@documentation-robotics/cli 0.1.8 → 0.1.9

package/dist/commands/version.js

@@ -2,7 +2,7 @@ import ansis from "ansis";
 import { getCliBundledSpecVersion } from "../utils/spec-version.js";
 import { isTelemetryBuiltIn, isTelemetryConfigured } from "../telemetry/detect.js";
 import { getSpecReferencePath, getModelPath } from "../utils/project-paths.js";
-const gitHash = "f413188", cliVersion = "0.1.8";
+const gitHash = "5345bf8", cliVersion = "0.1.9";
 async function versionCommand() {
   const specVersion = getCliBundledSpecVersion(), telemetryBuiltIn = isTelemetryBuiltIn(), telemetryConfigured = await isTelemetryConfigured();
   let telemetryStatus;

package/dist/core/layers.js

@@ -1,6 +1,7 @@
 const CANONICAL_LAYER_NAMES = [
   "motivation",
   "business",
+  "product",
   "security",
   "application",
   "technology",

package/dist/core/layers.js.map

@@ -1,7 +1,7 @@
 {
   "version": 3,
   "sources": ["../../src/core/layers.ts"],
-  "sourcesContent": ["/**\n * Canonical layer names and ordering for the 12-layer architecture model.\n * This is the source of truth for layer naming and ordering.\n */\n\nexport const CANONICAL_LAYER_NAMES = [\n  'motivation',\n  'business',\n  'security',\n  'application',\n  'technology',\n  'api',\n  'data-model',\n  'data-store',\n  'ux',\n  'navigation',\n  'apm',\n  'testing'\n] as const;\n\nexport type CanonicalLayerName = (typeof CANONICAL_LAYER_NAMES)[number];\n\n/**\n * Get the numeric order of a layer (1-12)\n */\nexport function getLayerOrder(layerName: string): number {\n  const index = CANONICAL_LAYER_NAMES.indexOf(layerName as CanonicalLayerName);\n  return index >= 0 ? index + 1 : -1;\n}\n\n/**\n * Get layer name by numeric order (1-12)\n */\nexport function getLayerByOrder(order: number): string | undefined {\n  if (order < 1 || order > CANONICAL_LAYER_NAMES.length) {\n    return undefined;\n  }\n  return CANONICAL_LAYER_NAMES[order - 1];\n}\n\n/**\n * Check if a layer name is valid (type predicate for compile-time narrowing)\n */\nexport function isValidLayerName(name: string): name is CanonicalLayerName {\n  return CANONICAL_LAYER_NAMES.includes(name as CanonicalLayerName);\n}\n"],
-  "mappings": "AAKO,MAAM,wBAAwB;EACnC;EACA;EACA;EACA;EACA;EACA;EACA;EACA;EACA;EACA;EACA;EACA;;AAQI,SAAU,cAAc,WAAiB;AAC7C,QAAM,QAAQ,sBAAsB,QAAQ,SAA+B;AAC3E,SAAO,SAAS,IAAI,QAAQ,IAAI;AAClC;AAKM,SAAU,gBAAgB,OAAa;AAC3C,MAAI,UAAQ,KAAK,QAAQ,sBAAsB;AAG/C,WAAO,sBAAsB,QAAQ,CAAC;AACxC;AAKM,SAAU,iBAAiB,MAAY;AAC3C,SAAO,sBAAsB,SAAS,IAA0B;AAClE;",
+  "sourcesContent": ["/**\n * Canonical layer names and ordering for the 13-layer architecture model.\n * This is the source of truth for layer naming and ordering.\n */\n\nexport const CANONICAL_LAYER_NAMES = [\n  'motivation',\n  'business',\n  'product',\n  'security',\n  'application',\n  'technology',\n  'api',\n  'data-model',\n  'data-store',\n  'ux',\n  'navigation',\n  'apm',\n  'testing'\n] as const;\n\nexport type CanonicalLayerName = (typeof CANONICAL_LAYER_NAMES)[number];\n\n/**\n * Get the numeric order of a layer (1-13)\n */\nexport function getLayerOrder(layerName: string): number {\n  const index = CANONICAL_LAYER_NAMES.indexOf(layerName as CanonicalLayerName);\n  return index >= 0 ? index + 1 : -1;\n}\n\n/**\n * Get layer name by numeric order (1-13)\n */\nexport function getLayerByOrder(order: number): string | undefined {\n  if (order < 1 || order > CANONICAL_LAYER_NAMES.length) {\n    return undefined;\n  }\n  return CANONICAL_LAYER_NAMES[order - 1];\n}\n\n/**\n * Check if a layer name is valid (type predicate for compile-time narrowing)\n */\nexport function isValidLayerName(name: string): name is CanonicalLayerName {\n  return CANONICAL_LAYER_NAMES.includes(name as CanonicalLayerName);\n}\n"],
+  "mappings": "AAKO,MAAM,wBAAwB;EACnC;EACA;EACA;EACA;EACA;EACA;EACA;EACA;EACA;EACA;EACA;EACA;EACA;;AAQI,SAAU,cAAc,WAAiB;AAC7C,QAAM,QAAQ,sBAAsB,QAAQ,SAA+B;AAC3E,SAAO,SAAS,IAAI,QAAQ,IAAI;AAClC;AAKM,SAAU,gBAAgB,OAAa;AAC3C,MAAI,UAAQ,KAAK,QAAQ,sBAAsB;AAG/C,WAAO,sBAAsB,QAAQ,CAAC;AACxC;AAKM,SAAU,iBAAiB,MAAY;AAC3C,SAAO,sBAAsB,SAAS,IAA0B;AAClE;",
   "names": []
 }

package/dist/core/migration-registry.js

@@ -80,6 +80,60 @@ class MigrationRegistry {
         filesModified: 0,
         description: "Spec version updated to 0.8.4 (Analyzer Infrastructure)"
       })
+    }), this.migrations.push({
+      fromVersion: "0.8.4",
+      toVersion: "0.9.0",
+      description: "Product Layer Introduction (Spec v0.9.0)",
+      apply: async (model) => {
+        const fs = await import("fs/promises"), pathModule = await import("path"), modelDir = `${model.rootPath}/documentation-robotics/model`;
+        let filesModified = 0;
+        try {
+          await fs.access(modelDir);
+        } catch (error) {
+          if (error.code === "ENOENT")
+            return {
+              migrationsApplied: 1,
+              filesModified: 0,
+              description: "Spec version updated to 0.9.0 (Product layer introduced; no model directories to migrate)"
+            };
+          throw error;
+        }
+        const renameMap = [
+          ["12_testing", "13_testing"],
+          ["11_apm", "12_apm"],
+          ["10_navigation", "11_navigation"],
+          ["09_ux", "10_ux"],
+          ["08_data-store", "09_data-store"],
+          ["07_data-model", "08_data-model"],
+          ["06_api", "07_api"],
+          ["05_technology", "06_technology"],
+          ["04_application", "05_application"],
+          ["03_security", "04_security"]
+        ], renameErrors = [];
+        for (const [oldName, newName] of renameMap) {
+          const oldPath = pathModule.join(modelDir, oldName), newPath = pathModule.join(modelDir, newName);
+          try {
+            await fs.rename(oldPath, newPath), filesModified++;
+          } catch (error) {
+            if (error.code === "ENOENT")
+              continue;
+            renameErrors.push(`Failed to rename ${oldName} to ${newName}: ${getErrorMessage(error)}`);
+          }
+        }
+        if (renameErrors.length > 0)
+          return {
+            migrationsApplied: 1,
+            filesModified,
+            description: "Spec version updated to 0.9.0 (Product layer introduced at layer 3; Security through Testing shifted from layers 3\u201312 to 4\u201313)",
+            error: renameErrors.join("; ")
+          };
+        const productPath = pathModule.join(modelDir, "03_product");
+        return await fs.mkdir(productPath, { recursive: !0 }), {
+          migrationsApplied: 1,
+          filesModified,
+          description: "Spec version updated to 0.9.0 (Product layer introduced at layer 3; Security through Testing shifted from layers 3\u201312 to 4\u201313)"
+        };
+      }
     });
   }
   /**
@@ -137,12 +191,15 @@ class MigrationRegistry {
       else
         try {
           const result = await migration.apply(model);
-          results.applied.push({
+          if (results.applied.push({
             from: migration.fromVersion,
             to: migration.toVersion,
             description: migration.description,
             changes: result
-          }), results.totalChanges += result.migrationsApplied, model.manifest.specVersion = migration.toVersion;
+          }), results.totalChanges += result.migrationsApplied, !result.error)
+            model.manifest.specVersion = migration.toVersion;
+          else
+            throw new Error(result.error);
         } catch (error) {
           throw new Error(`Migration ${migration.fromVersion} \u2192 ${migration.toVersion} failed: ${getErrorMessage(error)}`);
         }

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

@@ -1,7 +1,7 @@
 {
   "version": 3,
   "sources": ["../../src/core/migration-registry.ts"],
-  "sourcesContent": ["/**\n * Migration Registry - Manages version-based model migrations\n *\n * Handles sequential migrations from one spec version to another,\n * supporting the evolution of the architecture model specification.\n */\n\nimport type { Model } from \"./model.js\";\nimport { getErrorMessage } from \"../utils/errors.js\";\n\n/**\n * Represents a single version migration\n */\nexport interface Migration {\n  fromVersion: string;\n  toVersion: string;\n  description: string;\n  apply: (model: Model) => Promise<MigrationResult>;\n}\n\n/**\n * Result of applying a migration\n */\nexport interface MigrationResult {\n  migrationsApplied: number;\n  filesModified: number;\n  description: string;\n  error?: string;\n  details?: Record<string, unknown>;\n}\n\n/**\n * Migration Registry managing all available migrations\n */\nexport class MigrationRegistry {\n  private migrations: Migration[] = [];\n\n  constructor() {\n    this.registerMigrations();\n  }\n\n  /**\n   * Register all available migrations\n   */\n  private registerMigrations(): void {\n    // Migration from v0.5.0 to v0.6.0: Relationship Taxonomy\n    this.migrations.push({\n      fromVersion: \"0.5.0\",\n      toVersion: \"0.6.0\",\n      description: \"Relationship Taxonomy (Spec v0.6.0)\",\n      apply: async () => {\n        // This migration is opt-in - the new relationship taxonomy\n        // is fully backward compatible with existing models\n        return {\n          migrationsApplied: 1,\n          filesModified: 0,\n          description: \"Spec version updated to 0.6.0 (Relationship Taxonomy now available)\",\n        };\n      },\n    });\n\n    // Migration from v0.6.0 to v0.7.0: Layer Schema Relationship Metadata\n    this.migrations.push({\n      fromVersion: \"0.6.0\",\n      toVersion: \"0.7.0\",\n      description: \"Layer Schema Relationship Metadata (Spec v0.7.0)\",\n      apply: async () => {\n        // This migration updates layer schemas with relationship metadata sections\n        // - All 12 layer schemas now include layerMetadata, intraLayerRelationships, crossLayerRelationships\n        // - Deprecated link-registry.json (removed in v0.8.0)\n        // - Terminology change: \"cross-layer links\" \u2192 \"cross-layer relationships\"\n        // Fully backward compatible - existing models continue to work\n        return {\n          migrationsApplied: 1,\n          filesModified: 0,\n          description:\n            \"Spec version updated to 0.7.0 (Layer schemas now include relationship metadata sections)\",\n        };\n      },\n    });\n\n    // Migration from v0.7.0 to v0.7.1: Source Code Reference Infrastructure\n    this.migrations.push({\n      fromVersion: \"0.7.0\",\n      toVersion: \"0.7.1\",\n      description: \"Source Code Reference Infrastructure (Spec v0.7.1)\",\n      apply: async () => {\n        // This migration adds source code reference infrastructure\n        // - Common schema definitions in spec/schemas/common/\n        // - Source references integrated across 10 layers\n        // - Backward compatible - existing models continue to work\n        return {\n          migrationsApplied: 1,\n          filesModified: 0,\n          description: \"Spec version updated to 0.7.1 (Source Code Reference Infrastructure)\",\n        };\n      },\n    });\n\n    // Migration from v0.7.1 to v0.8.0: JSON Schema-Only Spec Architecture\n    this.migrations.push({\n      fromVersion: \"0.7.1\",\n      toVersion: \"0.8.0\",\n      description: \"JSON Schema-Only Spec Architecture (Spec v0.8.0)\",\n      apply: async () => {\n        // Spec architecture refactored to JSON Schema-only model:\n        // - Node type definitions moved to spec/schemas/nodes/{layer}/*.node.schema.json\n        // - Relationship definitions moved to spec/schemas/relationships/{layer}/*.relationship.schema.json\n        // - Predicates relocated to spec/schemas/base/predicates.json\n        // This is a spec architecture change only - model data files are fully backward compatible\n        return {\n          migrationsApplied: 1,\n          filesModified: 0,\n          description: \"Spec version updated to 0.8.0 (JSON Schema-Only Spec Architecture)\",\n        };\n      },\n    });\n\n    // Migration from v0.8.0 to v0.8.1: Expanded Relationship Coverage and Node Improvements\n    this.migrations.push({\n      fromVersion: \"0.8.0\",\n      toVersion: \"0.8.1\",\n      description: \"Expanded Relationship Coverage and Node Improvements (Spec v0.8.1)\",\n      apply: async () => {\n        // Spec enhancements only - no model data format changes:\n        // - 733 new relationship schemas added across all 12 layers\n        // - Node type descriptions improved for all 12 layers\n        // - Enum-masquerader node types consolidated into parent attributes\n        // - Existing models continue to work without modification\n        return {\n          migrationsApplied: 1,\n          filesModified: 0,\n          description: \"Spec version updated to 0.8.1 (Expanded Relationship Coverage and Node Improvements)\",\n        };\n      },\n    });\n\n    // Migration from v0.8.1 to v0.8.2: UUID/Path identifier separation\n    this.migrations.push({\n      fromVersion: \"0.8.1\",\n      toVersion: \"0.8.2\",\n      description: \"UUID/Path identifier separation (Spec v0.8.2)\",\n      apply: async () => {\n        // The path field is now required on all spec nodes (spec-node.schema.json).\n        // Existing elements are migrated automatically on load in model.ts (loadLayer):\n        // - Elements with slug-format id: slug moved to path, deterministic UUID assigned to id\n        // - Elements with UUID id but no path: path derived from layer_id.type.kebab(name)\n        // No manual data file changes needed; migration runs transparently on next load/save.\n        return {\n          migrationsApplied: 1,\n          filesModified: 0,\n          description: \"Spec version updated to 0.8.2 (UUID/Path identifier separation)\",\n        };\n      },\n    });\n\n    // Migration from v0.8.2 to v0.8.3: Inter-layer Relationship Schemas and APM Node Types\n    this.migrations.push({\n      fromVersion: \"0.8.2\",\n      toVersion: \"0.8.3\",\n      description: \"Inter-layer Relationship Schemas and APM Node Types (Spec v0.8.3)\",\n      apply: async () => {\n        // Major expansion of inter-layer relationship coverage and APM layer:\n        // - 495 new inter-layer relationship schemas across all 12 layers\n        // - Total relationship count increased from 969 to 1,447\n        // - 2 new APM node types: apm.alert and apm.dashboard\n        // - Backward compatible - existing models continue to work without modification\n        return {\n          migrationsApplied: 1,\n          filesModified: 0,\n          description: \"Spec version updated to 0.8.3 (Inter-layer Relationship Schemas and APM Node Types)\",\n        };\n      },\n    });\n\n    // Migration from v0.8.3 to v0.8.4: Analyzer Infrastructure (CBM Mapping)\n    this.migrations.push({\n      fromVersion: \"0.8.3\",\n      toVersion: \"0.8.4\",\n      description: \"Analyzer Infrastructure (Spec v0.8.4)\",\n      apply: async () => {\n        // Introduces spec/analyzers/ with codebase-memory (CBM) mapping:\n        // - New analyzer adapter foundation and full analyzer subcommands\n        // - dr analyzer verify with changeset awareness\n        // - Claude Code integration commands (/dr-verify, /dr-map, dr-extractor)\n        // - No model data format changes; existing models are fully compatible\n        return {\n          migrationsApplied: 1,\n          filesModified: 0,\n          description: \"Spec version updated to 0.8.4 (Analyzer Infrastructure)\",\n        };\n      },\n    });\n  }\n\n  /**\n   * Get the latest available specification version\n   */\n  getLatestVersion(): string {\n    if (this.migrations.length === 0) {\n      return \"0.7.0\";\n    }\n\n    // Return the highest toVersion from all migrations\n    const versions = this.migrations.map((m) => m.toVersion);\n    return versions.sort().reverse()[0];\n  }\n\n  /**\n   * Get the sequence of migrations needed from one version to another\n   */\n  getMigrationPath(fromVersion: string, toVersion?: string): Migration[] {\n    const targetVersion = toVersion || this.getLatestVersion();\n\n    if (this.compareVersions(fromVersion, targetVersion) >= 0) {\n      return [];\n    }\n\n    const path: Migration[] = [];\n    let current = fromVersion;\n\n    // Sort migrations by fromVersion\n    const sortedMigrations = [...this.migrations].sort((a, b) =>\n      this.compareVersions(a.fromVersion, b.fromVersion)\n    );\n\n    for (const migration of sortedMigrations) {\n      // Check if this migration is in our path\n      if (\n        this.compareVersions(current, migration.fromVersion) >= 0 &&\n        this.compareVersions(current, migration.toVersion) < 0 &&\n        this.compareVersions(migration.toVersion, targetVersion) <= 0\n      ) {\n        path.push(migration);\n        current = migration.toVersion;\n      }\n    }\n\n    return path;\n  }\n\n  /**\n   * Check if a model requires migration\n   */\n  requiresMigration(currentVersion: string): boolean {\n    const path = this.getMigrationPath(currentVersion);\n    return path.length > 0;\n  }\n\n  /**\n   * Apply all migrations in sequence\n   */\n  async applyMigrations(\n    model: Model,\n    options: {\n      fromVersion: string;\n      toVersion?: string;\n      dryRun?: boolean;\n      validate?: boolean;\n    }\n  ): Promise<ApplyMigrationsResult> {\n    const path = this.getMigrationPath(options.fromVersion, options.toVersion);\n    const targetVersion = options.toVersion || this.getLatestVersion();\n\n    if (path.length === 0) {\n      return {\n        applied: [],\n        currentVersion: options.fromVersion,\n        targetVersion,\n        totalChanges: 0,\n      };\n    }\n\n    const results: ApplyMigrationsResult = {\n      applied: [],\n      currentVersion: options.fromVersion,\n      targetVersion,\n      totalChanges: 0,\n    };\n\n    for (const migration of path) {\n      if (!options.dryRun) {\n        try {\n          const result = await migration.apply(model);\n\n          results.applied.push({\n            from: migration.fromVersion,\n            to: migration.toVersion,\n            description: migration.description,\n            changes: result,\n          });\n\n          results.totalChanges += result.migrationsApplied;\n\n          // Update model's spec version\n          model.manifest.specVersion = migration.toVersion;\n        } catch (error) {\n          throw new Error(\n            `Migration ${migration.fromVersion} \u2192 ${migration.toVersion} failed: ${\n              getErrorMessage(error)\n            }`\n          );\n        }\n      } else {\n        // Dry run - just record what would happen\n        results.applied.push({\n          from: migration.fromVersion,\n          to: migration.toVersion,\n          description: migration.description,\n          dryRun: true,\n        });\n      }\n    }\n\n    return results;\n  }\n\n  /**\n   * Get a summary of migrations that would be applied\n   */\n  getMigrationSummary(\n    fromVersion: string,\n    toVersion?: string\n  ): {\n    currentVersion: string;\n    targetVersion: string;\n    migrationsNeeded: number;\n    migrations: Array<{\n      from: string;\n      to: string;\n      description: string;\n    }>;\n  } {\n    const path = this.getMigrationPath(fromVersion, toVersion);\n    const targetVersion = toVersion || this.getLatestVersion();\n\n    return {\n      currentVersion: fromVersion,\n      targetVersion,\n      migrationsNeeded: path.length,\n      migrations: path.map((m) => ({\n        from: m.fromVersion,\n        to: m.toVersion,\n        description: m.description,\n      })),\n    };\n  }\n\n  /**\n   * Compare two version strings\n   * Returns: -1 if a < b, 0 if a == b, 1 if a > b\n   */\n  private compareVersions(a: string, b: string): number {\n    const aParts = a.split(\".\").map(Number);\n    const bParts = b.split(\".\").map(Number);\n\n    const maxLength = Math.max(aParts.length, bParts.length);\n\n    for (let i = 0; i < maxLength; i++) {\n      const aPart = aParts[i] || 0;\n      const bPart = bParts[i] || 0;\n\n      if (aPart < bPart) return -1;\n      if (aPart > bPart) return 1;\n    }\n\n    return 0;\n  }\n}\n\n/**\n * Result of applying multiple migrations\n */\nexport interface ApplyMigrationsResult {\n  applied: Array<{\n    from: string;\n    to: string;\n    description: string;\n    changes?: MigrationResult;\n    dryRun?: boolean;\n  }>;\n  currentVersion: string;\n  targetVersion: string;\n  totalChanges: number;\n}\n"],
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+  "sourcesContent": ["/**\n * Migration Registry - Manages version-based model migrations\n *\n * Handles sequential migrations from one spec version to another,\n * supporting the evolution of the architecture model specification.\n */\n\nimport type { Model } from \"./model.js\";\nimport { getErrorMessage } from \"../utils/errors.js\";\n\n/**\n * Represents a single version migration\n */\nexport interface Migration {\n  fromVersion: string;\n  toVersion: string;\n  description: string;\n  apply: (model: Model) => Promise<MigrationResult>;\n}\n\n/**\n * Result of applying a migration\n */\nexport interface MigrationResult {\n  migrationsApplied: number;\n  filesModified: number;\n  description: string;\n  error?: string;\n  details?: Record<string, unknown>;\n}\n\n/**\n * Migration Registry managing all available migrations\n */\nexport class MigrationRegistry {\n  private migrations: Migration[] = [];\n\n  constructor() {\n    this.registerMigrations();\n  }\n\n  /**\n   * Register all available migrations\n   */\n  private registerMigrations(): void {\n    // Migration from v0.5.0 to v0.6.0: Relationship Taxonomy\n    this.migrations.push({\n      fromVersion: \"0.5.0\",\n      toVersion: \"0.6.0\",\n      description: \"Relationship Taxonomy (Spec v0.6.0)\",\n      apply: async () => {\n        // This migration is opt-in - the new relationship taxonomy\n        // is fully backward compatible with existing models\n        return {\n          migrationsApplied: 1,\n          filesModified: 0,\n          description: \"Spec version updated to 0.6.0 (Relationship Taxonomy now available)\",\n        };\n      },\n    });\n\n    // Migration from v0.6.0 to v0.7.0: Layer Schema Relationship Metadata\n    this.migrations.push({\n      fromVersion: \"0.6.0\",\n      toVersion: \"0.7.0\",\n      description: \"Layer Schema Relationship Metadata (Spec v0.7.0)\",\n      apply: async () => {\n        // This migration updates layer schemas with relationship metadata sections\n        // - All 12 layer schemas now include layerMetadata, intraLayerRelationships, crossLayerRelationships\n        // - Deprecated link-registry.json (removed in v0.8.0)\n        // - Terminology change: \"cross-layer links\" \u2192 \"cross-layer relationships\"\n        // Fully backward compatible - existing models continue to work\n        return {\n          migrationsApplied: 1,\n          filesModified: 0,\n          description:\n            \"Spec version updated to 0.7.0 (Layer schemas now include relationship metadata sections)\",\n        };\n      },\n    });\n\n    // Migration from v0.7.0 to v0.7.1: Source Code Reference Infrastructure\n    this.migrations.push({\n      fromVersion: \"0.7.0\",\n      toVersion: \"0.7.1\",\n      description: \"Source Code Reference Infrastructure (Spec v0.7.1)\",\n      apply: async () => {\n        // This migration adds source code reference infrastructure\n        // - Common schema definitions in spec/schemas/common/\n        // - Source references integrated across 10 layers\n        // - Backward compatible - existing models continue to work\n        return {\n          migrationsApplied: 1,\n          filesModified: 0,\n          description: \"Spec version updated to 0.7.1 (Source Code Reference Infrastructure)\",\n        };\n      },\n    });\n\n    // Migration from v0.7.1 to v0.8.0: JSON Schema-Only Spec Architecture\n    this.migrations.push({\n      fromVersion: \"0.7.1\",\n      toVersion: \"0.8.0\",\n      description: \"JSON Schema-Only Spec Architecture (Spec v0.8.0)\",\n      apply: async () => {\n        // Spec architecture refactored to JSON Schema-only model:\n        // - Node type definitions moved to spec/schemas/nodes/{layer}/*.node.schema.json\n        // - Relationship definitions moved to spec/schemas/relationships/{layer}/*.relationship.schema.json\n        // - Predicates relocated to spec/schemas/base/predicates.json\n        // This is a spec architecture change only - model data files are fully backward compatible\n        return {\n          migrationsApplied: 1,\n          filesModified: 0,\n          description: \"Spec version updated to 0.8.0 (JSON Schema-Only Spec Architecture)\",\n        };\n      },\n    });\n\n    // Migration from v0.8.0 to v0.8.1: Expanded Relationship Coverage and Node Improvements\n    this.migrations.push({\n      fromVersion: \"0.8.0\",\n      toVersion: \"0.8.1\",\n      description: \"Expanded Relationship Coverage and Node Improvements (Spec v0.8.1)\",\n      apply: async () => {\n        // Spec enhancements only - no model data format changes:\n        // - 733 new relationship schemas added across all 12 layers\n        // - Node type descriptions improved for all 12 layers\n        // - Enum-masquerader node types consolidated into parent attributes\n        // - Existing models continue to work without modification\n        return {\n          migrationsApplied: 1,\n          filesModified: 0,\n          description: \"Spec version updated to 0.8.1 (Expanded Relationship Coverage and Node Improvements)\",\n        };\n      },\n    });\n\n    // Migration from v0.8.1 to v0.8.2: UUID/Path identifier separation\n    this.migrations.push({\n      fromVersion: \"0.8.1\",\n      toVersion: \"0.8.2\",\n      description: \"UUID/Path identifier separation (Spec v0.8.2)\",\n      apply: async () => {\n        // The path field is now required on all spec nodes (spec-node.schema.json).\n        // Existing elements are migrated automatically on load in model.ts (loadLayer):\n        // - Elements with slug-format id: slug moved to path, deterministic UUID assigned to id\n        // - Elements with UUID id but no path: path derived from layer_id.type.kebab(name)\n        // No manual data file changes needed; migration runs transparently on next load/save.\n        return {\n          migrationsApplied: 1,\n          filesModified: 0,\n          description: \"Spec version updated to 0.8.2 (UUID/Path identifier separation)\",\n        };\n      },\n    });\n\n    // Migration from v0.8.2 to v0.8.3: Inter-layer Relationship Schemas and APM Node Types\n    this.migrations.push({\n      fromVersion: \"0.8.2\",\n      toVersion: \"0.8.3\",\n      description: \"Inter-layer Relationship Schemas and APM Node Types (Spec v0.8.3)\",\n      apply: async () => {\n        // Major expansion of inter-layer relationship coverage and APM layer:\n        // - 495 new inter-layer relationship schemas across all 12 layers\n        // - Total relationship count increased from 969 to 1,447\n        // - 2 new APM node types: apm.alert and apm.dashboard\n        // - Backward compatible - existing models continue to work without modification\n        return {\n          migrationsApplied: 1,\n          filesModified: 0,\n          description: \"Spec version updated to 0.8.3 (Inter-layer Relationship Schemas and APM Node Types)\",\n        };\n      },\n    });\n\n    // Migration from v0.8.3 to v0.8.4: Analyzer Infrastructure (CBM Mapping)\n    this.migrations.push({\n      fromVersion: \"0.8.3\",\n      toVersion: \"0.8.4\",\n      description: \"Analyzer Infrastructure (Spec v0.8.4)\",\n      apply: async () => {\n        // Introduces spec/analyzers/ with codebase-memory (CBM) mapping:\n        // - New analyzer adapter foundation and full analyzer subcommands\n        // - dr analyzer verify with changeset awareness\n        // - Claude Code integration commands (/dr-verify, /dr-map, dr-extractor)\n        // - No model data format changes; existing models are fully compatible\n        return {\n          migrationsApplied: 1,\n          filesModified: 0,\n          description: \"Spec version updated to 0.8.4 (Analyzer Infrastructure)\",\n        };\n      },\n    });\n\n    // Migration from v0.8.4 to v0.9.0: Product Layer Introduction\n    this.migrations.push({\n      fromVersion: \"0.8.4\",\n      toVersion: \"0.9.0\",\n      description: \"Product Layer Introduction (Spec v0.9.0)\",\n      apply: async (model: Model) => {\n        const fs = await import(\"fs/promises\");\n        const pathModule = await import(\"path\");\n\n        const modelDir = `${model.rootPath}/documentation-robotics/model`;\n        let filesModified = 0;\n\n        try {\n          // Verify model directory exists\n          await fs.access(modelDir);\n        } catch (error) {\n          const err = error as { code?: string };\n          // ENOENT means the directory doesn't exist - nothing to migrate\n          if (err.code === \"ENOENT\") {\n            return {\n              migrationsApplied: 1,\n              filesModified: 0,\n              description:\n                \"Spec version updated to 0.9.0 (Product layer introduced; no model directories to migrate)\",\n            };\n          }\n          // Re-throw other errors (e.g., EACCES for permission denied)\n          throw error;\n        }\n\n        // Rename existing layer directories: shift from 03-12 to 04-13\n        // Must do this in reverse order (12\u219213, 11\u219212, ..., 03\u219204) to avoid conflicts\n        const renameMap = [\n          [\"12_testing\", \"13_testing\"],\n          [\"11_apm\", \"12_apm\"],\n          [\"10_navigation\", \"11_navigation\"],\n          [\"09_ux\", \"10_ux\"],\n          [\"08_data-store\", \"09_data-store\"],\n          [\"07_data-model\", \"08_data-model\"],\n          [\"06_api\", \"07_api\"],\n          [\"05_technology\", \"06_technology\"],\n          [\"04_application\", \"05_application\"],\n          [\"03_security\", \"04_security\"],\n        ];\n\n        const renameErrors: string[] = [];\n\n        for (const [oldName, newName] of renameMap) {\n          const oldPath = pathModule.join(modelDir, oldName);\n          const newPath = pathModule.join(modelDir, newName);\n\n          try {\n            await fs.rename(oldPath, newPath);\n            filesModified++;\n          } catch (error) {\n            const err = error as { code?: string };\n            // ENOENT is expected when a directory hasn't been created yet\n            if (err.code === \"ENOENT\") {\n              continue;\n            }\n            // Track non-ENOENT errors to report them in the result\n            renameErrors.push(\n              `Failed to rename ${oldName} to ${newName}: ${getErrorMessage(error)}`\n            );\n          }\n        }\n\n        // If there were any rename failures, include them in the error field\n        if (renameErrors.length > 0) {\n          return {\n            migrationsApplied: 1,\n            filesModified,\n            description:\n              \"Spec version updated to 0.9.0 (Product layer introduced at layer 3; Security through Testing shifted from layers 3\u201312 to 4\u201313)\",\n            error: renameErrors.join(\"; \"),\n          };\n        }\n\n        // Create new product layer directory (it will be empty for now)\n        // recursive: true handles EEXIST, so no catch needed\n        const productPath = pathModule.join(modelDir, \"03_product\");\n        await fs.mkdir(productPath, { recursive: true });\n\n        return {\n          migrationsApplied: 1,\n          filesModified,\n          description:\n            \"Spec version updated to 0.9.0 (Product layer introduced at layer 3; Security through Testing shifted from layers 3\u201312 to 4\u201313)\",\n        };\n      },\n    });\n  }\n\n  /**\n   * Get the latest available specification version\n   */\n  getLatestVersion(): string {\n    if (this.migrations.length === 0) {\n      return \"0.7.0\";\n    }\n\n    // Return the highest toVersion from all migrations\n    const versions = this.migrations.map((m) => m.toVersion);\n    return versions.sort().reverse()[0];\n  }\n\n  /**\n   * Get the sequence of migrations needed from one version to another\n   */\n  getMigrationPath(fromVersion: string, toVersion?: string): Migration[] {\n    const targetVersion = toVersion || this.getLatestVersion();\n\n    if (this.compareVersions(fromVersion, targetVersion) >= 0) {\n      return [];\n    }\n\n    const path: Migration[] = [];\n    let current = fromVersion;\n\n    // Sort migrations by fromVersion\n    const sortedMigrations = [...this.migrations].sort((a, b) =>\n      this.compareVersions(a.fromVersion, b.fromVersion)\n    );\n\n    for (const migration of sortedMigrations) {\n      // Check if this migration is in our path\n      if (\n        this.compareVersions(current, migration.fromVersion) >= 0 &&\n        this.compareVersions(current, migration.toVersion) < 0 &&\n        this.compareVersions(migration.toVersion, targetVersion) <= 0\n      ) {\n        path.push(migration);\n        current = migration.toVersion;\n      }\n    }\n\n    return path;\n  }\n\n  /**\n   * Check if a model requires migration\n   */\n  requiresMigration(currentVersion: string): boolean {\n    const path = this.getMigrationPath(currentVersion);\n    return path.length > 0;\n  }\n\n  /**\n   * Apply all migrations in sequence\n   */\n  async applyMigrations(\n    model: Model,\n    options: {\n      fromVersion: string;\n      toVersion?: string;\n      dryRun?: boolean;\n      validate?: boolean;\n    }\n  ): Promise<ApplyMigrationsResult> {\n    const path = this.getMigrationPath(options.fromVersion, options.toVersion);\n    const targetVersion = options.toVersion || this.getLatestVersion();\n\n    if (path.length === 0) {\n      return {\n        applied: [],\n        currentVersion: options.fromVersion,\n        targetVersion,\n        totalChanges: 0,\n      };\n    }\n\n    const results: ApplyMigrationsResult = {\n      applied: [],\n      currentVersion: options.fromVersion,\n      targetVersion,\n      totalChanges: 0,\n    };\n\n    for (const migration of path) {\n      if (!options.dryRun) {\n        try {\n          const result = await migration.apply(model);\n\n          results.applied.push({\n            from: migration.fromVersion,\n            to: migration.toVersion,\n            description: migration.description,\n            changes: result,\n          });\n\n          results.totalChanges += result.migrationsApplied;\n\n          // Only update model's spec version if migration succeeded (no error field)\n          if (!result.error) {\n            model.manifest.specVersion = migration.toVersion;\n          } else {\n            // If migration has errors, throw to prevent partial success state\n            throw new Error(result.error);\n          }\n        } catch (error) {\n          throw new Error(\n            `Migration ${migration.fromVersion} \u2192 ${migration.toVersion} failed: ${\n              getErrorMessage(error)\n            }`\n          );\n        }\n      } else {\n        // Dry run - just record what would happen\n        results.applied.push({\n          from: migration.fromVersion,\n          to: migration.toVersion,\n          description: migration.description,\n          dryRun: true,\n        });\n      }\n    }\n\n    return results;\n  }\n\n  /**\n   * Get a summary of migrations that would be applied\n   */\n  getMigrationSummary(\n    fromVersion: string,\n    toVersion?: string\n  ): {\n    currentVersion: string;\n    targetVersion: string;\n    migrationsNeeded: number;\n    migrations: Array<{\n      from: string;\n      to: string;\n      description: string;\n    }>;\n  } {\n    const path = this.getMigrationPath(fromVersion, toVersion);\n    const targetVersion = toVersion || this.getLatestVersion();\n\n    return {\n      currentVersion: fromVersion,\n      targetVersion,\n      migrationsNeeded: path.length,\n      migrations: path.map((m) => ({\n        from: m.fromVersion,\n        to: m.toVersion,\n        description: m.description,\n      })),\n    };\n  }\n\n  /**\n   * Compare two version strings\n   * Returns: -1 if a < b, 0 if a == b, 1 if a > b\n   */\n  private compareVersions(a: string, b: string): number {\n    const aParts = a.split(\".\").map(Number);\n    const bParts = b.split(\".\").map(Number);\n\n    const maxLength = Math.max(aParts.length, bParts.length);\n\n    for (let i = 0; i < maxLength; i++) {\n      const aPart = aParts[i] || 0;\n      const bPart = bParts[i] || 0;\n\n      if (aPart < bPart) return -1;\n      if (aPart > bPart) return 1;\n    }\n\n    return 0;\n  }\n}\n\n/**\n * Result of applying multiple migrations\n */\nexport interface ApplyMigrationsResult {\n  applied: Array<{\n    from: string;\n    to: string;\n    description: string;\n    changes?: MigrationResult;\n    dryRun?: boolean;\n  }>;\n  currentVersion: string;\n  targetVersion: string;\n  totalChanges: number;\n}\n"],
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package/dist/core/model.js

@@ -314,22 +314,9 @@ class Model {
       },
       documentation: ".dr/README.md",
       layers: {}
-    }, layerOrder = [
-      "motivation",
-      "business",
-      "security",
-      "application",
-      "technology",
-      "api",
-      "data-model",
-      "data-store",
-      "ux",
-      "navigation",
-      "apm",
-      "testing"
-    ];
-    for (let i = 0; i < layerOrder.length; i++) {
-      const layerName = layerOrder[i], layer = this.layers.get(layerName), orderNum = String(i + 1).padStart(2, "0");
+    };
+    for (let i = 0; i < CANONICAL_LAYER_NAMES.length; i++) {
+      const layerName = CANONICAL_LAYER_NAMES[i], layer = this.layers.get(layerName), orderNum = String(i + 1).padStart(2, "0");
       yamlData.layers[layerName] = {
         order: i + 1,
         name: layerName.charAt(0).toUpperCase() + layerName.slice(1).replace("-", " "),

package/dist/core/model.js.map

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