@documentation-robotics/cli 0.1.9 → 0.1.11

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Files changed (21) hide show
  1. package/dist/cli.js +18 -2
  2. package/dist/cli.js.map +2 -2
  3. package/dist/commands/repair.js +62 -0
  4. package/dist/commands/repair.js.map +7 -0
  5. package/dist/commands/version.js +1 -1
  6. package/dist/core/attribute-collision-repair.js +73 -0
  7. package/dist/core/attribute-collision-repair.js.map +7 -0
  8. package/dist/core/model.js +10 -7
  9. package/dist/core/model.js.map +2 -2
  10. package/dist/telemetry/index.js +1 -1
  11. package/dist/utils/spec-version.js +1 -1
  12. package/dist/utils/spec-version.js.map +2 -2
  13. package/dist/viewer/README.md +6 -6
  14. package/dist/viewer/assets/main-BRPZyc36.css +1 -0
  15. package/dist/viewer/assets/main-BrpLargo.js +81 -0
  16. package/dist/viewer/index.html +2 -2
  17. package/dist/viewer/manifest.json +10 -10
  18. package/dist/viewer/version.json +1 -1
  19. package/package.json +9 -9
  20. package/dist/viewer/assets/main-D114QwJo.css +0 -1
  21. package/dist/viewer/assets/main-DyuokeQj.js +0 -81
package/dist/core/model.js.map CHANGED
@@ -1,7 +1,7 @@
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  {
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  "version": 3,
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  "sources": ["../../src/core/model.ts"],
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- "sourcesContent": ["import { Layer } from \"./layer.js\";\nimport { Manifest } from \"./manifest.js\";\nimport { Element } from \"./element.js\";\nimport { GraphModel, type GraphEdge } from \"./graph-model.js\";\nimport { VirtualProjectionEngine } from \"./virtual-projection.js\";\nimport { StagedChangesetStorage } from \"./staged-changeset-storage.js\";\nimport { Relationships } from \"./relationships.js\";\nimport { CANONICAL_LAYER_NAMES } from \"./layers.js\";\nimport type { StagedChange } from \"./changeset.js\";\nimport { ensureDir, writeFile } from \"../utils/file-io.js\";\nimport { getCliVersion } from \"../utils/spec-version.js\";\nimport { startSpan, endSpan, startActiveSpan } from \"../telemetry/index.js\";\nimport { findProjectRoot } from \"../utils/project-paths.js\";\nimport { getNodeType } from \"../generated/node-types.js\";\nimport type { SpecNodeId } from \"../generated/node-types.js\";\nimport type { ManifestData, ModelOptions } from \"../types/index.js\";\nimport path from \"node:path\";\nimport fs from \"node:fs/promises\";\nimport crypto from \"node:crypto\";\n\n/**\n * Derive a deterministic UUID from a path string using SHA-256.\n * Produces a stable UUID4-like value so migration doesn't regenerate UUIDs on every load.\n */\nfunction deterministicUUID(path: string): string {\n const hash = crypto.createHash(\"sha256\").update(path).digest(\"hex\");\n return [\n hash.slice(0, 8),\n hash.slice(8, 12),\n \"4\" + hash.slice(13, 16), // version 4 marker\n ((parseInt(hash.slice(16, 18), 16) & 0x3f) | 0x80).toString(16) + hash.slice(18, 20), // variant\n hash.slice(20, 32),\n ].join(\"-\");\n}\n\n/**\n * Convert a PascalCase title to snake_case.\n * Handles acronyms correctly: \"UXApplication\" \u2192 \"ux_application\", \"OpenAPIDocument\" \u2192 \"open_api_document\".\n */\nfunction titleToSnakeCase(title: string): string {\n return title\n .replace(/([A-Z]+)([A-Z][a-z])/g, \"$1_$2\") // \"APIDoc\" \u2192 \"API_Doc\"\n .replace(/([a-z\\d])([A-Z])/g, \"$1_$2\") // \"appComponent\" \u2192 \"app_Component\"\n .toLowerCase();\n}\n\n/**\n * Derive a snake_case file stem for a given element type.\n * Uses the spec node title for accurate word boundaries (e.g., \"InputSpacePartition\" \u2192 \"input_space_partition\").\n * Falls back to the raw type string when the title is unavailable.\n */\nfunction typeToSnakeStem(specNodeId: string | undefined, type: string): string {\n if (specNodeId) {\n const nodeType = getNodeType(specNodeId as SpecNodeId);\n if (nodeType?.title) {\n return titleToSnakeCase(nodeType.title);\n }\n }\n return type;\n}\n\n// Fallback for runtime environments where TELEMETRY_ENABLED is not defined by esbuild\ndeclare const TELEMETRY_ENABLED: boolean | undefined;\nconst isTelemetryEnabled = typeof TELEMETRY_ENABLED !== \"undefined\" ? TELEMETRY_ENABLED : false;\n\n/**\n * Model class representing the complete architecture model\n * Uses GraphModel internally for graph-based storage\n */\nexport class Model {\n rootPath: string;\n manifest: Manifest;\n graph: GraphModel;\n layers: Map<string, Layer>;\n relationships: Relationships;\n lazyLoad: boolean;\n private loadedLayers: Set<string>;\n private virtualProjectionEngine?: VirtualProjectionEngine;\n /** ID of the currently active changeset, or null if none is active. Set during load(). */\n private _activeChangesetId: string | null = null;\n /** Layer names that exist only in staged changes (not yet committed to base model). */\n private _stagedLayerNames: Set<string> = new Set();\n\n constructor(rootPath: string, manifest: Manifest, options: ModelOptions = {}) {\n this.rootPath = rootPath;\n this.manifest = manifest;\n this.graph = new GraphModel();\n this.layers = new Map();\n this.relationships = new Relationships();\n this.lazyLoad = options.lazyLoad ?? false;\n this.loadedLayers = new Set();\n }\n\n /**\n * Get the committed base layer (no staging projection).\n * Used internally by VirtualProjectionEngine and commit() to access the raw base model\n * without triggering infinite recursion or double-projection.\n */\n async getBaseLayer(name: string): Promise<Layer | undefined> {\n if (this.lazyLoad && !this.loadedLayers.has(name)) {\n await this.loadLayer(name);\n }\n return this.layers.get(name);\n }\n\n /**\n * Get a layer, transparently merging staged changes when an active changeset exists.\n * Falls back to the committed base layer if no changeset is active or projection fails.\n */\n async getLayer(name: string): Promise<Layer | undefined> {\n if (this.lazyLoad && !this.loadedLayers.has(name)) {\n await this.loadLayer(name);\n }\n\n // If an active changeset is present, return a projected (base + staged) layer\n if (this._activeChangesetId) {\n try {\n return await this.getVirtualProjectionEngine().projectLayer(\n this,\n this._activeChangesetId,\n name\n );\n } catch {\n // Fall back to base layer on projection failure (e.g. corrupt changeset)\n return this.layers.get(name);\n }\n }\n\n return this.layers.get(name);\n }\n\n /**\n * Get an element by ID across all layers\n * Supports both UUID and semantic ID (layer.type.kebab-name) lookup\n */\n getElementById(id: string): Element | undefined {\n for (const layer of this.layers.values()) {\n const element = layer.getElement(id);\n if (element) {\n return element;\n }\n }\n return undefined;\n }\n\n /**\n * Get virtual projection engine (lazily initialized)\n */\n getVirtualProjectionEngine(): VirtualProjectionEngine {\n if (!this.virtualProjectionEngine) {\n this.virtualProjectionEngine = new VirtualProjectionEngine(this.rootPath);\n }\n return this.virtualProjectionEngine;\n }\n\n /**\n * Returns the active changeset ID, or null if no changeset is active.\n * Used by commands that need to project the full model (e.g. validate).\n */\n getActiveChangesetId(): string | null {\n return this._activeChangesetId;\n }\n\n /**\n * Load a layer from disk (model/XX_layername/*.yaml files)\n */\n async loadLayer(name: string): Promise<void> {\n await startActiveSpan(\"layer.load\", async (layerSpan) => {\n const fs = await import(\"fs/promises\");\n const yaml = await import(\"yaml\");\n\n let layerPath: string | null = null;\n\n // Auto-discover by scanning directory with naming convention\n const modelDir = `${this.rootPath}/documentation-robotics/model`;\n\n try {\n const entries = await fs.readdir(modelDir, { withFileTypes: true });\n const layerDir = entries.find(\n (e) =>\n e.isDirectory() && e.name.match(/^\\d{2}_/) && e.name.replace(/^\\d{2}_/, \"\") === name\n );\n\n if (layerDir) {\n layerPath = `${modelDir}/${layerDir.name}`;\n }\n } catch {\n // Model directory doesn't exist or can't be read\n }\n\n if (!layerPath) {\n return; // Layer directory not found\n }\n\n const layer = new Layer(name, this.graph);\n let parseErrorCount = 0;\n\n // Load all YAML files in the layer directory\n const files = await fs.readdir(layerPath);\n for (const file of files) {\n if (file.endsWith(\".yaml\") || file.endsWith(\".yml\")) {\n const filePath = `${layerPath}/${file}`;\n try {\n const yamlContent = await fs.readFile(filePath, \"utf-8\");\n const elements = yaml.parse(yamlContent);\n\n // Add each element from the YAML file\n if (elements && typeof elements === \"object\") {\n for (const [key, element] of Object.entries(elements)) {\n if (element && typeof element === \"object\") {\n const el: any = element;\n\n // Derive id, path, and type using the 3-case migration logic:\n // Case 1: element already has both id (UUID) and path \u2192 use as-is\n // Case 2: element.id looks like a slug (layer.type.name) \u2192 move to path, generate UUID\n // Case 3: element has UUID id but no path \u2192 derive path from layer_id.type.kebab(name)\n const isSlugPattern = /^[a-z][a-z0-9-]*\\.[a-z][a-z0-9-]*\\.[a-z][a-z0-9-]*$/.test(el.id || \"\");\n const isUUIDPattern = /^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$/i.test(el.id || \"\");\n\n let elementId: string;\n let elementPath: string;\n let extractedType: string | undefined = undefined;\n\n if (el.path && isUUIDPattern) {\n // Case 1: already has both path and UUID id\n elementId = el.id;\n elementPath = el.path;\n const pathParts = el.path.split(\".\");\n if (pathParts.length >= 3) extractedType = pathParts[1];\n } else if (el.path && !isUUIDPattern) {\n // Has a path but id is not a UUID \u2014 migrate id to deterministic UUID\n elementPath = el.path;\n elementId = deterministicUUID(el.path);\n const pathParts = el.path.split(\".\");\n if (pathParts.length >= 3) extractedType = pathParts[1];\n } else if (isSlugPattern) {\n // Case 2: slug-looking id \u2192 move to path, generate deterministic UUID\n elementPath = el.id;\n elementId = deterministicUUID(el.id);\n const parts = el.id.split(\".\");\n if (parts.length >= 3) extractedType = parts[1];\n } else if (isUUIDPattern) {\n // Case 3: UUID id, no path \u2192 derive path\n elementId = el.id;\n const layerId = el.layer_id || name;\n const rawType = el.type || \"\";\n const rawName = el.name || key;\n const kebabName = rawName.toLowerCase().replace(/[\\s_]+/g, \"-\").replace(/[^a-z0-9-]/g, \"\").replace(/-+/g, \"-\").replace(/^-+|-+$/g, \"\");\n elementPath = `${layerId}.${rawType}.${kebabName}`;\n extractedType = rawType || undefined;\n } else {\n // Fallback: derive a path from available data, generate deterministic UUID\n const layerId = el.layer_id || name;\n const rawType = el.type || (typeof el.id === \"string\" && el.id.includes(\".\") ? el.id.split(\".\")[1] : \"\") || \"\";\n const rawName = el.name || key;\n const kebabName = rawName.toLowerCase().replace(/[\\s_]+/g, \"-\").replace(/[^a-z0-9-]/g, \"\").replace(/-+/g, \"-\").replace(/^-+|-+$/g, \"\") || \"unknown\";\n elementPath = `${layerId}.${rawType || \"element\"}.${kebabName}`;\n elementId = deterministicUUID(elementPath);\n if (rawType) extractedType = rawType;\n else if (typeof el.id === \"string\" && el.id.includes(\".\")) {\n const parts = el.id.split(\".\");\n if (parts.length >= 3) extractedType = parts[1];\n }\n }\n\n const elementName = el.name || key;\n const elementType = el.type || extractedType;\n const layerId = el.layer_id || name;\n\n const newElement = new Element({\n id: elementId,\n path: elementPath,\n spec_node_id: el.spec_node_id,\n layer_id: layerId,\n attributes: el.attributes,\n source_reference: el.source_reference,\n metadata: el.metadata,\n name: elementName,\n type: elementType,\n description: el.description || \"\",\n relationships: el.relationships || [],\n references: el.references || [],\n layer: layerId,\n } as any);\n layer.addElement(newElement);\n }\n }\n }\n } catch (fileError) {\n // Log YAML parsing errors but continue loading other files\n const errorMsg = fileError instanceof Error ? fileError.message : String(fileError);\n console.error(`Warning: Failed to parse ${filePath}: ${errorMsg}`);\n parseErrorCount++;\n // Continue with next file\n }\n }\n }\n\n // If we had parse errors, add a note to the layer\n if (parseErrorCount > 0) {\n console.error(\n `Warning: Layer '${name}' loaded with ${parseErrorCount} YAML parse error(s)`\n );\n }\n\n this.layers.set(name, layer);\n this.loadedLayers.add(name);\n\n layerSpan.setAttribute(\"layer.element_count\", layer.elements.size);\n }, { \"layer.name\": name });\n }\n\n /**\n * Add a layer to the model\n */\n addLayer(layer: Layer): void {\n // If the layer has elements in its isolated graph, migrate them to the model's graph\n if (layer.graph.getNodeCount() > 0) {\n for (const node of layer.graph.nodes.values()) {\n this.graph.addNode(node);\n }\n for (const edge of layer.graph.edges.values()) {\n this.graph.addEdge(edge);\n }\n }\n // Ensure layer uses the model's graph for future operations\n layer.graph = this.graph;\n this.layers.set(layer.name, layer);\n this.loadedLayers.add(layer.name);\n }\n\n /**\n * Get all layer names, including layers that exist only in staged changes.\n * When an active changeset introduces elements for a layer with no committed data,\n * that layer name is included so findElementLayer() and other callers can discover it.\n */\n getLayerNames(): string[] {\n const base = Array.from(this.layers.keys());\n if (this._stagedLayerNames.size === 0) {\n return base;\n }\n // Include staged-only layers (layers that have staged elements but no committed elements)\n const staged = Array.from(this._stagedLayerNames).filter((l) => !this.layers.has(l));\n return [...base, ...staged];\n }\n\n /**\n * Save a layer to disk (model/XX_layername/*.yaml)\n */\n async saveLayer(name: string): Promise<void> {\n const layer = this.layers.get(name);\n if (!layer) {\n throw new Error(`Layer ${name} not found`);\n }\n\n const fs = await import(\"fs/promises\");\n const yaml = await import(\"yaml\");\n\n let layerPath: string | null = null;\n\n // Discover by scanning directory\n const modelDir = `${this.rootPath}/documentation-robotics/model`;\n\n try {\n const entries = await fs.readdir(modelDir, { withFileTypes: true });\n const layerDir = entries.find(\n (e) =>\n e.isDirectory() && e.name.match(/^\\d{2}_/) && e.name.replace(/^\\d{2}_/, \"\") === name\n );\n\n if (layerDir) {\n layerPath = `${modelDir}/${layerDir.name}`;\n }\n } catch {\n // Model directory doesn't exist or can't be read\n }\n\n // If still not found, create using default format\n if (!layerPath) {\n // Find the order number for this layer\n // Handle layer names with or without numeric prefix (e.g., \"motivation\" or \"01-motivation\")\n const layerNameWithoutPrefix = name.replace(/^\\d{2}-/, \"\");\n const index = CANONICAL_LAYER_NAMES.indexOf(layerNameWithoutPrefix as typeof CANONICAL_LAYER_NAMES[number]);\n if (index >= 0) {\n const orderNum = String(index + 1).padStart(2, \"0\");\n layerPath = `${this.rootPath}/documentation-robotics/model/${orderNum}_${layerNameWithoutPrefix}`;\n await ensureDir(layerPath);\n } else {\n throw new Error(`Unknown layer ${name} and no path configured in manifest`);\n }\n }\n\n // Delete all existing YAML files in the layer directory to ensure\n // we don't keep stale files after element deletion\n try {\n const existingFiles = await fs.readdir(layerPath);\n for (const file of existingFiles) {\n if (file.endsWith(\".yaml\") || file.endsWith(\".yml\")) {\n await fs.unlink(`${layerPath}/${file}`);\n }\n }\n } catch (err) {\n // Only ignore \"directory not found\" errors \u2014 re-throw permission/I/O errors\n const isNotFoundError = (err as any)?.code === \"ENOENT\";\n if (!isNotFoundError) {\n throw new Error(\n `Failed to clean existing YAML files: ${err instanceof Error ? err.message : String(err)}`\n );\n }\n }\n\n // Group elements by type, computing the snake_case file stem from the spec node title\n const elementsByType = new Map<string, { stem: string; elements: Element[] }>();\n for (const element of layer.elements.values()) {\n const typeKey = element.type;\n if (!elementsByType.has(typeKey)) {\n const stem = typeToSnakeStem(element.spec_node_id, element.type);\n elementsByType.set(typeKey, { stem, elements: [] });\n }\n elementsByType.get(typeKey)!.elements.push(element);\n }\n\n // Internal graph fields \u2014 never written to YAML\n const INTERNAL_FIELDS = new Set([\n \"__references__\", \"__relationships__\",\n \"source\", \"x-source-reference\",\n ]);\n\n // Write each type to its own YAML file\n for (const [, { stem, elements }] of elementsByType) {\n const filename = `${stem}.yaml`;\n const filePath = `${layerPath}/${filename}`;\n\n // Convert elements to spec-node format YAML\n const yamlData: any = {};\n for (const element of elements) {\n const json = element.toJSON();\n\n // Clean attributes: remove graph-internal keys that should not be persisted\n const cleanAttrs = json.attributes\n ? Object.fromEntries(\n Object.entries(json.attributes).filter(([k]) => !INTERNAL_FIELDS.has(k))\n )\n : undefined;\n\n // Use path as YAML key (human-readable); fall back to id for elements without path\n const key = element.path || element.id;\n yamlData[key] = {\n id: json.id,\n path: json.path,\n spec_node_id: json.spec_node_id,\n type: json.type,\n layer_id: json.layer_id,\n name: json.name,\n ...(json.description && { description: json.description }),\n ...(cleanAttrs && Object.keys(cleanAttrs).length > 0 && { attributes: cleanAttrs }),\n ...(json.source_reference && { source_reference: json.source_reference }),\n ...(json.metadata && { metadata: json.metadata }),\n ...(json.references && json.references.length > 0 && { references: json.references }),\n // Relationships are now stored in centralized relationships.yaml, not inline\n };\n }\n\n await writeFile(filePath, yaml.stringify(yamlData));\n }\n\n layer.markClean();\n }\n\n /**\n * Save model (saves all dirty layers and manifest)\n */\n async save(): Promise<void> {\n await this.saveDirtyLayers();\n await this.saveManifest();\n }\n\n /**\n * Save all dirty layers to disk\n */\n async saveDirtyLayers(): Promise<void> {\n // Count dirty layers before operation\n let dirtyLayerCount = 0;\n for (const layer of this.layers.values()) {\n if (layer.isDirty()) {\n dirtyLayerCount++;\n }\n }\n\n const span = isTelemetryEnabled\n ? startSpan(\"model.save\", {\n \"model.path\": this.rootPath,\n \"model.dirty_layer_count\": dirtyLayerCount,\n })\n : null;\n\n try {\n for (const layer of this.layers.values()) {\n if (layer.isDirty()) {\n await this.saveLayer(layer.name);\n }\n }\n } finally {\n if (isTelemetryEnabled) {\n endSpan(span);\n }\n }\n }\n\n /**\n * Save the manifest to disk (documentation-robotics/model/manifest.yaml)\n */\n async saveManifest(): Promise<void> {\n this.manifest.updateModified();\n const yaml = await import(\"yaml\");\n const manifestPath = `${this.rootPath}/documentation-robotics/model/manifest.yaml`;\n\n // Convert to YAML format\n const yamlData: any = {\n version: this.manifest.version,\n schema: \"documentation-robotics-v1\",\n cli_version: getCliVersion(),\n spec_version: this.manifest.specVersion,\n created: this.manifest.created,\n updated: this.manifest.modified,\n project: {\n name: this.manifest.name,\n description: this.manifest.description,\n version: this.manifest.version,\n },\n documentation: \".dr/README.md\",\n layers: {},\n };\n\n // Generate layer structure from current model state\n for (let i = 0; i < CANONICAL_LAYER_NAMES.length; i++) {\n const layerName = CANONICAL_LAYER_NAMES[i];\n const layer = this.layers.get(layerName);\n const orderNum = String(i + 1).padStart(2, \"0\");\n\n yamlData.layers[layerName] = {\n order: i + 1,\n name: layerName.charAt(0).toUpperCase() + layerName.slice(1).replace(\"-\", \" \"),\n path: `documentation-robotics/model/${orderNum}_${layerName}/`,\n enabled: true,\n ...(layer && { elements: this.getLayerElementCounts(layer) }),\n };\n }\n\n if (this.manifest.changeset_history && this.manifest.changeset_history.length > 0) {\n yamlData.changeset_history = this.manifest.changeset_history;\n }\n\n await ensureDir(`${this.rootPath}/documentation-robotics/model`);\n await writeFile(manifestPath, yaml.stringify(yamlData));\n }\n\n private getLayerElementCounts(layer: Layer): Record<string, number> {\n const counts: Record<string, number> = {};\n for (const element of layer.elements.values()) {\n counts[element.type] = (counts[element.type] || 0) + 1;\n }\n return counts;\n }\n\n /**\n * Load relationships from relationships.yaml\n */\n async loadRelationships(): Promise<void> {\n const fs = await import(\"fs/promises\");\n const yaml = await import(\"yaml\");\n const relationshipsPath = `${this.rootPath}/documentation-robotics/model/relationships.yaml`;\n\n let data: any;\n try {\n const yamlContent = await fs.readFile(relationshipsPath, \"utf-8\");\n data = yaml.parse(yamlContent);\n } catch (err) {\n // If file doesn't exist, that's okay - start with empty relationships\n if ((err as any).code !== \"ENOENT\") {\n // But if it's a different error (YAML parse, permission denied, etc), throw it\n // so the caller knows about the issue\n throw new Error(\n `Failed to load relationships.yaml: ${err instanceof Error ? err.message : String(err)}`\n );\n }\n // ENOENT: file doesn't exist, return with empty relationships\n return;\n }\n\n // Validate that parsed content is an array\n if (!Array.isArray(data)) {\n const typeLabel = data === null ? \"null\" : typeof data;\n console.warn(\n `Warning: relationships.yaml contains non-array content (received ${typeLabel}). Expected an array of relationships. Skipping relationship loading.`\n );\n return;\n }\n\n this.relationships = Relationships.fromArray(data);\n // Sync relationships to graph as a secondary in-memory index.\n // addEdge() may throw if nodes from other layers haven't been loaded yet;\n // failures are silently skipped \u2014 this.relationships holds the primary data.\n for (let i = 0; i < data.length; i++) {\n const rel = data[i];\n const edge: GraphEdge = {\n id: `rel-${i}-${crypto.randomBytes(4).toString(\"hex\")}`,\n source: rel.source,\n destination: rel.target,\n predicate: rel.predicate,\n properties: rel.properties,\n category: rel.category,\n };\n try {\n this.graph.addEdge(edge);\n } catch {\n // Silently skip edges whose nodes haven't been loaded yet.\n // The primary relationship data lives in this.relationships; the graph\n // is a secondary index. Cross-layer relationships referencing nodes from\n // unloaded layers are expected during partial model construction.\n }\n }\n }\n\n /**\n * Save relationships to relationships.yaml\n */\n async saveRelationships(): Promise<void> {\n const fs = await import(\"fs/promises\");\n const yaml = await import(\"yaml\");\n const relationshipsPath = `${this.rootPath}/documentation-robotics/model/relationships.yaml`;\n\n await ensureDir(`${this.rootPath}/documentation-robotics/model`);\n\n const data = this.relationships.toArray();\n\n // Add header comment with timestamp to ensure file always changes\n const timestamp = new Date().toISOString();\n const header = `# Intra-layer relationships\n# Format: source_id -> predicate -> target_id\n# Last updated: ${timestamp}\n\n`;\n const yamlContent = header + yaml.stringify(data);\n\n await fs.writeFile(relationshipsPath, yamlContent, \"utf-8\");\n this.relationships.markClean();\n }\n\n /**\n * Resolve model paths (private helper)\n *\n * @param startPath - Starting path for search\n * @returns Project root and manifest path\n */\n private static async resolveModelPaths(startPath?: string): Promise<{\n projectRoot: string;\n manifestPath: string;\n }> {\n const searchPath = startPath || process.cwd();\n\n // Optional override via env var (highest priority)\n if (process.env.DR_MODEL_PATH) {\n const envPath = path.resolve(process.env.DR_MODEL_PATH);\n let manifestPath: string;\n\n if (envPath.endsWith(\"manifest.yaml\")) {\n manifestPath = envPath;\n } else if (envPath.endsWith(\"model\")) {\n manifestPath = path.join(envPath, \"manifest.yaml\");\n } else {\n manifestPath = path.join(envPath, \"documentation-robotics\", \"model\", \"manifest.yaml\");\n }\n\n try {\n await fs.access(manifestPath);\n const projectRoot = path.dirname(path.dirname(path.dirname(manifestPath)));\n return { projectRoot, manifestPath: path.normalize(manifestPath) };\n } catch {\n throw new Error(`Model not found at DR_MODEL_PATH: ${process.env.DR_MODEL_PATH}`);\n }\n }\n\n // Use findProjectRoot to locate documentation_robotics/ folder\n const projectRoot = await findProjectRoot(searchPath);\n\n if (!projectRoot) {\n throw new Error(\n \"No DR project found. Could not find documentation_robotics/ folder.\\n\" +\n 'Run \"dr init\" to create a new project, or navigate to a directory containing a DR project.'\n );\n }\n\n const manifestPath = path.join(projectRoot, \"documentation-robotics\", \"model\", \"manifest.yaml\");\n\n try {\n await fs.access(manifestPath);\n return { projectRoot, manifestPath };\n } catch {\n throw new Error(\n `Found documentation_robotics/ at ${projectRoot} but no model found. ` +\n `Expected: ${manifestPath}\\n` +\n `Run \"dr init\" to create a model.`\n );\n }\n }\n\n /**\n * Load a model from disk\n *\n * Expected structure:\n * <project-root>/\n * \u2514\u2500\u2500 documentation_robotics/\n * \u2514\u2500\u2500 model/\n * \u2514\u2500\u2500 manifest.yaml\n *\n * @param startPath - Starting path for project search (defaults to process.cwd())\n * @param options - Model loading options\n * @returns Loaded Model instance\n */\n static async load(startPath?: string, options: ModelOptions = {}): Promise<Model> {\n return startActiveSpan(\"model.load\", async (span) => {\n // Resolve project root and manifest path\n const { projectRoot, manifestPath } = await Model.resolveModelPaths(startPath);\n\n const yaml = await import(\"yaml\");\n\n // Load manifest from resolved path\n const yamlContent = await fs.readFile(manifestPath, \"utf-8\");\n const manifestYaml = yaml.parse(yamlContent);\n\n // Convert manifest to internal format\n const manifestData: any = {\n name: manifestYaml.project?.name || \"Unnamed Model\",\n description: manifestYaml.project?.description || \"\",\n version: manifestYaml.project?.version || manifestYaml.version || \"0.1.0\",\n specVersion: manifestYaml.spec_version || \"0.6.0\",\n created: manifestYaml.created || new Date().toISOString(),\n modified: manifestYaml.updated || new Date().toISOString(),\n };\n const manifest = new Manifest(manifestData);\n const model = new Model(projectRoot, manifest, options);\n\n // Load all available layers if lazyLoad is false\n if (!options.lazyLoad) {\n try {\n // If manifest has layer definitions, use those\n if (manifestYaml.layers) {\n for (const layerName of Object.keys(manifestYaml.layers)) {\n const layerConfig = manifestYaml.layers[layerName];\n if (layerConfig.enabled !== false) {\n if (!options.layers || options.layers.includes(layerName)) {\n await model.loadLayer(layerName);\n }\n }\n }\n } else {\n // Otherwise scan for layer directories\n const modelDir = manifestPath.replace(\"/manifest.yaml\", \"\");\n const entries = await fs.readdir(modelDir, { withFileTypes: true });\n\n for (const entry of entries) {\n if (entry.isDirectory() && entry.name.match(/^\\d{2}_/)) {\n const layerName = entry.name.replace(/^\\d{2}_/, \"\");\n if (!options.layers || options.layers.includes(layerName)) {\n await model.loadLayer(layerName);\n }\n }\n }\n }\n } catch (e) {\n // Check if this is a \"directory not found\" error (expected case)\n const isNotFoundError = (e as any)?.code === \"ENOENT\";\n if (!isNotFoundError) {\n // Re-throw non-ENOENT errors: permission errors, YAML parsing failures, I/O errors, etc.\n throw new Error(\n `Failed to load layers: ${e instanceof Error ? e.message : String(e)}`\n );\n }\n // ENOENT is expected if layer directory doesn't exist yet, so just continue\n }\n }\n\n // Load relationships from relationships.yaml\n await model.loadRelationships();\n\n // Check for active changeset and pre-load staged metadata for transparent projection.\n // This enables getLayer() to return projected views and getLayerNames() to include\n // layers that exist only in staged changes.\n const activePath = path.join(\n projectRoot,\n \"documentation-robotics\",\n \"changesets\",\n \".active\"\n );\n try {\n const activeContent = await fs.readFile(activePath, \"utf-8\");\n const activeId = activeContent.trim();\n if (activeId) {\n model._activeChangesetId = activeId;\n const storage = new StagedChangesetStorage(projectRoot);\n const changeset = await storage.load(activeId);\n if (changeset) {\n for (const change of changeset.changes as StagedChange[]) {\n // Track layer names for getLayerNames()\n if (\n change.type === \"add\" ||\n change.type === \"update\" ||\n change.type === \"delete\"\n ) {\n model._stagedLayerNames.add(change.layerName);\n }\n\n // Inject staged relationship-adds into model.relationships so that\n // read commands (list, show, export) transparently see staged relationships.\n if (change.type === \"relationship-add\" && change.after) {\n const rel = change.after as {\n source: string;\n target: string;\n predicate: string;\n layer: string;\n targetLayer?: string;\n category?: \"structural\" | \"behavioral\";\n properties?: Record<string, unknown>;\n };\n // Only inject if not already in relationships.yaml (prevents duplicates\n // if .active file is stale after a partial commit or manual edit).\n const alreadyPresent = model.relationships.find(\n rel.source,\n rel.target,\n rel.predicate\n );\n if (alreadyPresent.length === 0) {\n model.relationships.add({\n source: rel.source,\n target: rel.target,\n predicate: rel.predicate,\n layer: rel.layer,\n ...(rel.targetLayer ? { targetLayer: rel.targetLayer } : {}),\n category: rel.category ?? \"structural\",\n ...(rel.properties ? { properties: rel.properties } : {}),\n });\n }\n }\n\n // Remove staged relationship-deletes from model.relationships so that\n // read commands see the relationship as already deleted.\n if (change.type === \"relationship-delete\" && change.before) {\n const rel = change.before as {\n source: string;\n target: string;\n predicate?: string;\n };\n model.relationships.delete(rel.source, rel.target, rel.predicate);\n }\n }\n }\n }\n } catch {\n // No active changeset or unreadable \u2014 proceed with base model only\n model._activeChangesetId = null;\n }\n\n // Count total entities across all layers\n let entityCount = 0;\n for (const layer of model.layers.values()) {\n entityCount += layer.elements.size;\n }\n\n span.setAttribute(\"model.entity_count\", entityCount);\n span.setAttribute(\"model.layer_count\", model.layers.size);\n\n return model;\n }, {\n \"model.path\": startPath || process.cwd(),\n \"model.type\": \"dr\",\n });\n }\n\n /**\n * Initialize a new model in a directory\n */\n static async init(\n rootPath: string,\n manifestData: ManifestData,\n options: ModelOptions = {}\n ): Promise<Model> {\n // Create model directory structure\n await ensureDir(`${rootPath}/documentation-robotics/model`);\n\n for (let i = 0; i < CANONICAL_LAYER_NAMES.length; i++) {\n const orderNum = String(i + 1).padStart(2, \"0\");\n const layerName = CANONICAL_LAYER_NAMES[i];\n await ensureDir(`${rootPath}/documentation-robotics/model/${orderNum}_${layerName}`);\n }\n\n const manifest = new Manifest(manifestData);\n const model = new Model(rootPath, manifest, options);\n\n await model.saveManifest();\n\n return model;\n }\n\n /**\n * Graph-based API methods for querying the model\n * These methods delegate to the underlying GraphModel for efficient queries\n */\n\n /**\n * Get a node by its UUID\n */\n getNode(id: string) {\n return this.graph.getNode(id);\n }\n\n /**\n * Get all nodes in a specific layer\n */\n getNodesByLayer(layerId: string) {\n return this.graph.getNodesByLayer(layerId);\n }\n\n /**\n * Get all nodes of a specific type\n */\n getNodesByType(type: string) {\n return this.graph.getNodesByType(type);\n }\n\n /**\n * Get all edges (relationships) in the model\n */\n getAllEdges() {\n return this.graph.getAllEdges();\n }\n\n /**\n * Get edges originating from a specific node\n */\n getEdgesFrom(nodeId: string, predicate?: string) {\n return this.graph.getEdgesFrom(nodeId, predicate);\n }\n\n /**\n * Get edges terminating at a specific node\n */\n getEdgesTo(nodeId: string, predicate?: string) {\n return this.graph.getEdgesTo(nodeId, predicate);\n }\n\n /**\n * Get edges between two specific nodes\n */\n getEdgesBetween(sourceId: string, destinationId: string, predicate?: string) {\n return this.graph.getEdgesBetween(sourceId, destinationId, predicate);\n }\n\n /**\n * Traverse the graph starting from a node, following a specific predicate\n */\n async traverse(startNodeId: string, predicate: string, maxDepth: number = 10) {\n return this.graph.traverse(startNodeId, predicate, maxDepth);\n }\n\n /**\n * Create a backup of the current model state\n * Used for rollback support in migration operations\n *\n * @param label Descriptive label for the backup (e.g., \"pre-migration\")\n * @returns Path to the backup directory\n */\n async createBackup(label: string): Promise<string> {\n const timestamp = new Date().toISOString().replace(/[:.]/g, \"-\");\n const backupDir = path.join(this.rootPath, \".dr-backups\", `${label}-${timestamp}`);\n\n // Create backup directory\n await ensureDir(backupDir);\n\n // Backup layers directory\n const layersSource = path.join(this.rootPath, \"documentation-robotics\", \"model\");\n const layersBackup = path.join(backupDir, \"layers\");\n if (await this.directoryExists(layersSource)) {\n await this.copyDirectory(layersSource, layersBackup);\n }\n\n // Backup manifest\n const manifestSource = path.join(this.rootPath, \"documentation-robotics\", \"model\", \"manifest.yaml\");\n const manifestBackup = path.join(backupDir, \"manifest.yaml\");\n if (await this.fileExists(manifestSource)) {\n await fs.copyFile(manifestSource, manifestBackup);\n }\n\n return backupDir;\n }\n\n /**\n * Restore model from a backup directory\n * Used for rollback after failed migrations\n *\n * @param backupPath Path to the backup directory\n */\n async restoreFromBackup(backupPath: string): Promise<void> {\n // Restore layers\n const layersBackup = path.join(backupPath, \"layers\");\n const layersTarget = path.join(this.rootPath, \"documentation-robotics\", \"model\");\n if (await this.directoryExists(layersBackup)) {\n await this.copyDirectory(layersBackup, layersTarget);\n }\n\n // Restore manifest\n const manifestBackup = path.join(backupPath, \"manifest.yaml\");\n const manifestTarget = path.join(this.rootPath, \"documentation-robotics\", \"model\", \"manifest.yaml\");\n if (await this.fileExists(manifestBackup)) {\n await fs.copyFile(manifestBackup, manifestTarget);\n }\n\n // Reload model to refresh in-memory state\n const reloadedModel = await Model.load(this.rootPath, { lazyLoad: this.lazyLoad });\n this.layers = reloadedModel.layers;\n this.manifest = reloadedModel.manifest;\n this.graph = reloadedModel.graph;\n this.relationships = reloadedModel.relationships;\n }\n\n /**\n * Save dirty layers with atomic write semantics\n * Writes to temporary file first, then renames on success to ensure data safety\n *\n * @throws Error if atomic write fails\n */\n async saveDirtyLayersAtomic(): Promise<void> {\n // First, save all layers to temporary files\n const tempLayerWrites: Array<{ layer: Layer; tempPath: string }> = [];\n\n try {\n for (const layer of this.layers.values()) {\n if (layer.isDirty()) {\n const layerPath = path.join(\n this.rootPath,\n \"documentation-robotics\",\n \"model\",\n `${layer.name}_layer`\n );\n\n const tempPath = `${layerPath}.tmp`;\n await ensureDir(tempPath);\n\n // Write layer elements to temp directory\n for (const element of layer.elements.values()) {\n const elementPath = path.join(tempPath, `${element.path || element.id}.json`);\n const content = JSON.stringify(element.toJSON(), null, 2);\n await writeFile(elementPath, content);\n }\n\n tempLayerWrites.push({ layer, tempPath });\n }\n }\n\n // All temp writes succeeded, now commit by renaming\n for (const { layer, tempPath } of tempLayerWrites) {\n const layerPath = path.join(\n this.rootPath,\n \"documentation-robotics\",\n \"model\",\n `${layer.name}_layer`\n );\n\n // Remove old directory and rename temp to actual\n if (await this.directoryExists(layerPath)) {\n await fs.rm(layerPath, { recursive: true, force: true });\n }\n await fs.rename(tempPath, layerPath);\n }\n } catch (error) {\n // Cleanup any temp directories on failure\n for (const { tempPath } of tempLayerWrites) {\n if (await this.directoryExists(tempPath)) {\n await fs.rm(tempPath, { recursive: true, force: true });\n }\n }\n throw error;\n }\n }\n\n /**\n * Helper: Check if file exists\n */\n private async fileExists(filePath: string): Promise<boolean> {\n try {\n await fs.access(filePath);\n return true;\n } catch {\n return false;\n }\n }\n\n /**\n * Helper: Check if directory exists\n */\n private async directoryExists(dirPath: string): Promise<boolean> {\n try {\n const stat = await fs.stat(dirPath);\n return stat.isDirectory();\n } catch {\n return false;\n }\n }\n\n /**\n * Helper: Recursively copy directory\n */\n private async copyDirectory(src: string, dest: string): Promise<void> {\n await ensureDir(dest);\n const entries = await fs.readdir(src, { withFileTypes: true });\n\n for (const entry of entries) {\n const srcPath = path.join(src, entry.name);\n const destPath = path.join(dest, entry.name);\n\n if (entry.isDirectory()) {\n await this.copyDirectory(srcPath, destPath);\n } else {\n await fs.copyFile(srcPath, destPath);\n }\n }\n }\n}\n"],
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+ "sourcesContent": ["import { Layer } from \"./layer.js\";\nimport { Manifest } from \"./manifest.js\";\nimport { Element } from \"./element.js\";\nimport { GraphModel, type GraphEdge } from \"./graph-model.js\";\nimport { VirtualProjectionEngine } from \"./virtual-projection.js\";\nimport { StagedChangesetStorage } from \"./staged-changeset-storage.js\";\nimport { Relationships } from \"./relationships.js\";\nimport { CANONICAL_LAYER_NAMES } from \"./layers.js\";\nimport type { StagedChange } from \"./changeset.js\";\nimport { ensureDir, writeFile } from \"../utils/file-io.js\";\nimport { getCliVersion } from \"../utils/spec-version.js\";\nimport { startSpan, endSpan, startActiveSpan } from \"../telemetry/index.js\";\nimport { findProjectRoot } from \"../utils/project-paths.js\";\nimport { getNodeType } from \"../generated/node-types.js\";\nimport type { SpecNodeId } from \"../generated/node-types.js\";\nimport type { ManifestData, ModelOptions } from \"../types/index.js\";\nimport path from \"node:path\";\nimport fs from \"node:fs/promises\";\nimport crypto from \"node:crypto\";\n\n/**\n * Derive a deterministic UUID from a path string using SHA-256.\n * Produces a stable UUID4-like value so migration doesn't regenerate UUIDs on every load.\n */\nfunction deterministicUUID(path: string): string {\n const hash = crypto.createHash(\"sha256\").update(path).digest(\"hex\");\n return [\n hash.slice(0, 8),\n hash.slice(8, 12),\n \"4\" + hash.slice(13, 16), // version 4 marker\n ((parseInt(hash.slice(16, 18), 16) & 0x3f) | 0x80).toString(16) + hash.slice(18, 20), // variant\n hash.slice(20, 32),\n ].join(\"-\");\n}\n\n/**\n * Convert a PascalCase title to snake_case.\n * Handles acronyms correctly: \"UXApplication\" \u2192 \"ux_application\", \"OpenAPIDocument\" \u2192 \"open_api_document\".\n */\nfunction titleToSnakeCase(title: string): string {\n return title\n .replace(/([A-Z]+)([A-Z][a-z])/g, \"$1_$2\") // \"APIDoc\" \u2192 \"API_Doc\"\n .replace(/([a-z\\d])([A-Z])/g, \"$1_$2\") // \"appComponent\" \u2192 \"app_Component\"\n .toLowerCase();\n}\n\n/**\n * Derive a snake_case file stem for a given element type.\n * Uses the spec node title for accurate word boundaries (e.g., \"InputSpacePartition\" \u2192 \"input_space_partition\").\n * Falls back to the raw type string when the title is unavailable.\n */\nfunction typeToSnakeStem(specNodeId: string | undefined, type: string): string {\n if (specNodeId) {\n const nodeType = getNodeType(specNodeId as SpecNodeId);\n if (nodeType?.title) {\n return titleToSnakeCase(nodeType.title);\n }\n }\n return type;\n}\n\n/**\n * Graph-internal bookkeeping keys that `layer.ts`'s node<->Element conversion stuffs into the\n * same flat `attributes`/`properties` bag the underlying graph structure uses for everything\n * (it has no separate channel for them) \u2014 `__references__`/`__relationships__` mirror\n * `element.references`/`element.relationships`, which are real, separately-typed fields on\n * `Element` and get serialized to their own place (references inline, relationships to\n * relationships.yaml). These must never reach the 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 either\n * name. Contrast with the *type-blind* set this replaced, which also unconditionally stripped\n * plain `\"source\"`/`\"x-source-reference\"` \u2014 both of which ARE legitimate, sometimes-required\n * domain attributes on 41 node schemas across 8 layers (e.g. security.accesscondition.source),\n * and neither of which is ever actually used as internal bookkeeping anywhere in this codebase.\n * That collision silently destroyed real data on every save for any element of one of those 41\n * types, without ever failing validation (validation runs on the in-memory element, before this\n * stripping) \u2014 see CHANGELOG for the incident this fixes.\n */\nconst ALWAYS_INTERNAL_ATTRIBUTE_KEYS = new Set([\"__references__\", \"__relationships__\"]);\n\n/**\n * Whether `key` should survive persistence in `specNodeId`'s `attributes`.\n *\n * Only ever strips the two confirmed-always-internal keys above, and even then only when the\n * node type's OWN schema doesn't declare that name as a real attribute \u2014 so if some future\n * schema ever legitimately needs an attribute literally called `__references__` (unlikely, but\n * the whole point of this function is to not have to trust \"unlikely\" again), it still survives.\n * Nothing else is ever stripped: the class of bug this fixes was a hardcoded, type-blind\n * reserved-word blocklist making that same \"trust the list, not the schema\" mistake for\n * `source`/`x-source-reference`. Consulting the schema instead of a fixed string list is what\n * keeps this from silently recurring for some other attribute name in the future.\n */\nfunction isPersistableAttribute(specNodeId: string | undefined, key: string): boolean {\n if (!ALWAYS_INTERNAL_ATTRIBUTE_KEYS.has(key)) return true;\n if (!specNodeId) return false;\n const nodeType = getNodeType(specNodeId as SpecNodeId);\n if (!nodeType) return false;\n return nodeType.requiredAttributes.includes(key) || nodeType.optionalAttributes.includes(key);\n}\n\n// Fallback for runtime environments where TELEMETRY_ENABLED is not defined by esbuild\ndeclare const TELEMETRY_ENABLED: boolean | undefined;\nconst isTelemetryEnabled = typeof TELEMETRY_ENABLED !== \"undefined\" ? TELEMETRY_ENABLED : false;\n\n/**\n * Model class representing the complete architecture model\n * Uses GraphModel internally for graph-based storage\n */\nexport class Model {\n rootPath: string;\n manifest: Manifest;\n graph: GraphModel;\n layers: Map<string, Layer>;\n relationships: Relationships;\n lazyLoad: boolean;\n private loadedLayers: Set<string>;\n private virtualProjectionEngine?: VirtualProjectionEngine;\n /** ID of the currently active changeset, or null if none is active. Set during load(). */\n private _activeChangesetId: string | null = null;\n /** Layer names that exist only in staged changes (not yet committed to base model). */\n private _stagedLayerNames: Set<string> = new Set();\n\n constructor(rootPath: string, manifest: Manifest, options: ModelOptions = {}) {\n this.rootPath = rootPath;\n this.manifest = manifest;\n this.graph = new GraphModel();\n this.layers = new Map();\n this.relationships = new Relationships();\n this.lazyLoad = options.lazyLoad ?? false;\n this.loadedLayers = new Set();\n }\n\n /**\n * Get the committed base layer (no staging projection).\n * Used internally by VirtualProjectionEngine and commit() to access the raw base model\n * without triggering infinite recursion or double-projection.\n */\n async getBaseLayer(name: string): Promise<Layer | undefined> {\n if (this.lazyLoad && !this.loadedLayers.has(name)) {\n await this.loadLayer(name);\n }\n return this.layers.get(name);\n }\n\n /**\n * Get a layer, transparently merging staged changes when an active changeset exists.\n * Falls back to the committed base layer if no changeset is active or projection fails.\n */\n async getLayer(name: string): Promise<Layer | undefined> {\n if (this.lazyLoad && !this.loadedLayers.has(name)) {\n await this.loadLayer(name);\n }\n\n // If an active changeset is present, return a projected (base + staged) layer\n if (this._activeChangesetId) {\n try {\n return await this.getVirtualProjectionEngine().projectLayer(\n this,\n this._activeChangesetId,\n name\n );\n } catch {\n // Fall back to base layer on projection failure (e.g. corrupt changeset)\n return this.layers.get(name);\n }\n }\n\n return this.layers.get(name);\n }\n\n /**\n * Get an element by ID across all layers\n * Supports both UUID and semantic ID (layer.type.kebab-name) lookup\n */\n getElementById(id: string): Element | undefined {\n for (const layer of this.layers.values()) {\n const element = layer.getElement(id);\n if (element) {\n return element;\n }\n }\n return undefined;\n }\n\n /**\n * Get virtual projection engine (lazily initialized)\n */\n getVirtualProjectionEngine(): VirtualProjectionEngine {\n if (!this.virtualProjectionEngine) {\n this.virtualProjectionEngine = new VirtualProjectionEngine(this.rootPath);\n }\n return this.virtualProjectionEngine;\n }\n\n /**\n * Returns the active changeset ID, or null if no changeset is active.\n * Used by commands that need to project the full model (e.g. validate).\n */\n getActiveChangesetId(): string | null {\n return this._activeChangesetId;\n }\n\n /**\n * Load a layer from disk (model/XX_layername/*.yaml files)\n */\n async loadLayer(name: string): Promise<void> {\n await startActiveSpan(\"layer.load\", async (layerSpan) => {\n const fs = await import(\"fs/promises\");\n const yaml = await import(\"yaml\");\n\n let layerPath: string | null = null;\n\n // Auto-discover by scanning directory with naming convention\n const modelDir = `${this.rootPath}/documentation-robotics/model`;\n\n try {\n const entries = await fs.readdir(modelDir, { withFileTypes: true });\n const layerDir = entries.find(\n (e) =>\n e.isDirectory() && e.name.match(/^\\d{2}_/) && e.name.replace(/^\\d{2}_/, \"\") === name\n );\n\n if (layerDir) {\n layerPath = `${modelDir}/${layerDir.name}`;\n }\n } catch {\n // Model directory doesn't exist or can't be read\n }\n\n if (!layerPath) {\n return; // Layer directory not found\n }\n\n const layer = new Layer(name, this.graph);\n let parseErrorCount = 0;\n\n // Load all YAML files in the layer directory\n const files = await fs.readdir(layerPath);\n for (const file of files) {\n if (file.endsWith(\".yaml\") || file.endsWith(\".yml\")) {\n const filePath = `${layerPath}/${file}`;\n try {\n const yamlContent = await fs.readFile(filePath, \"utf-8\");\n const elements = yaml.parse(yamlContent);\n\n // Add each element from the YAML file\n if (elements && typeof elements === \"object\") {\n for (const [key, element] of Object.entries(elements)) {\n if (element && typeof element === \"object\") {\n const el: any = element;\n\n // Derive id, path, and type using the 3-case migration logic:\n // Case 1: element already has both id (UUID) and path \u2192 use as-is\n // Case 2: element.id looks like a slug (layer.type.name) \u2192 move to path, generate UUID\n // Case 3: element has UUID id but no path \u2192 derive path from layer_id.type.kebab(name)\n const isSlugPattern = /^[a-z][a-z0-9-]*\\.[a-z][a-z0-9-]*\\.[a-z][a-z0-9-]*$/.test(el.id || \"\");\n const isUUIDPattern = /^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$/i.test(el.id || \"\");\n\n let elementId: string;\n let elementPath: string;\n let extractedType: string | undefined = undefined;\n\n if (el.path && isUUIDPattern) {\n // Case 1: already has both path and UUID id\n elementId = el.id;\n elementPath = el.path;\n const pathParts = el.path.split(\".\");\n if (pathParts.length >= 3) extractedType = pathParts[1];\n } else if (el.path && !isUUIDPattern) {\n // Has a path but id is not a UUID \u2014 migrate id to deterministic UUID\n elementPath = el.path;\n elementId = deterministicUUID(el.path);\n const pathParts = el.path.split(\".\");\n if (pathParts.length >= 3) extractedType = pathParts[1];\n } else if (isSlugPattern) {\n // Case 2: slug-looking id \u2192 move to path, generate deterministic UUID\n elementPath = el.id;\n elementId = deterministicUUID(el.id);\n const parts = el.id.split(\".\");\n if (parts.length >= 3) extractedType = parts[1];\n } else if (isUUIDPattern) {\n // Case 3: UUID id, no path \u2192 derive path\n elementId = el.id;\n const layerId = el.layer_id || name;\n const rawType = el.type || \"\";\n const rawName = el.name || key;\n const kebabName = rawName.toLowerCase().replace(/[\\s_]+/g, \"-\").replace(/[^a-z0-9-]/g, \"\").replace(/-+/g, \"-\").replace(/^-+|-+$/g, \"\");\n elementPath = `${layerId}.${rawType}.${kebabName}`;\n extractedType = rawType || undefined;\n } else {\n // Fallback: derive a path from available data, generate deterministic UUID\n const layerId = el.layer_id || name;\n const rawType = el.type || (typeof el.id === \"string\" && el.id.includes(\".\") ? el.id.split(\".\")[1] : \"\") || \"\";\n const rawName = el.name || key;\n const kebabName = rawName.toLowerCase().replace(/[\\s_]+/g, \"-\").replace(/[^a-z0-9-]/g, \"\").replace(/-+/g, \"-\").replace(/^-+|-+$/g, \"\") || \"unknown\";\n elementPath = `${layerId}.${rawType || \"element\"}.${kebabName}`;\n elementId = deterministicUUID(elementPath);\n if (rawType) extractedType = rawType;\n else if (typeof el.id === \"string\" && el.id.includes(\".\")) {\n const parts = el.id.split(\".\");\n if (parts.length >= 3) extractedType = parts[1];\n }\n }\n\n const elementName = el.name || key;\n const elementType = el.type || extractedType;\n const layerId = el.layer_id || name;\n\n const newElement = new Element({\n id: elementId,\n path: elementPath,\n spec_node_id: el.spec_node_id,\n layer_id: layerId,\n attributes: el.attributes,\n source_reference: el.source_reference,\n metadata: el.metadata,\n name: elementName,\n type: elementType,\n description: el.description || \"\",\n relationships: el.relationships || [],\n references: el.references || [],\n layer: layerId,\n } as any);\n layer.addElement(newElement);\n }\n }\n }\n } catch (fileError) {\n // Log YAML parsing errors but continue loading other files\n const errorMsg = fileError instanceof Error ? fileError.message : String(fileError);\n console.error(`Warning: Failed to parse ${filePath}: ${errorMsg}`);\n parseErrorCount++;\n // Continue with next file\n }\n }\n }\n\n // If we had parse errors, add a note to the layer\n if (parseErrorCount > 0) {\n console.error(\n `Warning: Layer '${name}' loaded with ${parseErrorCount} YAML parse error(s)`\n );\n }\n\n this.layers.set(name, layer);\n this.loadedLayers.add(name);\n\n layerSpan.setAttribute(\"layer.element_count\", layer.elements.size);\n }, { \"layer.name\": name });\n }\n\n /**\n * Add a layer to the model\n */\n addLayer(layer: Layer): void {\n // If the layer has elements in its isolated graph, migrate them to the model's graph\n if (layer.graph.getNodeCount() > 0) {\n for (const node of layer.graph.nodes.values()) {\n this.graph.addNode(node);\n }\n for (const edge of layer.graph.edges.values()) {\n this.graph.addEdge(edge);\n }\n }\n // Ensure layer uses the model's graph for future operations\n layer.graph = this.graph;\n this.layers.set(layer.name, layer);\n this.loadedLayers.add(layer.name);\n }\n\n /**\n * Get all layer names, including layers that exist only in staged changes.\n * When an active changeset introduces elements for a layer with no committed data,\n * that layer name is included so findElementLayer() and other callers can discover it.\n */\n getLayerNames(): string[] {\n const base = Array.from(this.layers.keys());\n if (this._stagedLayerNames.size === 0) {\n return base;\n }\n // Include staged-only layers (layers that have staged elements but no committed elements)\n const staged = Array.from(this._stagedLayerNames).filter((l) => !this.layers.has(l));\n return [...base, ...staged];\n }\n\n /**\n * Save a layer to disk (model/XX_layername/*.yaml)\n */\n async saveLayer(name: string): Promise<void> {\n const layer = this.layers.get(name);\n if (!layer) {\n throw new Error(`Layer ${name} not found`);\n }\n\n const fs = await import(\"fs/promises\");\n const yaml = await import(\"yaml\");\n\n let layerPath: string | null = null;\n\n // Discover by scanning directory\n const modelDir = `${this.rootPath}/documentation-robotics/model`;\n\n try {\n const entries = await fs.readdir(modelDir, { withFileTypes: true });\n const layerDir = entries.find(\n (e) =>\n e.isDirectory() && e.name.match(/^\\d{2}_/) && e.name.replace(/^\\d{2}_/, \"\") === name\n );\n\n if (layerDir) {\n layerPath = `${modelDir}/${layerDir.name}`;\n }\n } catch {\n // Model directory doesn't exist or can't be read\n }\n\n // If still not found, create using default format\n if (!layerPath) {\n // Find the order number for this layer\n // Handle layer names with or without numeric prefix (e.g., \"motivation\" or \"01-motivation\")\n const layerNameWithoutPrefix = name.replace(/^\\d{2}-/, \"\");\n const index = CANONICAL_LAYER_NAMES.indexOf(layerNameWithoutPrefix as typeof CANONICAL_LAYER_NAMES[number]);\n if (index >= 0) {\n const orderNum = String(index + 1).padStart(2, \"0\");\n layerPath = `${this.rootPath}/documentation-robotics/model/${orderNum}_${layerNameWithoutPrefix}`;\n await ensureDir(layerPath);\n } else {\n throw new Error(`Unknown layer ${name} and no path configured in manifest`);\n }\n }\n\n // Delete all existing YAML files in the layer directory to ensure\n // we don't keep stale files after element deletion\n try {\n const existingFiles = await fs.readdir(layerPath);\n for (const file of existingFiles) {\n if (file.endsWith(\".yaml\") || file.endsWith(\".yml\")) {\n await fs.unlink(`${layerPath}/${file}`);\n }\n }\n } catch (err) {\n // Only ignore \"directory not found\" errors \u2014 re-throw permission/I/O errors\n const isNotFoundError = (err as any)?.code === \"ENOENT\";\n if (!isNotFoundError) {\n throw new Error(\n `Failed to clean existing YAML files: ${err instanceof Error ? err.message : String(err)}`\n );\n }\n }\n\n // Group elements by type, computing the snake_case file stem from the spec node title\n const elementsByType = new Map<string, { stem: string; elements: Element[] }>();\n for (const element of layer.elements.values()) {\n const typeKey = element.type;\n if (!elementsByType.has(typeKey)) {\n const stem = typeToSnakeStem(element.spec_node_id, element.type);\n elementsByType.set(typeKey, { stem, elements: [] });\n }\n elementsByType.get(typeKey)!.elements.push(element);\n }\n\n // Write each type to its own YAML file\n for (const [, { stem, elements }] of elementsByType) {\n const filename = `${stem}.yaml`;\n const filePath = `${layerPath}/${filename}`;\n\n // Convert elements to spec-node format YAML\n const yamlData: any = {};\n for (const element of elements) {\n const json = element.toJSON();\n\n // Clean attributes: remove graph-internal keys that should not be persisted \u2014 see\n // isPersistableAttribute's own doc for why this checks the schema rather than a\n // hardcoded name list.\n const cleanAttrs = json.attributes\n ? Object.fromEntries(\n Object.entries(json.attributes).filter(([k]) =>\n isPersistableAttribute(json.spec_node_id, k)\n )\n )\n : undefined;\n\n // Use path as YAML key (human-readable); fall back to id for elements without path\n const key = element.path || element.id;\n yamlData[key] = {\n id: json.id,\n path: json.path,\n spec_node_id: json.spec_node_id,\n type: json.type,\n layer_id: json.layer_id,\n name: json.name,\n ...(json.description && { description: json.description }),\n ...(cleanAttrs && Object.keys(cleanAttrs).length > 0 && { attributes: cleanAttrs }),\n ...(json.source_reference && { source_reference: json.source_reference }),\n ...(json.metadata && { metadata: json.metadata }),\n ...(json.references && json.references.length > 0 && { references: json.references }),\n // Relationships are now stored in centralized relationships.yaml, not inline\n };\n }\n\n await writeFile(filePath, yaml.stringify(yamlData));\n }\n\n layer.markClean();\n }\n\n /**\n * Save model (saves all dirty layers and manifest)\n */\n async save(): Promise<void> {\n await this.saveDirtyLayers();\n await this.saveManifest();\n }\n\n /**\n * Save all dirty layers to disk\n */\n async saveDirtyLayers(): Promise<void> {\n // Count dirty layers before operation\n let dirtyLayerCount = 0;\n for (const layer of this.layers.values()) {\n if (layer.isDirty()) {\n dirtyLayerCount++;\n }\n }\n\n const span = isTelemetryEnabled\n ? startSpan(\"model.save\", {\n \"model.path\": this.rootPath,\n \"model.dirty_layer_count\": dirtyLayerCount,\n })\n : null;\n\n try {\n for (const layer of this.layers.values()) {\n if (layer.isDirty()) {\n await this.saveLayer(layer.name);\n }\n }\n } finally {\n if (isTelemetryEnabled) {\n endSpan(span);\n }\n }\n }\n\n /**\n * Save the manifest to disk (documentation-robotics/model/manifest.yaml)\n */\n async saveManifest(): Promise<void> {\n this.manifest.updateModified();\n const yaml = await import(\"yaml\");\n const manifestPath = `${this.rootPath}/documentation-robotics/model/manifest.yaml`;\n\n // Convert to YAML format\n const yamlData: any = {\n version: this.manifest.version,\n schema: \"documentation-robotics-v1\",\n cli_version: getCliVersion(),\n spec_version: this.manifest.specVersion,\n created: this.manifest.created,\n updated: this.manifest.modified,\n project: {\n name: this.manifest.name,\n description: this.manifest.description,\n version: this.manifest.version,\n },\n documentation: \".dr/README.md\",\n layers: {},\n };\n\n // Generate layer structure from current model state\n for (let i = 0; i < CANONICAL_LAYER_NAMES.length; i++) {\n const layerName = CANONICAL_LAYER_NAMES[i];\n const layer = this.layers.get(layerName);\n const orderNum = String(i + 1).padStart(2, \"0\");\n\n yamlData.layers[layerName] = {\n order: i + 1,\n name: layerName.charAt(0).toUpperCase() + layerName.slice(1).replace(\"-\", \" \"),\n path: `documentation-robotics/model/${orderNum}_${layerName}/`,\n enabled: true,\n ...(layer && { elements: this.getLayerElementCounts(layer) }),\n };\n }\n\n if (this.manifest.changeset_history && this.manifest.changeset_history.length > 0) {\n yamlData.changeset_history = this.manifest.changeset_history;\n }\n\n await ensureDir(`${this.rootPath}/documentation-robotics/model`);\n await writeFile(manifestPath, yaml.stringify(yamlData));\n }\n\n private getLayerElementCounts(layer: Layer): Record<string, number> {\n const counts: Record<string, number> = {};\n for (const element of layer.elements.values()) {\n counts[element.type] = (counts[element.type] || 0) + 1;\n }\n return counts;\n }\n\n /**\n * Load relationships from relationships.yaml\n */\n async loadRelationships(): Promise<void> {\n const fs = await import(\"fs/promises\");\n const yaml = await import(\"yaml\");\n const relationshipsPath = `${this.rootPath}/documentation-robotics/model/relationships.yaml`;\n\n let data: any;\n try {\n const yamlContent = await fs.readFile(relationshipsPath, \"utf-8\");\n data = yaml.parse(yamlContent);\n } catch (err) {\n // If file doesn't exist, that's okay - start with empty relationships\n if ((err as any).code !== \"ENOENT\") {\n // But if it's a different error (YAML parse, permission denied, etc), throw it\n // so the caller knows about the issue\n throw new Error(\n `Failed to load relationships.yaml: ${err instanceof Error ? err.message : String(err)}`\n );\n }\n // ENOENT: file doesn't exist, return with empty relationships\n return;\n }\n\n // Validate that parsed content is an array\n if (!Array.isArray(data)) {\n const typeLabel = data === null ? \"null\" : typeof data;\n console.warn(\n `Warning: relationships.yaml contains non-array content (received ${typeLabel}). Expected an array of relationships. Skipping relationship loading.`\n );\n return;\n }\n\n this.relationships = Relationships.fromArray(data);\n // Sync relationships to graph as a secondary in-memory index.\n // addEdge() may throw if nodes from other layers haven't been loaded yet;\n // failures are silently skipped \u2014 this.relationships holds the primary data.\n for (let i = 0; i < data.length; i++) {\n const rel = data[i];\n const edge: GraphEdge = {\n id: `rel-${i}-${crypto.randomBytes(4).toString(\"hex\")}`,\n source: rel.source,\n destination: rel.target,\n predicate: rel.predicate,\n properties: rel.properties,\n category: rel.category,\n };\n try {\n this.graph.addEdge(edge);\n } catch {\n // Silently skip edges whose nodes haven't been loaded yet.\n // The primary relationship data lives in this.relationships; the graph\n // is a secondary index. Cross-layer relationships referencing nodes from\n // unloaded layers are expected during partial model construction.\n }\n }\n }\n\n /**\n * Save relationships to relationships.yaml\n */\n async saveRelationships(): Promise<void> {\n const fs = await import(\"fs/promises\");\n const yaml = await import(\"yaml\");\n const relationshipsPath = `${this.rootPath}/documentation-robotics/model/relationships.yaml`;\n\n await ensureDir(`${this.rootPath}/documentation-robotics/model`);\n\n const data = this.relationships.toArray();\n\n // Add header comment with timestamp to ensure file always changes\n const timestamp = new Date().toISOString();\n const header = `# Intra-layer relationships\n# Format: source_id -> predicate -> target_id\n# Last updated: ${timestamp}\n\n`;\n const yamlContent = header + yaml.stringify(data);\n\n await fs.writeFile(relationshipsPath, yamlContent, \"utf-8\");\n this.relationships.markClean();\n }\n\n /**\n * Resolve model paths (private helper)\n *\n * @param startPath - Starting path for search\n * @returns Project root and manifest path\n */\n private static async resolveModelPaths(startPath?: string): Promise<{\n projectRoot: string;\n manifestPath: string;\n }> {\n const searchPath = startPath || process.cwd();\n\n // Optional override via env var (highest priority)\n if (process.env.DR_MODEL_PATH) {\n const envPath = path.resolve(process.env.DR_MODEL_PATH);\n let manifestPath: string;\n\n if (envPath.endsWith(\"manifest.yaml\")) {\n manifestPath = envPath;\n } else if (envPath.endsWith(\"model\")) {\n manifestPath = path.join(envPath, \"manifest.yaml\");\n } else {\n manifestPath = path.join(envPath, \"documentation-robotics\", \"model\", \"manifest.yaml\");\n }\n\n try {\n await fs.access(manifestPath);\n const projectRoot = path.dirname(path.dirname(path.dirname(manifestPath)));\n return { projectRoot, manifestPath: path.normalize(manifestPath) };\n } catch {\n throw new Error(`Model not found at DR_MODEL_PATH: ${process.env.DR_MODEL_PATH}`);\n }\n }\n\n // Use findProjectRoot to locate documentation_robotics/ folder\n const projectRoot = await findProjectRoot(searchPath);\n\n if (!projectRoot) {\n throw new Error(\n \"No DR project found. Could not find documentation_robotics/ folder.\\n\" +\n 'Run \"dr init\" to create a new project, or navigate to a directory containing a DR project.'\n );\n }\n\n const manifestPath = path.join(projectRoot, \"documentation-robotics\", \"model\", \"manifest.yaml\");\n\n try {\n await fs.access(manifestPath);\n return { projectRoot, manifestPath };\n } catch {\n throw new Error(\n `Found documentation_robotics/ at ${projectRoot} but no model found. ` +\n `Expected: ${manifestPath}\\n` +\n `Run \"dr init\" to create a model.`\n );\n }\n }\n\n /**\n * Load a model from disk\n *\n * Expected structure:\n * <project-root>/\n * \u2514\u2500\u2500 documentation_robotics/\n * \u2514\u2500\u2500 model/\n * \u2514\u2500\u2500 manifest.yaml\n *\n * @param startPath - Starting path for project search (defaults to process.cwd())\n * @param options - Model loading options\n * @returns Loaded Model instance\n */\n static async load(startPath?: string, options: ModelOptions = {}): Promise<Model> {\n return startActiveSpan(\"model.load\", async (span) => {\n // Resolve project root and manifest path\n const { projectRoot, manifestPath } = await Model.resolveModelPaths(startPath);\n\n const yaml = await import(\"yaml\");\n\n // Load manifest from resolved path\n const yamlContent = await fs.readFile(manifestPath, \"utf-8\");\n const manifestYaml = yaml.parse(yamlContent);\n\n // Convert manifest to internal format\n const manifestData: any = {\n name: manifestYaml.project?.name || \"Unnamed Model\",\n description: manifestYaml.project?.description || \"\",\n version: manifestYaml.project?.version || manifestYaml.version || \"0.1.0\",\n specVersion: manifestYaml.spec_version || \"0.6.0\",\n created: manifestYaml.created || new Date().toISOString(),\n modified: manifestYaml.updated || new Date().toISOString(),\n };\n const manifest = new Manifest(manifestData);\n const model = new Model(projectRoot, manifest, options);\n\n // Load all available layers if lazyLoad is false\n if (!options.lazyLoad) {\n try {\n // If manifest has layer definitions, use those\n if (manifestYaml.layers) {\n for (const layerName of Object.keys(manifestYaml.layers)) {\n const layerConfig = manifestYaml.layers[layerName];\n if (layerConfig.enabled !== false) {\n if (!options.layers || options.layers.includes(layerName)) {\n await model.loadLayer(layerName);\n }\n }\n }\n } else {\n // Otherwise scan for layer directories\n const modelDir = manifestPath.replace(\"/manifest.yaml\", \"\");\n const entries = await fs.readdir(modelDir, { withFileTypes: true });\n\n for (const entry of entries) {\n if (entry.isDirectory() && entry.name.match(/^\\d{2}_/)) {\n const layerName = entry.name.replace(/^\\d{2}_/, \"\");\n if (!options.layers || options.layers.includes(layerName)) {\n await model.loadLayer(layerName);\n }\n }\n }\n }\n } catch (e) {\n // Check if this is a \"directory not found\" error (expected case)\n const isNotFoundError = (e as any)?.code === \"ENOENT\";\n if (!isNotFoundError) {\n // Re-throw non-ENOENT errors: permission errors, YAML parsing failures, I/O errors, etc.\n throw new Error(\n `Failed to load layers: ${e instanceof Error ? e.message : String(e)}`\n );\n }\n // ENOENT is expected if layer directory doesn't exist yet, so just continue\n }\n }\n\n // Load relationships from relationships.yaml\n await model.loadRelationships();\n\n // Check for active changeset and pre-load staged metadata for transparent projection.\n // This enables getLayer() to return projected views and getLayerNames() to include\n // layers that exist only in staged changes.\n const activePath = path.join(\n projectRoot,\n \"documentation-robotics\",\n \"changesets\",\n \".active\"\n );\n try {\n const activeContent = await fs.readFile(activePath, \"utf-8\");\n const activeId = activeContent.trim();\n if (activeId) {\n model._activeChangesetId = activeId;\n const storage = new StagedChangesetStorage(projectRoot);\n const changeset = await storage.load(activeId);\n if (changeset) {\n for (const change of changeset.changes as StagedChange[]) {\n // Track layer names for getLayerNames()\n if (\n change.type === \"add\" ||\n change.type === \"update\" ||\n change.type === \"delete\"\n ) {\n model._stagedLayerNames.add(change.layerName);\n }\n\n // Inject staged relationship-adds into model.relationships so that\n // read commands (list, show, export) transparently see staged relationships.\n if (change.type === \"relationship-add\" && change.after) {\n const rel = change.after as {\n source: string;\n target: string;\n predicate: string;\n layer: string;\n targetLayer?: string;\n category?: \"structural\" | \"behavioral\";\n properties?: Record<string, unknown>;\n };\n // Only inject if not already in relationships.yaml (prevents duplicates\n // if .active file is stale after a partial commit or manual edit).\n const alreadyPresent = model.relationships.find(\n rel.source,\n rel.target,\n rel.predicate\n );\n if (alreadyPresent.length === 0) {\n model.relationships.add({\n source: rel.source,\n target: rel.target,\n predicate: rel.predicate,\n layer: rel.layer,\n ...(rel.targetLayer ? { targetLayer: rel.targetLayer } : {}),\n category: rel.category ?? \"structural\",\n ...(rel.properties ? { properties: rel.properties } : {}),\n });\n }\n }\n\n // Remove staged relationship-deletes from model.relationships so that\n // read commands see the relationship as already deleted.\n if (change.type === \"relationship-delete\" && change.before) {\n const rel = change.before as {\n source: string;\n target: string;\n predicate?: string;\n };\n model.relationships.delete(rel.source, rel.target, rel.predicate);\n }\n }\n }\n }\n } catch {\n // No active changeset or unreadable \u2014 proceed with base model only\n model._activeChangesetId = null;\n }\n\n // Count total entities across all layers\n let entityCount = 0;\n for (const layer of model.layers.values()) {\n entityCount += layer.elements.size;\n }\n\n span.setAttribute(\"model.entity_count\", entityCount);\n span.setAttribute(\"model.layer_count\", model.layers.size);\n\n return model;\n }, {\n \"model.path\": startPath || process.cwd(),\n \"model.type\": \"dr\",\n });\n }\n\n /**\n * Initialize a new model in a directory\n */\n static async init(\n rootPath: string,\n manifestData: ManifestData,\n options: ModelOptions = {}\n ): Promise<Model> {\n // Create model directory structure\n await ensureDir(`${rootPath}/documentation-robotics/model`);\n\n for (let i = 0; i < CANONICAL_LAYER_NAMES.length; i++) {\n const orderNum = String(i + 1).padStart(2, \"0\");\n const layerName = CANONICAL_LAYER_NAMES[i];\n await ensureDir(`${rootPath}/documentation-robotics/model/${orderNum}_${layerName}`);\n }\n\n const manifest = new Manifest(manifestData);\n const model = new Model(rootPath, manifest, options);\n\n await model.saveManifest();\n\n return model;\n }\n\n /**\n * Graph-based API methods for querying the model\n * These methods delegate to the underlying GraphModel for efficient queries\n */\n\n /**\n * Get a node by its UUID\n */\n getNode(id: string) {\n return this.graph.getNode(id);\n }\n\n /**\n * Get all nodes in a specific layer\n */\n getNodesByLayer(layerId: string) {\n return this.graph.getNodesByLayer(layerId);\n }\n\n /**\n * Get all nodes of a specific type\n */\n getNodesByType(type: string) {\n return this.graph.getNodesByType(type);\n }\n\n /**\n * Get all edges (relationships) in the model\n */\n getAllEdges() {\n return this.graph.getAllEdges();\n }\n\n /**\n * Get edges originating from a specific node\n */\n getEdgesFrom(nodeId: string, predicate?: string) {\n return this.graph.getEdgesFrom(nodeId, predicate);\n }\n\n /**\n * Get edges terminating at a specific node\n */\n getEdgesTo(nodeId: string, predicate?: string) {\n return this.graph.getEdgesTo(nodeId, predicate);\n }\n\n /**\n * Get edges between two specific nodes\n */\n getEdgesBetween(sourceId: string, destinationId: string, predicate?: string) {\n return this.graph.getEdgesBetween(sourceId, destinationId, predicate);\n }\n\n /**\n * Traverse the graph starting from a node, following a specific predicate\n */\n async traverse(startNodeId: string, predicate: string, maxDepth: number = 10) {\n return this.graph.traverse(startNodeId, predicate, maxDepth);\n }\n\n /**\n * Create a backup of the current model state\n * Used for rollback support in migration operations\n *\n * @param label Descriptive label for the backup (e.g., \"pre-migration\")\n * @returns Path to the backup directory\n */\n async createBackup(label: string): Promise<string> {\n const timestamp = new Date().toISOString().replace(/[:.]/g, \"-\");\n const backupDir = path.join(this.rootPath, \".dr-backups\", `${label}-${timestamp}`);\n\n // Create backup directory\n await ensureDir(backupDir);\n\n // Backup layers directory\n const layersSource = path.join(this.rootPath, \"documentation-robotics\", \"model\");\n const layersBackup = path.join(backupDir, \"layers\");\n if (await this.directoryExists(layersSource)) {\n await this.copyDirectory(layersSource, layersBackup);\n }\n\n // Backup manifest\n const manifestSource = path.join(this.rootPath, \"documentation-robotics\", \"model\", \"manifest.yaml\");\n const manifestBackup = path.join(backupDir, \"manifest.yaml\");\n if (await this.fileExists(manifestSource)) {\n await fs.copyFile(manifestSource, manifestBackup);\n }\n\n return backupDir;\n }\n\n /**\n * Restore model from a backup directory\n * Used for rollback after failed migrations\n *\n * @param backupPath Path to the backup directory\n */\n async restoreFromBackup(backupPath: string): Promise<void> {\n // Restore layers\n const layersBackup = path.join(backupPath, \"layers\");\n const layersTarget = path.join(this.rootPath, \"documentation-robotics\", \"model\");\n if (await this.directoryExists(layersBackup)) {\n await this.copyDirectory(layersBackup, layersTarget);\n }\n\n // Restore manifest\n const manifestBackup = path.join(backupPath, \"manifest.yaml\");\n const manifestTarget = path.join(this.rootPath, \"documentation-robotics\", \"model\", \"manifest.yaml\");\n if (await this.fileExists(manifestBackup)) {\n await fs.copyFile(manifestBackup, manifestTarget);\n }\n\n // Reload model to refresh in-memory state\n const reloadedModel = await Model.load(this.rootPath, { lazyLoad: this.lazyLoad });\n this.layers = reloadedModel.layers;\n this.manifest = reloadedModel.manifest;\n this.graph = reloadedModel.graph;\n this.relationships = reloadedModel.relationships;\n }\n\n /**\n * Save dirty layers with atomic write semantics\n * Writes to temporary file first, then renames on success to ensure data safety\n *\n * @throws Error if atomic write fails\n */\n async saveDirtyLayersAtomic(): Promise<void> {\n // First, save all layers to temporary files\n const tempLayerWrites: Array<{ layer: Layer; tempPath: string }> = [];\n\n try {\n for (const layer of this.layers.values()) {\n if (layer.isDirty()) {\n const layerPath = path.join(\n this.rootPath,\n \"documentation-robotics\",\n \"model\",\n `${layer.name}_layer`\n );\n\n const tempPath = `${layerPath}.tmp`;\n await ensureDir(tempPath);\n\n // Write layer elements to temp directory\n for (const element of layer.elements.values()) {\n const elementPath = path.join(tempPath, `${element.path || element.id}.json`);\n const content = JSON.stringify(element.toJSON(), null, 2);\n await writeFile(elementPath, content);\n }\n\n tempLayerWrites.push({ layer, tempPath });\n }\n }\n\n // All temp writes succeeded, now commit by renaming\n for (const { layer, tempPath } of tempLayerWrites) {\n const layerPath = path.join(\n this.rootPath,\n \"documentation-robotics\",\n \"model\",\n `${layer.name}_layer`\n );\n\n // Remove old directory and rename temp to actual\n if (await this.directoryExists(layerPath)) {\n await fs.rm(layerPath, { recursive: true, force: true });\n }\n await fs.rename(tempPath, layerPath);\n }\n } catch (error) {\n // Cleanup any temp directories on failure\n for (const { tempPath } of tempLayerWrites) {\n if (await this.directoryExists(tempPath)) {\n await fs.rm(tempPath, { recursive: true, force: true });\n }\n }\n throw error;\n }\n }\n\n /**\n * Helper: Check if file exists\n */\n private async fileExists(filePath: string): Promise<boolean> {\n try {\n await fs.access(filePath);\n return true;\n } catch {\n return false;\n }\n }\n\n /**\n * Helper: Check if directory exists\n */\n private async directoryExists(dirPath: string): Promise<boolean> {\n try {\n const stat = await fs.stat(dirPath);\n return stat.isDirectory();\n } catch {\n return false;\n }\n }\n\n /**\n * Helper: Recursively copy directory\n */\n private async copyDirectory(src: string, dest: string): Promise<void> {\n await ensureDir(dest);\n const entries = await fs.readdir(src, { withFileTypes: true });\n\n for (const entry of entries) {\n const srcPath = path.join(src, entry.name);\n const destPath = path.join(dest, entry.name);\n\n if (entry.isDirectory()) {\n await this.copyDirectory(srcPath, destPath);\n } else {\n await fs.copyFile(srcPath, destPath);\n }\n }\n }\n}\n"],
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6
6
  "names": ["path", "fs", "layerId", "manifestPath"]
7
7
  }
package/dist/telemetry/index.js CHANGED
@@ -21,7 +21,7 @@ async function initTelemetry() {
21
21
  `), process.stderr.write(` - Logs endpoint: ${otlpConfig.logsEndpoint}
22
22
  `), process.stderr.write(` - Service name: ${otlpConfig.serviceName}
23
23
  `));
24
- const cliVersion = "0.1.9";
24
+ const cliVersion = "0.1.11";
25
25
  let projectName = "unknown";
26
26
  try {
27
27
  const [{ readFileSync, existsSync }, { parse }] = await Promise.all([
package/dist/utils/spec-version.js CHANGED
@@ -1,6 +1,6 @@
1
1
  import { readJSON, fileExists } from "./file-io.js";
2
2
  import { join } from "path";
3
- const CLI_VERSION = "0.1.9", BUNDLED_SPEC_VERSION = "0.9.0";
3
+ const CLI_VERSION = "0.1.11", BUNDLED_SPEC_VERSION = "0.9.0";
4
4
  function getCliVersion() {
5
5
  return CLI_VERSION;
6
6
  }
package/dist/utils/spec-version.js.map CHANGED
@@ -1,7 +1,7 @@
1
1
  {
2
2
  "version": 3,
3
3
  "sources": ["../../src/utils/spec-version.ts"],
4
- "sourcesContent": ["/**\n * Spec Version Utilities\n *\n * Manages spec version information for the CLI\n */\n\nimport { readJSON, fileExists } from \"./file-io.js\";\nimport { join } from \"path\";\n\n/**\n * CLI version\n * This should match the version in ../package.json\n * Updated during release process\n */\nconst CLI_VERSION = \"0.1.9\";\n\n/**\n * Bundled spec version\n * This should match the version in ../../../spec/VERSION\n * Updated during build process\n */\nconst BUNDLED_SPEC_VERSION = \"0.9.0\";\n\n/**\n * Get the CLI version\n *\n * @returns CLI version string\n */\nexport function getCliVersion(): string {\n return CLI_VERSION;\n}\n\n/**\n * Get the CLI's bundled spec version\n *\n * This is the version of the DR specification that is bundled with this CLI.\n * It represents what version of the spec this CLI supports.\n *\n * @returns Bundled spec version string\n */\nexport function getCliBundledSpecVersion(): string {\n return BUNDLED_SPEC_VERSION;\n}\n\n/**\n * Read spec version from .dr/manifest.json (installed spec reference)\n *\n * @param drPath - Path to .dr/ directory\n * @returns Spec version from .dr/manifest.json, or null if not found\n */\nexport async function getInstalledSpecVersion(drPath: string): Promise<string | null> {\n const manifestPath = join(drPath, \"manifest.json\");\n\n if (!(await fileExists(manifestPath))) {\n return null;\n }\n\n try {\n const manifest = await readJSON<{ specVersion?: string }>(manifestPath);\n return manifest.specVersion || null;\n } catch {\n return null;\n }\n}\n\n/**\n * Read spec version from documentation_robotics/model/manifest.yaml\n *\n * @param modelPath - Path to model directory\n * @returns Spec version from model manifest, or null if not found\n */\nexport async function getModelSpecVersion(modelPath: string): Promise<string | null> {\n const manifestPath = join(modelPath, \"manifest.yaml\");\n\n if (!(await fileExists(manifestPath))) {\n return null;\n }\n\n try {\n // Use YAML parser\n const yaml = await import(\"yaml\");\n const fs = await import(\"fs/promises\");\n const content = await fs.readFile(manifestPath, \"utf-8\");\n const manifest = yaml.parse(content) as { spec_version?: string; specVersion?: string };\n // Check snake_case first (Python CLI format), then camelCase (legacy)\n return manifest.spec_version || manifest.specVersion || null;\n } catch {\n return null;\n }\n}\n"],
5
- "mappings": "AAMA,SAAS,UAAU,kBAAkB;AACrC,SAAS,YAAY;AAOrB,MAAM,cAAc,SAOd,uBAAuB;AAOvB,SAAU,gBAAa;AAC3B,SAAO;AACT;AAUM,SAAU,2BAAwB;AACtC,SAAO;AACT;AAQA,eAAsB,wBAAwB,QAAc;AAC1D,QAAM,eAAe,KAAK,QAAQ,eAAe;AAEjD,MAAI,CAAE,MAAM,WAAW,YAAY;AACjC,WAAO;AAGT,MAAI;AAEF,YADiB,MAAM,SAAmC,YAAY,GACtD,eAAe;EACjC,QAAQ;AACN,WAAO;EACT;AACF;AAQA,eAAsB,oBAAoB,WAAiB;AACzD,QAAM,eAAe,KAAK,WAAW,eAAe;AAEpD,MAAI,CAAE,MAAM,WAAW,YAAY;AACjC,WAAO;AAGT,MAAI;AAEF,UAAM,OAAO,MAAM,OAAO,MAAM,GAE1B,UAAU,OADL,MAAM,OAAO,aAAa,GACZ,SAAS,cAAc,OAAO,GACjD,WAAW,KAAK,MAAM,OAAO;AAEnC,WAAO,SAAS,gBAAgB,SAAS,eAAe;EAC1D,QAAQ;AACN,WAAO;EACT;AACF;",
4
+ "sourcesContent": ["/**\n * Spec Version Utilities\n *\n * Manages spec version information for the CLI\n */\n\nimport { readJSON, fileExists } from \"./file-io.js\";\nimport { join } from \"path\";\n\n/**\n * CLI version\n * This should match the version in ../package.json\n * Updated during release process\n */\nconst CLI_VERSION = \"0.1.11\";\n\n/**\n * Bundled spec version\n * This should match the version in ../../../spec/VERSION\n * Updated during build process\n */\nconst BUNDLED_SPEC_VERSION = \"0.9.0\";\n\n/**\n * Get the CLI version\n *\n * @returns CLI version string\n */\nexport function getCliVersion(): string {\n return CLI_VERSION;\n}\n\n/**\n * Get the CLI's bundled spec version\n *\n * This is the version of the DR specification that is bundled with this CLI.\n * It represents what version of the spec this CLI supports.\n *\n * @returns Bundled spec version string\n */\nexport function getCliBundledSpecVersion(): string {\n return BUNDLED_SPEC_VERSION;\n}\n\n/**\n * Read spec version from .dr/manifest.json (installed spec reference)\n *\n * @param drPath - Path to .dr/ directory\n * @returns Spec version from .dr/manifest.json, or null if not found\n */\nexport async function getInstalledSpecVersion(drPath: string): Promise<string | null> {\n const manifestPath = join(drPath, \"manifest.json\");\n\n if (!(await fileExists(manifestPath))) {\n return null;\n }\n\n try {\n const manifest = await readJSON<{ specVersion?: string }>(manifestPath);\n return manifest.specVersion || null;\n } catch {\n return null;\n }\n}\n\n/**\n * Read spec version from documentation_robotics/model/manifest.yaml\n *\n * @param modelPath - Path to model directory\n * @returns Spec version from model manifest, or null if not found\n */\nexport async function getModelSpecVersion(modelPath: string): Promise<string | null> {\n const manifestPath = join(modelPath, \"manifest.yaml\");\n\n if (!(await fileExists(manifestPath))) {\n return null;\n }\n\n try {\n // Use YAML parser\n const yaml = await import(\"yaml\");\n const fs = await import(\"fs/promises\");\n const content = await fs.readFile(manifestPath, \"utf-8\");\n const manifest = yaml.parse(content) as { spec_version?: string; specVersion?: string };\n // Check snake_case first (Python CLI format), then camelCase (legacy)\n return manifest.spec_version || manifest.specVersion || null;\n } catch {\n return null;\n }\n}\n"],
5
+ "mappings": "AAMA,SAAS,UAAU,kBAAkB;AACrC,SAAS,YAAY;AAOrB,MAAM,cAAc,UAOd,uBAAuB;AAOvB,SAAU,gBAAa;AAC3B,SAAO;AACT;AAUM,SAAU,2BAAwB;AACtC,SAAO;AACT;AAQA,eAAsB,wBAAwB,QAAc;AAC1D,QAAM,eAAe,KAAK,QAAQ,eAAe;AAEjD,MAAI,CAAE,MAAM,WAAW,YAAY;AACjC,WAAO;AAGT,MAAI;AAEF,YADiB,MAAM,SAAmC,YAAY,GACtD,eAAe;EACjC,QAAQ;AACN,WAAO;EACT;AACF;AAQA,eAAsB,oBAAoB,WAAiB;AACzD,QAAM,eAAe,KAAK,WAAW,eAAe;AAEpD,MAAI,CAAE,MAAM,WAAW,YAAY;AACjC,WAAO;AAGT,MAAI;AAEF,UAAM,OAAO,MAAM,OAAO,MAAM,GAE1B,UAAU,OADL,MAAM,OAAO,aAAa,GACZ,SAAS,cAAc,OAAO,GACjD,WAAW,KAAK,MAAM,OAAO;AAEnC,WAAO,SAAS,gBAAgB,SAAS,eAAe;EAC1D,QAAQ;AACN,WAAO;EACT;AACF;",
6
6
  "names": []
7
7
  }
package/dist/viewer/README.md CHANGED
@@ -4,15 +4,15 @@ This directory contains the pre-built embedded viewer for the Documentation Robo
4
4
 
5
5
  ## Bundle Information
6
6
 
7
- - **Version:** 0.5.1
8
- - **Build Date:** 2026-08-14T17:01:17.395Z
9
- - **Total Size:** 1.18 MB
10
- - **Estimated Gzip:** 375.5 KB
7
+ - **Version:** 0.6.0
8
+ - **Build Date:** 2026-08-19T11:56:19.998Z
9
+ - **Total Size:** 1.24 MB
10
+ - **Estimated Gzip:** 392.89 KB
11
11
 
12
12
  ## Files
13
13
 
14
- - `assets/main-DyuokeQj.js` (787.76 KB)
15
- - `assets/main-D114QwJo.css` (181.95 KB)
14
+ - `assets/main-BrpLargo.js` (832.61 KB)
15
+ - `assets/main-BRPZyc36.css` (193.2 KB)
16
16
  - `fonts/inter/Inter-SemiBold.woff2` (23.88 KB)
17
17
  - `fonts/inter/Inter-ExtraBold.woff2` (23.83 KB)
18
18
  - `fonts/inter/Inter-Bold.woff2` (23.79 KB)