.stagedAddToFoldInto(activeChangeset, element);
+      if (add) {
+        await this.stagingManager.restage(activeChangeset.id, add.elementId, {
+          type: "add",
+          elementId: add.elementId,
+          layerName: add.layerName,
+          ...add.before !== void 0 ? { before: add.before } : {},
+          after: foldIntoSnapshot(add.after, this.context.before, this.context.after),
+          timestamp: (/* @__PURE__ */ new Date()).toISOString()
+        }), this.foldedIntoAdd = !0;
+        return;
+      }
+      await this.stagingManager.stage(activeChangeset.id, {
         type: "update",
         elementId: this.context.elementId,
         layerName: this.context.layerName,
@@ -93,7 +141,7 @@ class MutationHandler {
    */
   async executeDelete(element) {
     this.context.element = element, this.context.before = element.toJSON(), this.context.after = void 0;
-    const activeChangeset = await this.stagingManager.getActive();
+    const identifiers = elementIdentifiers(element, this.context.elementId), activeChangeset = await this.stagingManager.getActive();
     if (activeChangeset && activeChangeset.status === "staged") {
       await this.stagingManager.stage(activeChangeset.id, {
         type: "delete",
@@ -102,13 +150,29 @@ class MutationHandler {
         before: this.context.before,
         timestamp: (/* @__PURE__ */ new Date()).toISOString()
       });
+      const ids = new Set(identifiers), alreadyStaged = new Set(activeChangeset.changes.filter((change) => change.type === "relationship-delete").map((change) => change.elementId)), dangling = this.context.model.relationships.getAll().filter((rel) => ids.has(rel.source) || ids.has(rel.target)).filter((rel) => !alreadyStaged.has(`${rel.source}::${rel.predicate}::${rel.target}`));
+      for (const rel of dangling)
+        alreadyStaged.add(`${rel.source}::${rel.predicate}::${rel.target}`), await this.stagingManager.stage(activeChangeset.id, {
+          type: "relationship-delete",
+          elementId: `${rel.source}::${rel.predicate}::${rel.target}`,
+          layerName: rel.layer,
+          before: {
+            source: rel.source,
+            target: rel.target,
+            predicate: rel.predicate,
+            layer: rel.layer,
+            ...rel.targetLayer ? { targetLayer: rel.targetLayer } : {},
+            ...rel.properties ? { properties: rel.properties } : {}
+          },
+          timestamp: (/* @__PURE__ */ new Date()).toISOString()
+        });
       return;
     }
     if (!(await this.context.model.getLayer(this.context.layerName)).deleteElement(element.path || element.id))
       throw new CLIError(`Failed to delete element ${this.context.elementId}`, 1, [
         "Element may have already been deleted"
       ]);
-    this.context.model.relationships.deleteForElement(this.context.elementId), await this._persistChanges("delete");
+    this.context.model.relationships.deleteForElement(identifiers), await this._persistChanges("delete");
   }
   /**
    * Execute all registered steps and persist
@@ -138,7 +202,7 @@ class MutationHandler {
   async _executeBasePath(mutator, type) {
     if (!this.context.element)
       throw new CLIError("Element not set", 1);
-    this.context.before === void 0 && (this.context.before = this.context.element.toJSON()), this.context.after === void 0 && (this.context.after = { ...this.context.before }), await mutator(this.context.element, this.context.after), await this._persistChanges(type);
+    this.context.before === void 0 && (this.context.before = this.context.element.toJSON()), this.context.after === void 0 && (this.context.after = { ...this.context.before }), await mutator(this.context.element, this.context.after), this.changedFields = changedFields(this.context.before, this.context.after), await this._persistChanges(type);
   }
   /**
    * Persist changes to disk
@@ -152,7 +216,7 @@ class MutationHandler {
     try {
       await this.context.model.saveLayer(this.context.layerName), type === "delete" && this.context.model.relationships.isDirty() && await this.context.model.saveRelationships(), await this.context.model.saveManifest();
     } catch (error) {
-      throw new CLIError(`Failed to persist changes: ${getErrorMessage(error)}`, 1, ["Check that the model directory is writable", "Verify the model is not corrupted"]);
+      throw error instanceof ChangesetOnlyError ? error : new CLIError(`Failed to persist changes: ${getErrorMessage(error)}`, 1, ["Check that the model directory is writable", "Verify the model is not corrupted"]);
     }
     try {
       const orchestrator = new ModelReportOrchestrator(this.context.model, this.context.model.rootPath);
@@ -174,6 +238,7 @@ class MutationHandler {
   }
 }
 export {
-  MutationHandler
+  MutationHandler,
+  foldIntoSnapshot
 };
 //# sourceMappingURL=mutation-handler.js.map