@documentation-robotics/cli 0.2.0 → 0.4.0

package/dist/core/relationships.js

@@ -1,3 +1,9 @@
+function elementIdentifiers(element, ...extra) {
+  const ids = /* @__PURE__ */ new Set();
+  for (const candidate of [element.id, element.path, ...extra])
+    typeof candidate == "string" && candidate.length > 0 && ids.add(candidate);
+  return [...ids];
+}
 class Relationships {
   relationships = [];
   dirty = !1;
@@ -20,14 +26,29 @@ class Relationships {
     return deletedCount > 0 && (this.dirty = !0), deletedCount;
   }
   /**
-   * Delete all relationships involving an element (as source or target)
+   * Delete all relationships involving an element (as source or target).
+   *
+   * A row may name an element by its UUID `id` or by its dotted `path`, so callers
+   * should pass every identifier the element is known by (see
+   * `elementIdentifiers()`); any row whose source or target matches one of them
+   * is removed.
    */
   deleteForElement(elementId) {
-    const initialLength = this.relationships.length;
-    this.relationships = this.relationships.filter((rel) => rel.source !== elementId && rel.target !== elementId);
+    const ids = new Set((Array.isArray(elementId) ? elementId : [elementId]).filter((id) => !!id)), initialLength = this.relationships.length;
+    this.relationships = this.relationships.filter((rel) => !ids.has(rel.source) && !ids.has(rel.target));
     const deletedCount = initialLength - this.relationships.length;
     return this.dirty = !0, deletedCount;
   }
+  /**
+   * Keep only the relationships for which `keep` returns true, preserving order.
+   * Returns the number of relationships removed.
+   */
+  retain(keep) {
+    const initialLength = this.relationships.length;
+    this.relationships = this.relationships.filter(keep);
+    const removedCount = initialLength - this.relationships.length;
+    return removedCount > 0 && (this.dirty = !0), removedCount;
+  }
   /**
    * Get all relationships for an element
    */
@@ -73,6 +94,7 @@ class Relationships {
   }
 }
 export {
-  Relationships
+  Relationships,
+  elementIdentifiers
 };
 //# sourceMappingURL=relationships.js.map

package/dist/core/relationships.js.map

@@ -1,7 +1,7 @@
 {
   "version": 3,
   "sources": ["../../src/core/relationships.ts"],
-  "sourcesContent": ["/**\n * Relationships management for intra-layer and cross-layer relationships\n */\n\nexport interface Relationship {\n  source: string;\n  predicate: string;\n  target: string;\n  category?: \"structural\" | \"behavioral\";\n  layer: string;\n  targetLayer?: string;\n  properties?: Record<string, unknown>;\n}\n\n/**\n * Relationships class for managing the central relationships.yaml file\n */\nexport class Relationships {\n  private relationships: Relationship[] = [];\n  private dirty: boolean = false;\n\n  constructor(relationships: Relationship[] = []) {\n    this.relationships = relationships;\n  }\n\n  /**\n   * Add a relationship\n   */\n  add(relationship: Relationship): void {\n    this.relationships.push(relationship);\n    this.dirty = true;\n  }\n\n  /**\n   * Delete relationships matching criteria\n   */\n  delete(source: string, target: string, predicate?: string): number {\n    const initialLength = this.relationships.length;\n    this.relationships = this.relationships.filter(\n      (rel) =>\n        !(\n          rel.source === source &&\n          rel.target === target &&\n          (!predicate || rel.predicate === predicate)\n        )\n    );\n    const deletedCount = initialLength - this.relationships.length;\n    if (deletedCount > 0) {\n      this.dirty = true;\n    }\n    return deletedCount;\n  }\n\n  /**\n   * Delete all relationships involving an element (as source or target)\n   */\n  deleteForElement(elementId: string): number {\n    const initialLength = this.relationships.length;\n    this.relationships = this.relationships.filter(\n      (rel) => rel.source !== elementId && rel.target !== elementId\n    );\n    const deletedCount = initialLength - this.relationships.length;\n    // Always mark as dirty to ensure file is rewritten (Python CLI behavior)\n    this.dirty = true;\n    return deletedCount;\n  }\n\n  /**\n   * Get all relationships for an element\n   */\n  getForElement(elementId: string): {\n    outgoing: Relationship[];\n    incoming: Relationship[];\n  } {\n    const outgoing = this.relationships.filter((rel) => rel.source === elementId);\n    const incoming = this.relationships.filter((rel) => rel.target === elementId);\n    return { outgoing, incoming };\n  }\n\n  /**\n   * Get all relationships\n   */\n  getAll(): Relationship[] {\n    return [...this.relationships];\n  }\n\n  /**\n   * Find relationships between two elements\n   */\n  find(source: string, target: string, predicate?: string): Relationship[] {\n    return this.relationships.filter(\n      (rel) =>\n        rel.source === source &&\n        rel.target === target &&\n        (!predicate || rel.predicate === predicate)\n    );\n  }\n\n  /**\n   * Check if relationships have unsaved changes\n   */\n  isDirty(): boolean {\n    return this.dirty;\n  }\n\n  /**\n   * Mark relationships as clean (no unsaved changes)\n   */\n  markClean(): void {\n    this.dirty = false;\n  }\n\n  /**\n   * Serialize to array for YAML\n   */\n  toArray(): Relationship[] {\n    return this.relationships;\n  }\n\n  /**\n   * Load from array (from YAML)\n   */\n  static fromArray(data: Relationship[]): Relationships {\n    return new Relationships(data);\n  }\n}\n"],
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+  "sourcesContent": ["/**\n * Relationships management for intra-layer and cross-layer relationships\n */\n\nexport interface Relationship {\n  source: string;\n  predicate: string;\n  target: string;\n  category?: \"structural\" | \"behavioral\";\n  layer: string;\n  targetLayer?: string;\n  properties?: Record<string, unknown>;\n}\n\n/**\n * Every identifier a relationship row may use to name an element: its UUID `id`\n * and its dotted `path`. Both forms are legal in relationships.yaml.\n */\nexport function elementIdentifiers(\n  element: { id?: unknown; path?: unknown },\n  ...extra: Array<string | undefined>\n): string[] {\n  const ids = new Set<string>();\n  for (const candidate of [element.id, element.path, ...extra]) {\n    if (typeof candidate === \"string\" && candidate.length > 0) {\n      ids.add(candidate);\n    }\n  }\n  return [...ids];\n}\n\n/**\n * Relationships class for managing the central relationships.yaml file\n */\nexport class Relationships {\n  private relationships: Relationship[] = [];\n  private dirty: boolean = false;\n\n  constructor(relationships: Relationship[] = []) {\n    this.relationships = relationships;\n  }\n\n  /**\n   * Add a relationship\n   */\n  add(relationship: Relationship): void {\n    this.relationships.push(relationship);\n    this.dirty = true;\n  }\n\n  /**\n   * Delete relationships matching criteria\n   */\n  delete(source: string, target: string, predicate?: string): number {\n    const initialLength = this.relationships.length;\n    this.relationships = this.relationships.filter(\n      (rel) =>\n        !(\n          rel.source === source &&\n          rel.target === target &&\n          (!predicate || rel.predicate === predicate)\n        )\n    );\n    const deletedCount = initialLength - this.relationships.length;\n    if (deletedCount > 0) {\n      this.dirty = true;\n    }\n    return deletedCount;\n  }\n\n  /**\n   * Delete all relationships involving an element (as source or target).\n   *\n   * A row may name an element by its UUID `id` or by its dotted `path`, so callers\n   * should pass every identifier the element is known by (see\n   * `elementIdentifiers()`); any row whose source or target matches one of them\n   * is removed.\n   */\n  deleteForElement(elementId: string | string[]): number {\n    const ids = new Set(\n      (Array.isArray(elementId) ? elementId : [elementId]).filter((id) => !!id)\n    );\n    const initialLength = this.relationships.length;\n    this.relationships = this.relationships.filter(\n      (rel) => !ids.has(rel.source) && !ids.has(rel.target)\n    );\n    const deletedCount = initialLength - this.relationships.length;\n    // Always mark as dirty to ensure file is rewritten (Python CLI behavior)\n    this.dirty = true;\n    return deletedCount;\n  }\n\n  /**\n   * Keep only the relationships for which `keep` returns true, preserving order.\n   * Returns the number of relationships removed.\n   */\n  retain(keep: (rel: Relationship) => boolean): number {\n    const initialLength = this.relationships.length;\n    this.relationships = this.relationships.filter(keep);\n    const removedCount = initialLength - this.relationships.length;\n    if (removedCount > 0) {\n      this.dirty = true;\n    }\n    return removedCount;\n  }\n\n  /**\n   * Get all relationships for an element\n   */\n  getForElement(elementId: string): {\n    outgoing: Relationship[];\n    incoming: Relationship[];\n  } {\n    const outgoing = this.relationships.filter((rel) => rel.source === elementId);\n    const incoming = this.relationships.filter((rel) => rel.target === elementId);\n    return { outgoing, incoming };\n  }\n\n  /**\n   * Get all relationships\n   */\n  getAll(): Relationship[] {\n    return [...this.relationships];\n  }\n\n  /**\n   * Find relationships between two elements\n   */\n  find(source: string, target: string, predicate?: string): Relationship[] {\n    return this.relationships.filter(\n      (rel) =>\n        rel.source === source &&\n        rel.target === target &&\n        (!predicate || rel.predicate === predicate)\n    );\n  }\n\n  /**\n   * Check if relationships have unsaved changes\n   */\n  isDirty(): boolean {\n    return this.dirty;\n  }\n\n  /**\n   * Mark relationships as clean (no unsaved changes)\n   */\n  markClean(): void {\n    this.dirty = false;\n  }\n\n  /**\n   * Serialize to array for YAML\n   */\n  toArray(): Relationship[] {\n    return this.relationships;\n  }\n\n  /**\n   * Load from array (from YAML)\n   */\n  static fromArray(data: Relationship[]): Relationships {\n    return new Relationships(data);\n  }\n}\n"],
+  "mappings": "AAkBM,SAAU,mBACd,YACG,OAAgC;AAEnC,QAAM,MAAM,oBAAI,IAAG;AACnB,aAAW,aAAa,CAAC,QAAQ,IAAI,QAAQ,MAAM,GAAG,KAAK;AACzD,IAAI,OAAO,aAAc,YAAY,UAAU,SAAS,KACtD,IAAI,IAAI,SAAS;AAGrB,SAAO,CAAC,GAAG,GAAG;AAChB;AAKM,MAAO,cAAa;EAChB,gBAAgC,CAAA;EAChC,QAAiB;EAEzB,YAAY,gBAAgC,CAAA,GAAE;AAC5C,SAAK,gBAAgB;EACvB;;;;EAKA,IAAI,cAA0B;AAC5B,SAAK,cAAc,KAAK,YAAY,GACpC,KAAK,QAAQ;EACf;;;;EAKA,OAAO,QAAgB,QAAgB,WAAkB;AACvD,UAAM,gBAAgB,KAAK,cAAc;AACzC,SAAK,gBAAgB,KAAK,cAAc,OACtC,CAAC,QACC,EACE,IAAI,WAAW,UACf,IAAI,WAAW,WACd,CAAC,aAAa,IAAI,cAAc,WAClC;AAEL,UAAM,eAAe,gBAAgB,KAAK,cAAc;AACxD,WAAI,eAAe,MACjB,KAAK,QAAQ,KAER;EACT;;;;;;;;;EAUA,iBAAiB,WAA4B;AAC3C,UAAM,MAAM,IAAI,KACb,MAAM,QAAQ,SAAS,IAAI,YAAY,CAAC,SAAS,GAAG,OAAO,CAAC,OAAO,CAAC,CAAC,EAAE,CAAC,GAErE,gBAAgB,KAAK,cAAc;AACzC,SAAK,gBAAgB,KAAK,cAAc,OACtC,CAAC,QAAQ,CAAC,IAAI,IAAI,IAAI,MAAM,KAAK,CAAC,IAAI,IAAI,IAAI,MAAM,CAAC;AAEvD,UAAM,eAAe,gBAAgB,KAAK,cAAc;AAExD,gBAAK,QAAQ,IACN;EACT;;;;;EAMA,OAAO,MAAoC;AACzC,UAAM,gBAAgB,KAAK,cAAc;AACzC,SAAK,gBAAgB,KAAK,cAAc,OAAO,IAAI;AACnD,UAAM,eAAe,gBAAgB,KAAK,cAAc;AACxD,WAAI,eAAe,MACjB,KAAK,QAAQ,KAER;EACT;;;;EAKA,cAAc,WAAiB;AAI7B,UAAM,WAAW,KAAK,cAAc,OAAO,CAAC,QAAQ,IAAI,WAAW,SAAS,GACtE,WAAW,KAAK,cAAc,OAAO,CAAC,QAAQ,IAAI,WAAW,SAAS;AAC5E,WAAO,EAAE,UAAU,SAAQ;EAC7B;;;;EAKA,SAAM;AACJ,WAAO,CAAC,GAAG,KAAK,aAAa;EAC/B;;;;EAKA,KAAK,QAAgB,QAAgB,WAAkB;AACrD,WAAO,KAAK,cAAc,OACxB,CAAC,QACC,IAAI,WAAW,UACf,IAAI,WAAW,WACd,CAAC,aAAa,IAAI,cAAc,UAAU;EAEjD;;;;EAKA,UAAO;AACL,WAAO,KAAK;EACd;;;;EAKA,YAAS;AACP,SAAK,QAAQ;EACf;;;;EAKA,UAAO;AACL,WAAO,KAAK;EACd;;;;EAKA,OAAO,UAAU,MAAoB;AACnC,WAAO,IAAI,cAAc,IAAI;EAC/B;;",
   "names": []
 }

package/dist/core/report-data-model.js

@@ -248,22 +248,16 @@ class ReportDataModel {
     return Math.round(specCompliant / analysis.totalRelationships * 100);
   }
   /**
-   * Calculate layer compliance score (directional compliance)
-   * Measures adherence to the higher -> lower layer reference rule
+   * Calculate layer compliance score: the share of cross-layer relationships between known
+   * layers whose predicate is in the catalog. There is no layer-direction rule; direction is a
+   * property of the predicate (spec/DESIGN_CHARTER.md).
    */
   calculateLayerComplianceScore(analysis) {
-    const validRelationships = analysis.classified.filter((rel) => {
-      const sourceOrder = getLayerOrder(rel.sourceLayer), targetOrder = getLayerOrder(rel.targetLayer);
-      return sourceOrder > 0 && targetOrder > 0;
-    });
-    if (validRelationships.length === 0)
+    const crossLayer = analysis.classified.filter((rel) => rel.isCrossLayer && getLayerOrder(rel.sourceLayer) > 0 && getLayerOrder(rel.targetLayer) > 0);
+    if (crossLayer.length === 0)
       return 100;
-    let compliantCount = 0;
-    for (const rel of validRelationships) {
-      const sourceOrder = getLayerOrder(rel.sourceLayer), targetOrder = getLayerOrder(rel.targetLayer);
-      sourceOrder >= targetOrder && compliantCount++;
-    }
-    return Math.round(compliantCount / validRelationships.length * 100);
+    const compliantCount = crossLayer.filter((rel) => rel.isSpecCompliant).length;
+    return Math.round(compliantCount / crossLayer.length * 100);
   }
   /**
    * Clear all cached data

package/dist/core/report-data-model.js.map

@@ -1,7 +1,7 @@
 {
   "version": 3,
   "sources": ["../../src/core/report-data-model.ts"],
-  "sourcesContent": ["/**\n * ReportDataModel - Unified reporting interface for architecture models\n *\n * Combines statistics collection, relationship classification, and data model analysis\n * to provide comprehensive insights into architecture model structure, quality, and completeness.\n */\n\nimport { Model } from \"./model.js\";\nimport { StatsCollector, ModelStats } from \"./stats-collector.js\";\nimport { RelationshipCatalog, RelationshipType, type Directionality } from \"./relationship-catalog.js\";\nimport { getLayerOrder } from \"./layers.js\";\nimport type { Relationship } from \"../types/index.js\";\n\n/**\n * Relationship with semantic classification metadata\n */\nexport interface ClassifiedRelationship {\n  id: string;\n  source: string; // Element ID\n  target: string; // Element ID\n  predicate: string;\n\n  // Classification\n  category: string; // e.g., \"structural\", \"behavioral\", \"dependency\"\n  archimateAlignment: string | null;\n\n  // Semantic properties\n  directionality: Directionality;\n  transitivity: boolean;\n  symmetry: boolean;\n  reflexivity?: boolean;\n\n  // Analysis\n  sourceLayer: string;\n  targetLayer: string;\n  isCrossLayer: boolean;\n  isSpecCompliant: boolean;\n}\n\n/**\n * Data model entity (Layer 7 specific)\n */\nexport interface DataModelEntity {\n  id: string;\n  name: string;\n  layer: string;\n  attributes: string[];\n  relatedEntities: string[];\n  isReferenced: boolean; // Referenced from other layers\n}\n\n/**\n * Data model layer specific insights\n *\n * Coverage metrics are percentages (0-100) representing data model completeness:\n * - entityCoverage: Percentage of entities referenced from higher layers\n * - attributeCoverage: Percentage of attributes populated across entities\n */\nexport interface DataModelInsights {\n  entityCount: number;\n  attributeCount: number;\n  relationshipCount: number;\n  entities: DataModelEntity[];\n\n  // Coverage metrics\n  entityCoverage: number;\n  attributeCoverage: number;\n\n  // Complexity\n  avgAttributesPerEntity: number;\n  maxAttributesPerEntity: number;\n  avgRelationshipsPerEntity: number;\n\n  // Quality\n  referencedEntities: number; // Entities referenced from higher layers\n  orphanedEntities: string[];\n}\n\n/**\n * Relationship analysis results\n */\nexport interface RelationshipAnalysis {\n  totalRelationships: number;\n  classified: ClassifiedRelationship[];\n  byCategory: Record<string, number>;\n  byPredicate: Record<string, number>;\n  crossLayerCount: number;\n  intraLayerCount: number;\n  circularDependencies: CircularPath[];\n}\n\n/**\n * Circular dependency detection result\n */\nexport interface CircularPath {\n  elements: string[];\n  predicates: string[];\n  pathLength: number;\n}\n\n/**\n * Quality metrics for the model\n *\n * Percentages (0-100) represent quality metrics:\n * - Coverage metrics (elementCoverage, relationshipCoverage, documentationCoverage, archimateCompliance, specCompliance, semanticConsistency):\n *   Express completeness or compliance as percentages\n * - Composition metrics (crossLayerReferenceHealth):\n *   Descriptive ratio of cross-layer to total relationships (not a quality indicator)\n * - Structural metrics (orphanedElements, circularDependencies):\n *   Count of problematic elements\n * - Compliance metrics (layerComplianceScore):\n *   Percentage of relationships following higher\u2192lower layer rule\n */\nexport interface QualityMetrics {\n  // Coverage\n  elementCoverage: number;\n  relationshipCoverage: number;\n  documentationCoverage: number;\n  layerCoverage: number;\n\n  // Structural quality\n  orphanedElements: number;\n  circularDependencies: number;\n\n  // Semantic quality\n  archimateCompliance: number;\n  specCompliance: number;\n  semanticConsistency: number;\n\n  // Layering quality\n  crossLayerReferenceHealth: number;\n  layerComplianceScore: number;\n}\n\n/**\n * Complete report containing statistics, relationships, data model insights, and quality metrics\n */\nexport interface ReportData {\n  timestamp: string;\n  statistics: ModelStats;\n  relationships: RelationshipAnalysis;\n  dataModel: DataModelInsights;\n  quality: QualityMetrics;\n}\n\n/**\n * Factory function to create a ClassifiedRelationship with enforced invariants\n *\n * Ensures that `isCrossLayer` correctly reflects whether sourceLayer !== targetLayer.\n * This prevents accidental bugs where the invariant could be violated.\n */\nexport function createClassifiedRelationship(\n  rel: Omit<ClassifiedRelationship, \"isCrossLayer\" | \"sourceLayer\" | \"targetLayer\">,\n  sourceLayer: string,\n  targetLayer: string\n): ClassifiedRelationship {\n  return {\n    ...rel,\n    sourceLayer,\n    targetLayer,\n    isCrossLayer: sourceLayer !== targetLayer,\n  };\n}\n\n/**\n * ReportDataModel class - Unified reporting interface\n */\nexport class ReportDataModel {\n  private model: Model;\n  private statsCollector: StatsCollector;\n  private relationshipCatalog: RelationshipCatalog;\n\n  private cachedStats: ModelStats | null = null;\n  private cachedRelationships: RelationshipAnalysis | null = null;\n  private cachedDataModel: DataModelInsights | null = null;\n  private cachedQuality: QualityMetrics | null = null;\n  private cachedReport: ReportData | null = null;\n\n  private relationshipTypeMap: Map<string, RelationshipType> = new Map();\n  private catalogLoaded = false;\n\n  constructor(model: Model) {\n    this.model = model;\n    this.statsCollector = new StatsCollector(model);\n    this.relationshipCatalog = new RelationshipCatalog();\n  }\n\n  /**\n   * Load the relationship catalog and build relationship type map\n   */\n  async loadCatalog(): Promise<void> {\n    if (this.catalogLoaded) return;\n\n    await this.relationshipCatalog.load();\n    const types = this.relationshipCatalog.getAllTypes();\n\n    for (const type of types) {\n      this.relationshipTypeMap.set(type.predicate, type);\n    }\n\n    this.catalogLoaded = true;\n  }\n\n  /**\n   * Collect all report data (statistics, relationships, data model, quality metrics)\n   */\n  async collect(): Promise<ReportData> {\n    if (this.cachedReport) {\n      return this.cachedReport;\n    }\n\n    try {\n      await this.loadCatalog();\n\n      const statistics = await this.getStatistics();\n      const relationships = await this.getRelationshipAnalysis();\n      const dataModel = await this.getDataModelInsights();\n      const quality = await this.getQualityMetrics();\n\n      this.cachedReport = {\n        timestamp: new Date().toISOString(),\n        statistics,\n        relationships,\n        dataModel,\n        quality,\n      };\n\n      return this.cachedReport;\n    } catch (error) {\n      throw new Error(\n        `Failed to collect report data: ${error instanceof Error ? error.message : String(error)}`,\n        { cause: error }\n      );\n    }\n  }\n\n  /**\n   * Get model statistics\n   */\n  async getStatistics(): Promise<ModelStats> {\n    if (this.cachedStats) {\n      return this.cachedStats;\n    }\n\n    this.cachedStats = await this.statsCollector.collect();\n    return this.cachedStats;\n  }\n\n  /**\n   * Get relationship analysis with classification\n   */\n  async getRelationshipAnalysis(): Promise<RelationshipAnalysis> {\n    if (this.cachedRelationships) {\n      return this.cachedRelationships;\n    }\n\n    await this.loadCatalog();\n\n    const allRelationships = this.model.relationships.getAll();\n    const classified: ClassifiedRelationship[] = [];\n    const byCategory: Record<string, number> = {};\n    const byPredicate: Record<string, number> = {};\n\n    let crossLayerCount = 0;\n    let intraLayerCount = 0;\n\n    for (let i = 0; i < allRelationships.length; i++) {\n      const rel = allRelationships[i];\n      const relationshipId = `${rel.source}\u2192${rel.predicate}\u2192${rel.target}`;\n      const classifiedRel = this.classifyRelationship(rel, relationshipId);\n      classified.push(classifiedRel);\n\n      // Count by category\n      if (!byCategory[classifiedRel.category]) {\n        byCategory[classifiedRel.category] = 0;\n      }\n      byCategory[classifiedRel.category]++;\n\n      // Count by predicate\n      if (!byPredicate[rel.predicate]) {\n        byPredicate[rel.predicate] = 0;\n      }\n      byPredicate[rel.predicate]++;\n\n      // Count cross vs intra-layer\n      if (classifiedRel.isCrossLayer) {\n        crossLayerCount++;\n      } else {\n        intraLayerCount++;\n      }\n    }\n\n    const circularDependencies = this.detectCircularDependencies(classified);\n\n    this.cachedRelationships = {\n      totalRelationships: allRelationships.length,\n      classified,\n      byCategory,\n      byPredicate,\n      crossLayerCount,\n      intraLayerCount,\n      circularDependencies,\n    };\n\n    return this.cachedRelationships;\n  }\n\n  /**\n   * Get relationships filtered by category\n   */\n  async getRelationshipsByCategory(category: string): Promise<ClassifiedRelationship[]> {\n    const analysis = await this.getRelationshipAnalysis();\n    return analysis.classified.filter((rel) => rel.category === category);\n  }\n\n  /**\n   * Get data model layer (Layer 7) specific insights\n   */\n  async getDataModelInsights(): Promise<DataModelInsights> {\n    if (this.cachedDataModel) {\n      return this.cachedDataModel;\n    }\n\n    const dataModelLayer = await this.model.getLayer(\"data-model\");\n    const entities: DataModelEntity[] = [];\n    let attributeCount = 0;\n\n    if (dataModelLayer) {\n      const elements = dataModelLayer.listElements();\n\n      // Get all references to data model entities from other layers\n      const referencesFrom = new Set<string>();\n      for (const layerName of this.model.getLayerNames()) {\n        if (layerName === \"data-model\") continue;\n        const layer = await this.model.getLayer(layerName);\n        if (!layer) continue;\n\n        for (const element of layer.listElements()) {\n          if (element.references) {\n            for (const ref of element.references) {\n              if (ref.target.startsWith(\"data-model.\")) {\n                referencesFrom.add(ref.target);\n              }\n            }\n          }\n        }\n      }\n\n      for (const element of elements) {\n        const attributes = element.attributes ? 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(entitiesWithAttributes / entityCount) * 100 : 0;\n\n    const avgAttrs = entityCount > 0 ? attributeCount / entityCount : 0;\n    const maxAttrs = Math.max(0, ...entities.map((e) => e.attributes.length));\n    const avgRels =\n      entityCount > 0 ? entities.reduce((sum, e) => sum + e.relatedEntities.length, 0) / entityCount : 0;\n\n    this.cachedDataModel = {\n      entityCount,\n      attributeCount,\n      relationshipCount: entities.reduce((sum, e) => sum + e.relatedEntities.length, 0),\n      entities,\n      entityCoverage: entityCount > 0 ? (referencedCount / entityCount) * 100 : 0,\n      attributeCoverage,\n      avgAttributesPerEntity: Math.round(avgAttrs * 10) / 10,\n      maxAttributesPerEntity: maxAttrs,\n      avgRelationshipsPerEntity: Math.round(avgRels * 10) / 10,\n      referencedEntities: referencedCount,\n      orphanedEntities: orphaned.map((e) => e.id),\n    };\n\n    return this.cachedDataModel;\n  }\n\n  /**\n   * Get quality metrics for the model\n   */\n  async getQualityMetrics(): Promise<QualityMetrics> {\n    if (this.cachedQuality) {\n      return this.cachedQuality;\n    }\n\n    const stats = await this.getStatistics();\n    const relationships = await this.getRelationshipAnalysis();\n\n    // Coverage metrics\n    const elementCoverage = stats.statistics.totalElements > 0 ? 100 : 0;\n    const relationshipCoverage =\n      stats.statistics.totalElements > 0\n        ? (stats.statistics.totalRelationships / stats.statistics.totalElements) * 100\n        : 0;\n    const documentationCoverage = this.calculateDocumentationCoverage(stats);\n    const layerCoverage =\n      stats.statistics.totalLayers > 0\n        ? (stats.statistics.populatedLayers / stats.statistics.totalLayers) * 100\n        : 0;\n\n    // Structural quality\n    const orphanedElements = stats.orphanedElements.length;\n    const circularDependencies = relationships.circularDependencies.length;\n\n    // Semantic quality - simplified calculation\n    const archimateCompliance = this.calculateArchimateCompliance(relationships);\n    const specCompliance = this.calculateSpecCompliance(relationships);\n    const semanticConsistency = (archimateCompliance + specCompliance) / 2;\n\n    // Layering quality\n    const crossLayerReferenceHealth =\n      relationships.totalRelationships > 0\n        ? (relationships.crossLayerCount / relationships.totalRelationships) * 100\n        : 0;\n\n    // Layer compliance score: proportion of relationships going higher -> lower\n    const layerComplianceScore = this.calculateLayerComplianceScore(relationships);\n\n    this.cachedQuality = {\n      elementCoverage,\n      relationshipCoverage: Math.min(100, relationshipCoverage),\n      documentationCoverage: Math.min(100, documentationCoverage),\n      layerCoverage: Math.min(100, layerCoverage),\n      orphanedElements,\n      circularDependencies,\n      archimateCompliance,\n      specCompliance,\n      semanticConsistency,\n      crossLayerReferenceHealth: Math.min(100, crossLayerReferenceHealth),\n      layerComplianceScore,\n    };\n\n    return this.cachedQuality;\n  }\n\n  /**\n   * Classify a single relationship with semantic metadata\n   */\n  private classifyRelationship(rel: Relationship, id: string): ClassifiedRelationship {\n    // Extract layer name from element ID (format: layer.type.name)\n    const sourceParts = rel.source.split(\".\");\n    const targetParts = rel.target.split(\".\");\n\n    // Validate element ID format: must have at least layer (part 0)\n    const sourceLayer = sourceParts[0];\n    const targetLayer = targetParts[0];\n\n    if (!sourceLayer || !targetLayer) {\n      // Log warning for malformed element IDs but continue with available data\n      // This allows partial analysis without breaking the entire report\n      console.warn(\n        `[REPORT_001] Malformed element ID format in relationship: ` +\n          `source=\"${rel.source}\" (${sourceParts.length} parts), ` +\n          `target=\"${rel.target}\" (${targetParts.length} parts). ` +\n          `Expected format: layer.type.name`\n      );\n    }\n\n    const relationshipType = this.relationshipTypeMap.get(rel.predicate);\n\n    // Determine spec compliance: unknown predicates are not compliant\n    const isSpecCompliant = relationshipType !== undefined;\n\n    return createClassifiedRelationship(\n      {\n        id,\n        source: rel.source,\n        target: rel.target,\n        predicate: rel.predicate,\n        category: relationshipType?.category || \"unknown\",\n        archimateAlignment: relationshipType?.archimateAlignment || null,\n        directionality: relationshipType?.semantics?.directionality || \"unidirectional\",\n        transitivity: relationshipType?.semantics?.transitivity || false,\n        symmetry: relationshipType?.semantics?.symmetry || false,\n        reflexivity: relationshipType?.semantics?.reflexivity,\n        isSpecCompliant,\n      },\n      sourceLayer,\n      targetLayer\n    );\n  }\n\n  /**\n   * Detect circular dependencies in relationships\n   * Max depth limit prevents stack overflow on complex graphs\n   */\n  private detectCircularDependencies(relationships: ClassifiedRelationship[]): CircularPath[] {\n    const MAX_SEARCH_DEPTH = 100;\n    const circularPaths: CircularPath[] = [];\n    const visited = new Set<string>();\n    const path: string[] = [];\n    const predicatePath: string[] = [];\n\n    for (const rel of relationships) {\n      if (!visited.has(rel.source)) {\n        this.findCircles(rel.source, relationships, visited, path, predicatePath, circularPaths, 0, MAX_SEARCH_DEPTH);\n      }\n    }\n\n    return circularPaths;\n  }\n\n  /**\n   * Helper to find circular paths using DFS with depth limit\n   */\n  private findCircles(\n    node: string,\n    relationships: ClassifiedRelationship[],\n    visited: Set<string>,\n    path: string[],\n    predicatePath: string[],\n    circularPaths: CircularPath[],\n    depth: number,\n    maxDepth: number\n  ): void {\n    // Prevent stack overflow on complex graphs\n    if (depth > maxDepth) {\n      return;\n    }\n    if (path.includes(node)) {\n      const circleStart = path.indexOf(node);\n      const circlePath = path.slice(circleStart);\n      const circlePredicates = predicatePath.slice(circleStart);\n\n      // Only add if not already found (use immutable sort for comparison)\n      const circleKey = [...circlePath].sort().join(\"\u2192\");\n      const isDuplicate = circularPaths.some(\n        (c) => [...c.elements].sort().join(\"\u2192\") === circleKey\n      );\n\n      if (!isDuplicate && circlePath.length > 1) {\n        circularPaths.push({\n          elements: circlePath,\n          predicates: circlePredicates,\n          pathLength: circlePath.length,\n        });\n      }\n      return;\n    }\n\n    if (visited.has(node)) {\n      return;\n    }\n\n    path.push(node);\n    visited.add(node);\n\n    // Find all outgoing edges from this node\n    for (const rel of relationships) {\n      if (rel.source === node) {\n        predicatePath.push(rel.predicate);\n        this.findCircles(rel.target, relationships, visited, path, predicatePath, circularPaths, depth + 1, maxDepth);\n        predicatePath.pop();\n      }\n    }\n\n    path.pop();\n    visited.delete(node); 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+  "sourcesContent": ["/**\n * ReportDataModel - Unified reporting interface for architecture models\n *\n * Combines statistics collection, relationship classification, and data model analysis\n * to provide comprehensive insights into architecture model structure, quality, and completeness.\n */\n\nimport { Model } from \"./model.js\";\nimport { StatsCollector, ModelStats } from \"./stats-collector.js\";\nimport { RelationshipCatalog, RelationshipType, type Directionality } from \"./relationship-catalog.js\";\nimport { getLayerOrder } from \"./layers.js\";\nimport type { Relationship } from \"../types/index.js\";\n\n/**\n * Relationship with semantic classification metadata\n */\nexport interface ClassifiedRelationship {\n  id: string;\n  source: string; // Element ID\n  target: string; // Element ID\n  predicate: string;\n\n  // Classification\n  category: string; // e.g., \"structural\", \"behavioral\", \"dependency\"\n  archimateAlignment: string | null;\n\n  // Semantic properties\n  directionality: Directionality;\n  transitivity: boolean;\n  symmetry: boolean;\n  reflexivity?: boolean;\n\n  // Analysis\n  sourceLayer: string;\n  targetLayer: string;\n  isCrossLayer: boolean;\n  isSpecCompliant: boolean;\n}\n\n/**\n * Data model entity (Layer 7 specific)\n */\nexport interface DataModelEntity {\n  id: string;\n  name: string;\n  layer: string;\n  attributes: string[];\n  relatedEntities: string[];\n  isReferenced: boolean; // Referenced from other layers\n}\n\n/**\n * Data model layer specific insights\n *\n * Coverage metrics are percentages (0-100) representing data model completeness:\n * - entityCoverage: Percentage of entities referenced from higher layers\n * - attributeCoverage: Percentage of attributes populated across entities\n */\nexport interface DataModelInsights {\n  entityCount: number;\n  attributeCount: number;\n  relationshipCount: number;\n  entities: DataModelEntity[];\n\n  // Coverage metrics\n  entityCoverage: number;\n  attributeCoverage: number;\n\n  // Complexity\n  avgAttributesPerEntity: number;\n  maxAttributesPerEntity: number;\n  avgRelationshipsPerEntity: number;\n\n  // Quality\n  referencedEntities: number; // Entities referenced from higher layers\n  orphanedEntities: string[];\n}\n\n/**\n * Relationship analysis results\n */\nexport interface RelationshipAnalysis {\n  totalRelationships: number;\n  classified: ClassifiedRelationship[];\n  byCategory: Record<string, number>;\n  byPredicate: Record<string, number>;\n  crossLayerCount: number;\n  intraLayerCount: number;\n  circularDependencies: CircularPath[];\n}\n\n/**\n * Circular dependency detection result\n */\nexport interface CircularPath {\n  elements: string[];\n  predicates: string[];\n  pathLength: number;\n}\n\n/**\n * Quality metrics for the model\n *\n * Percentages (0-100) represent quality metrics:\n * - Coverage metrics (elementCoverage, relationshipCoverage, documentationCoverage, archimateCompliance, specCompliance, semanticConsistency):\n *   Express completeness or compliance as percentages\n * - Composition metrics (crossLayerReferenceHealth):\n *   Descriptive ratio of cross-layer to total relationships (not a quality indicator)\n * - Structural metrics (orphanedElements, circularDependencies):\n *   Count of problematic elements\n * - Compliance metrics (layerComplianceScore):\n *   Percentage of cross-layer relationships whose predicate is in the catalog (direction is\n *   defined by the predicate, not by layer order; see spec/DESIGN_CHARTER.md)\n */\nexport interface QualityMetrics {\n  // Coverage\n  elementCoverage: number;\n  relationshipCoverage: number;\n  documentationCoverage: number;\n  layerCoverage: number;\n\n  // Structural quality\n  orphanedElements: number;\n  circularDependencies: number;\n\n  // Semantic quality\n  archimateCompliance: number;\n  specCompliance: number;\n  semanticConsistency: number;\n\n  // Layering quality\n  crossLayerReferenceHealth: number;\n  layerComplianceScore: number;\n}\n\n/**\n * Complete report containing statistics, relationships, data model insights, and quality metrics\n */\nexport interface ReportData {\n  timestamp: string;\n  statistics: ModelStats;\n  relationships: RelationshipAnalysis;\n  dataModel: DataModelInsights;\n  quality: QualityMetrics;\n}\n\n/**\n * Factory function to create a ClassifiedRelationship with enforced invariants\n *\n * Ensures that `isCrossLayer` correctly reflects whether sourceLayer !== targetLayer.\n * This prevents accidental bugs where the invariant could be violated.\n */\nexport function createClassifiedRelationship(\n  rel: Omit<ClassifiedRelationship, \"isCrossLayer\" | \"sourceLayer\" | \"targetLayer\">,\n  sourceLayer: string,\n  targetLayer: string\n): ClassifiedRelationship {\n  return {\n    ...rel,\n    sourceLayer,\n    targetLayer,\n    isCrossLayer: sourceLayer !== targetLayer,\n  };\n}\n\n/**\n * ReportDataModel class - Unified reporting interface\n */\nexport class ReportDataModel {\n  private model: Model;\n  private statsCollector: StatsCollector;\n  private relationshipCatalog: RelationshipCatalog;\n\n  private cachedStats: ModelStats | null = null;\n  private cachedRelationships: RelationshipAnalysis | null = null;\n  private cachedDataModel: DataModelInsights | null = null;\n  private cachedQuality: QualityMetrics | null = null;\n  private cachedReport: ReportData | null = null;\n\n  private relationshipTypeMap: Map<string, RelationshipType> = new Map();\n  private catalogLoaded = false;\n\n  constructor(model: Model) {\n    this.model = model;\n    this.statsCollector = new StatsCollector(model);\n    this.relationshipCatalog = new RelationshipCatalog();\n  }\n\n  /**\n   * Load the relationship catalog and build relationship type map\n   */\n  async loadCatalog(): Promise<void> {\n    if (this.catalogLoaded) return;\n\n    await this.relationshipCatalog.load();\n    const types = this.relationshipCatalog.getAllTypes();\n\n    for (const type of types) {\n      this.relationshipTypeMap.set(type.predicate, type);\n    }\n\n    this.catalogLoaded = true;\n  }\n\n  /**\n   * Collect all report data (statistics, relationships, data model, quality metrics)\n   */\n  async collect(): Promise<ReportData> {\n    if (this.cachedReport) {\n      return this.cachedReport;\n    }\n\n    try {\n      await this.loadCatalog();\n\n      const statistics = await this.getStatistics();\n      const relationships = await this.getRelationshipAnalysis();\n      const dataModel = await this.getDataModelInsights();\n      const quality = await this.getQualityMetrics();\n\n      this.cachedReport = {\n        timestamp: new Date().toISOString(),\n        statistics,\n        relationships,\n        dataModel,\n        quality,\n      };\n\n      return this.cachedReport;\n    } catch (error) {\n      throw new Error(\n        `Failed to collect report data: ${error instanceof Error ? error.message : String(error)}`,\n        { cause: error }\n      );\n    }\n  }\n\n  /**\n   * Get model statistics\n   */\n  async getStatistics(): Promise<ModelStats> {\n    if (this.cachedStats) {\n      return this.cachedStats;\n    }\n\n    this.cachedStats = await this.statsCollector.collect();\n    return this.cachedStats;\n  }\n\n  /**\n   * Get relationship analysis with classification\n   */\n  async getRelationshipAnalysis(): Promise<RelationshipAnalysis> {\n    if (this.cachedRelationships) {\n      return this.cachedRelationships;\n    }\n\n    await this.loadCatalog();\n\n    const allRelationships = this.model.relationships.getAll();\n    const classified: ClassifiedRelationship[] = [];\n    const byCategory: Record<string, number> = {};\n    const byPredicate: Record<string, number> = {};\n\n    let crossLayerCount = 0;\n    let intraLayerCount = 0;\n\n    for (let i = 0; i < allRelationships.length; i++) {\n      const rel = allRelationships[i];\n      const relationshipId = `${rel.source}\u2192${rel.predicate}\u2192${rel.target}`;\n      const classifiedRel = this.classifyRelationship(rel, relationshipId);\n      classified.push(classifiedRel);\n\n      // Count by category\n      if (!byCategory[classifiedRel.category]) {\n        byCategory[classifiedRel.category] = 0;\n      }\n      byCategory[classifiedRel.category]++;\n\n      // Count by predicate\n      if (!byPredicate[rel.predicate]) {\n        byPredicate[rel.predicate] = 0;\n      }\n      byPredicate[rel.predicate]++;\n\n      // Count cross vs intra-layer\n      if (classifiedRel.isCrossLayer) {\n        crossLayerCount++;\n      } else {\n        intraLayerCount++;\n      }\n    }\n\n    const circularDependencies = this.detectCircularDependencies(classified);\n\n    this.cachedRelationships = {\n      totalRelationships: allRelationships.length,\n      classified,\n      byCategory,\n      byPredicate,\n      crossLayerCount,\n      intraLayerCount,\n      circularDependencies,\n    };\n\n    return this.cachedRelationships;\n  }\n\n  /**\n   * Get relationships filtered by category\n   */\n  async getRelationshipsByCategory(category: string): Promise<ClassifiedRelationship[]> {\n    const analysis = await this.getRelationshipAnalysis();\n    return analysis.classified.filter((rel) => rel.category === category);\n  }\n\n  /**\n   * Get data model layer (Layer 7) specific insights\n   */\n  async getDataModelInsights(): Promise<DataModelInsights> {\n    if (this.cachedDataModel) {\n      return this.cachedDataModel;\n    }\n\n    const dataModelLayer = await this.model.getLayer(\"data-model\");\n    const entities: DataModelEntity[] = [];\n    let attributeCount = 0;\n\n    if (dataModelLayer) {\n      const elements = dataModelLayer.listElements();\n\n      // Get all references to data model entities from other layers\n      const referencesFrom = new Set<string>();\n      for (const layerName of this.model.getLayerNames()) {\n        if (layerName === \"data-model\") continue;\n        const layer = await this.model.getLayer(layerName);\n        if (!layer) continue;\n\n        for (const element of layer.listElements()) {\n          if (element.references) {\n            for (const ref of element.references) {\n              if (ref.target.startsWith(\"data-model.\")) {\n                referencesFrom.add(ref.target);\n              }\n            }\n          }\n        }\n      }\n\n      for (const element of elements) {\n        const attributes = element.attributes ? 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(entitiesWithAttributes / entityCount) * 100 : 0;\n\n    const avgAttrs = entityCount > 0 ? attributeCount / entityCount : 0;\n    const maxAttrs = Math.max(0, ...entities.map((e) => e.attributes.length));\n    const avgRels =\n      entityCount > 0 ? entities.reduce((sum, e) => sum + e.relatedEntities.length, 0) / entityCount : 0;\n\n    this.cachedDataModel = {\n      entityCount,\n      attributeCount,\n      relationshipCount: entities.reduce((sum, e) => sum + e.relatedEntities.length, 0),\n      entities,\n      entityCoverage: entityCount > 0 ? (referencedCount / entityCount) * 100 : 0,\n      attributeCoverage,\n      avgAttributesPerEntity: Math.round(avgAttrs * 10) / 10,\n      maxAttributesPerEntity: maxAttrs,\n      avgRelationshipsPerEntity: Math.round(avgRels * 10) / 10,\n      referencedEntities: referencedCount,\n      orphanedEntities: orphaned.map((e) => e.id),\n    };\n\n    return this.cachedDataModel;\n  }\n\n  /**\n   * Get quality metrics for the model\n   */\n  async getQualityMetrics(): Promise<QualityMetrics> {\n    if (this.cachedQuality) {\n      return this.cachedQuality;\n    }\n\n    const stats = await this.getStatistics();\n    const relationships = await this.getRelationshipAnalysis();\n\n    // Coverage metrics\n    const elementCoverage = stats.statistics.totalElements > 0 ? 100 : 0;\n    const relationshipCoverage =\n      stats.statistics.totalElements > 0\n        ? (stats.statistics.totalRelationships / stats.statistics.totalElements) * 100\n        : 0;\n    const documentationCoverage = this.calculateDocumentationCoverage(stats);\n    const layerCoverage =\n      stats.statistics.totalLayers > 0\n        ? (stats.statistics.populatedLayers / stats.statistics.totalLayers) * 100\n        : 0;\n\n    // Structural quality\n    const orphanedElements = stats.orphanedElements.length;\n    const circularDependencies = relationships.circularDependencies.length;\n\n    // Semantic quality - simplified calculation\n    const archimateCompliance = this.calculateArchimateCompliance(relationships);\n    const specCompliance = this.calculateSpecCompliance(relationships);\n    const semanticConsistency = (archimateCompliance + specCompliance) / 2;\n\n    // Layering quality\n    const crossLayerReferenceHealth =\n      relationships.totalRelationships > 0\n        ? (relationships.crossLayerCount / relationships.totalRelationships) * 100\n        : 0;\n\n    // Layer compliance score: cross-layer relationships whose predicate is in the catalog\n    const layerComplianceScore = this.calculateLayerComplianceScore(relationships);\n\n    this.cachedQuality = {\n      elementCoverage,\n      relationshipCoverage: Math.min(100, relationshipCoverage),\n      documentationCoverage: Math.min(100, documentationCoverage),\n      layerCoverage: Math.min(100, layerCoverage),\n      orphanedElements,\n      circularDependencies,\n      archimateCompliance,\n      specCompliance,\n      semanticConsistency,\n      crossLayerReferenceHealth: Math.min(100, crossLayerReferenceHealth),\n      layerComplianceScore,\n    };\n\n    return this.cachedQuality;\n  }\n\n  /**\n   * Classify a single relationship with semantic metadata\n   */\n  private classifyRelationship(rel: Relationship, id: string): ClassifiedRelationship {\n    // Extract layer name from element ID (format: layer.type.name)\n    const sourceParts = rel.source.split(\".\");\n    const targetParts = rel.target.split(\".\");\n\n    // Validate element ID format: must have at least layer (part 0)\n    const sourceLayer = sourceParts[0];\n    const targetLayer = targetParts[0];\n\n    if (!sourceLayer || !targetLayer) {\n      // Log warning for malformed element IDs but continue with available data\n      // This allows partial analysis without breaking the entire report\n      console.warn(\n        `[REPORT_001] Malformed element ID format in relationship: ` +\n          `source=\"${rel.source}\" (${sourceParts.length} parts), ` +\n          `target=\"${rel.target}\" (${targetParts.length} parts). ` +\n          `Expected format: layer.type.name`\n      );\n    }\n\n    const relationshipType = this.relationshipTypeMap.get(rel.predicate);\n\n    // Determine spec compliance: unknown predicates are not compliant\n    const isSpecCompliant = relationshipType !== undefined;\n\n    return createClassifiedRelationship(\n      {\n        id,\n        source: rel.source,\n        target: rel.target,\n        predicate: rel.predicate,\n        category: relationshipType?.category || \"unknown\",\n        archimateAlignment: relationshipType?.archimateAlignment || null,\n        directionality: relationshipType?.semantics?.directionality || \"unidirectional\",\n        transitivity: relationshipType?.semantics?.transitivity || false,\n        symmetry: relationshipType?.semantics?.symmetry || false,\n        reflexivity: relationshipType?.semantics?.reflexivity,\n        isSpecCompliant,\n      },\n      sourceLayer,\n      targetLayer\n    );\n  }\n\n  /**\n   * Detect circular dependencies in relationships\n   * Max depth limit prevents stack overflow on complex graphs\n   */\n  private detectCircularDependencies(relationships: ClassifiedRelationship[]): CircularPath[] {\n    const MAX_SEARCH_DEPTH = 100;\n    const circularPaths: CircularPath[] = [];\n    const visited = new Set<string>();\n    const path: string[] = [];\n    const predicatePath: string[] = [];\n\n    for (const rel of relationships) {\n      if (!visited.has(rel.source)) {\n        this.findCircles(rel.source, relationships, visited, path, predicatePath, circularPaths, 0, MAX_SEARCH_DEPTH);\n      }\n    }\n\n    return circularPaths;\n  }\n\n  /**\n   * Helper to find circular paths using DFS with depth limit\n   */\n  private findCircles(\n    node: string,\n    relationships: ClassifiedRelationship[],\n    visited: Set<string>,\n    path: string[],\n    predicatePath: string[],\n    circularPaths: CircularPath[],\n    depth: number,\n    maxDepth: number\n  ): void {\n    // Prevent stack overflow on complex graphs\n    if (depth > maxDepth) {\n      return;\n    }\n    if (path.includes(node)) {\n      const circleStart = path.indexOf(node);\n      const circlePath = path.slice(circleStart);\n      const circlePredicates = predicatePath.slice(circleStart);\n\n      // Only add if not already found (use immutable sort for comparison)\n      const circleKey = [...circlePath].sort().join(\"\u2192\");\n      const isDuplicate = circularPaths.some(\n        (c) => [...c.elements].sort().join(\"\u2192\") === circleKey\n      );\n\n      if (!isDuplicate && circlePath.length > 1) {\n        circularPaths.push({\n          elements: circlePath,\n          predicates: circlePredicates,\n          pathLength: circlePath.length,\n        });\n      }\n      return;\n    }\n\n    if (visited.has(node)) {\n      return;\n    }\n\n    path.push(node);\n    visited.add(node);\n\n    // Find all outgoing edges from this node\n    for (const rel of relationships) {\n      if (rel.source === node) {\n        predicatePath.push(rel.predicate);\n        this.findCircles(rel.target, relationships, visited, path, predicatePath, circularPaths, depth + 1, maxDepth);\n        predicatePath.pop();\n      }\n    }\n\n    path.pop();\n    visited.delete(node); 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There is no layer-direction rule; direction is a\n   * property of the predicate (spec/DESIGN_CHARTER.md).\n   */\n  private calculateLayerComplianceScore(analysis: RelationshipAnalysis): number {\n    const crossLayer = analysis.classified.filter(\n      (rel) =>\n        rel.isCrossLayer && getLayerOrder(rel.sourceLayer) > 0 && getLayerOrder(rel.targetLayer) > 0\n    );\n\n    if (crossLayer.length === 0) return 100;\n\n    const compliantCount = crossLayer.filter((rel) => rel.isSpecCompliant).length;\n    return Math.round((compliantCount / crossLayer.length) * 100);\n  }\n\n  /**\n   * Clear all cached data\n   */\n  clearCache(): void {\n    this.cachedStats = null;\n    this.cachedRelationships = null;\n    this.cachedDataModel = null;\n    this.cachedQuality = null;\n    this.cachedReport = null;\n  }\n\n  /**\n   * Get the relationship catalog\n   */\n  getCatalog(): RelationshipCatalog {\n    return this.relationshipCatalog;\n  }\n}\n"],
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   "names": []
 }

package/dist/core/staged-changeset-storage.js

@@ -4,8 +4,25 @@ import { FileLock } from "../utils/file-lock.js";
 import path from "path";
 import yaml from "yaml";
 import ansis from "ansis";
-import { Changeset } from "./changeset.js";
+import { Changeset, compactChange, nextSequenceNumber, sequenceOf, withSequenceNumbers } from "./changeset.js";
 import { getErrorMessage } from "../utils/errors.js";
+const MAX_UNSTAGED_TOMBSTONES = 200;
+function readTombstones(value, id) {
+  if (value == null)
+    return;
+  if (!Array.isArray(value)) {
+    console.warn(ansis.yellow(`\u26A0 Changeset '${id}': 'unstaged' in metadata.yaml is not a list; ignoring it`));
+    return;
+  }
+  const valid = value.filter((t) => !!t && typeof t == "object" && typeof t.sequence == "number" && typeof t.removedAt == "number" && !!t.change && typeof t.change == "object" && typeof t.change.type == "string" && typeof t.change.elementId == "string");
+  return valid.length < value.length && console.warn(ansis.yellow(`\u26A0 Changeset '${id}': ignoring ${value.length - valid.length} malformed 'unstaged' entr(ies) in metadata.yaml`)), valid;
+}
+function addTombstones(changeset, tombstones) {
+  if (changeset.unstaged = [...changeset.unstaged, ...tombstones], changeset.unstaged.length > MAX_UNSTAGED_TOMBSTONES) {
+    const dropped = changeset.unstaged.slice(0, changeset.unstaged.length - MAX_UNSTAGED_TOMBSTONES);
+    changeset.unstaged = changeset.unstaged.slice(-MAX_UNSTAGED_TOMBSTONES), changeset.unstagedPrunedThrough = Math.max(changeset.unstagedPrunedThrough ?? -1, ...dropped.map((t) => t.removedAt));
+  }
+}
 class StagedChangesetStorage {
   changesetsDir;
   constructor(rootPath) {
@@ -64,9 +81,11 @@ This may indicate disk failure or incomplete write. Check disk health and restor
         status: metadata.status,
         baseSnapshot: metadata.baseSnapshot,
         changes,
-        stats: metadata.stats || { additions: 0, modifications: 0, deletions: 0 }
-      };
-      return Changeset.fromJSON(data);
+        stats: metadata.stats || { additions: 0, modifications: 0, deletions: 0 },
+        ...typeof metadata.lastSequence == "number" ? { lastSequence: metadata.lastSequence } : {},
+        ...typeof metadata.unstagedPrunedThrough == "number" ? { unstagedPrunedThrough: metadata.unstagedPrunedThrough } : {}
+      }, unstaged = readTombstones(metadata.unstaged, id);
+      return unstaged && (data.unstaged = unstaged), Changeset.fromJSON(data);
     } catch (error) {
       throw new Error(`Failed to load changeset '${id}': YAML parsing failed.
 Error: ${getErrorMessage(error)}
@@ -85,7 +104,7 @@ This indicates file corruption. Try:
       throw new Error("Changeset must have an id to be saved in YAML format");
     const sanitizedId = this.sanitizeId(changeset.id), changesetPath = path.join(this.changesetsDir, sanitizedId);
     await ensureDir(changesetPath);
-    const metadata = {
+    const numbered = withSequenceNumbers(changeset.changes, nextSequenceNumber(changeset)), lastSequence = changeset.lastSequence !== void 0 ? Math.max(changeset.lastSequence, ...numbered.map((c) => c.sequenceNumber)) : void 0, metadata = {
       id: changeset.id,
       name: changeset.name,
       description: changeset.description,
@@ -93,9 +112,13 @@ This indicates file corruption. Try:
       modified: changeset.modified,
       status: changeset.status,
       baseSnapshot: changeset.baseSnapshot,
-      stats: changeset.stats || { additions: 0, modifications: 0, deletions: 0 }
+      stats: changeset.stats || { additions: 0, modifications: 0, deletions: 0 },
+      // Sequence bookkeeping (see nextSequenceNumber); absent on changesets never unstaged from.
+      ...lastSequence !== void 0 ? { lastSequence } : {},
+      ...changeset.unstagedPrunedThrough !== void 0 ? { unstagedPrunedThrough: changeset.unstagedPrunedThrough } : {},
+      ...changeset.unstaged.length > 0 ? { unstaged: changeset.unstaged } : {}
     };
-    await writeFile(path.join(changesetPath, "metadata.yaml"), yaml.stringify(metadata), "utf-8"), await writeFile(path.join(changesetPath, "changes.yaml"), yaml.stringify(changeset.changes), "utf-8");
+    await writeFile(path.join(changesetPath, "metadata.yaml"), yaml.stringify(metadata), "utf-8"), await writeFile(path.join(changesetPath, "changes.yaml"), yaml.stringify(numbered), "utf-8");
   }
   /**
    * List all staged changesets
@@ -154,11 +177,11 @@ Run 'dr changeset list' to see all changesets.`);
         const changeset = await this.load(id);
         if (!changeset)
           throw new Error(`Changeset '${id}' not found`);
-        const sequenceNumber = changeset.changes.length, stagedChange = {
+        const sequenceNumber = nextSequenceNumber(changeset), stagedChange = {
           ...change,
           sequenceNumber
         };
-        return changeset.changes.push(stagedChange), changeset.updateModified(), await this.save(changeset), sequenceNumber;
+        return changeset.changes = withSequenceNumbers(changeset.changes), changeset.changes.push(stagedChange), changeset.lastSequence = sequenceNumber, changeset.updateModified(), await this.save(changeset), sequenceNumber;
       });
     } catch (error) {
       const errorMessage = getErrorMessage(error);
@@ -177,6 +200,59 @@ To resolve:
   4. Retry the operation`);
       }
       throw new Error(`Failed to add change to changeset '${id}': ${errorMessage}
+Changeset path: ${changesetPath}`);
+    }
+  }
+  /**
+   * Add several changes, and rewrite some staged ones in place, in one write: one load and one save
+   * instead of one per change. Additions take the next sequence numbers in order; a rewrite keeps
+   * its change's number and leaves a tombstone, as {@link updateChange} does.
+   *
+   * @returns The sequence numbers assigned to the additions, in order
+   */
+  async addChanges(id, changes, rewrites = []) {
+    if (changes.length === 0 && rewrites.length === 0)
+      return [];
+    const changesetPath = this.getChangesetPath(id), lock = new FileLock(changesetPath);
+    try {
+      return await lock.withLock(async () => {
+        const changeset = await this.load(id);
+        if (!changeset)
+          throw new Error(`Changeset '${id}' not found`);
+        changeset.changes = withSequenceNumbers(changeset.changes, nextSequenceNumber(changeset));
+        for (const { elementId, change } of rewrites) {
+          const index = changeset.changes.findIndex((c) => c.elementId === elementId);
+          if (index === -1)
+            throw new Error(`No change for element '${elementId}' in changeset '${id}'`);
+          const existing = changeset.changes[index], rewrittenAt = nextSequenceNumber(changeset);
+          changeset.lastSequence = rewrittenAt, addTombstones(changeset, [
+            { sequence: existing.sequenceNumber, removedAt: rewrittenAt, change: compactChange(existing), rewritten: !0 }
+          ]), changeset.changes[index] = { ...existing, ...change, sequenceNumber: existing.sequenceNumber };
+        }
+        const numbers = [];
+        for (const change of changes) {
+          const sequenceNumber = nextSequenceNumber(changeset), staged = { ...change, sequenceNumber };
+          changeset.changes.push(staged), changeset.lastSequence = sequenceNumber, numbers.push(sequenceNumber);
+        }
+        return changeset.updateModified(), await this.save(changeset), numbers;
+      });
+    } catch (error) {
+      const errorMessage = getErrorMessage(error);
+      if (errorMessage.includes("lock") || errorMessage.includes("timeout")) {
+        const lockFilePath = path.join(changesetPath, ".lock");
+        throw new Error(`Failed to add changes to changeset '${id}': Lock acquisition failed.
+Error: ${errorMessage}
+
+This usually means another dr process is modifying this changeset.
+If no other processes are running, a stale lock file may exist.
+
+To resolve:
+  1. Wait for other operations to complete
+  2. Check for running dr processes: ps aux | grep dr
+  3. If no processes found, remove stale lock: rm "${lockFilePath}"
+  4. Retry the operation`);
+      }
+      throw new Error(`Failed to add changes to changeset '${id}': ${errorMessage}
 Changeset path: ${changesetPath}`);
     }
   }
@@ -188,17 +264,33 @@ Changeset path: ${changesetPath}`);
    * @throws {Error} If lock acquisition, changeset load, save, or lock release fails
    */
   async removeChange(id, elementId) {
-    const changesetPath = this.getChangesetPath(id), lock = new FileLock(changesetPath);
+    await this.removeChanges(id, [elementId]);
+  }
+  /**
+   * Remove every change to any of `elementIds` in one write. The removal is one revision: it takes
+   * one sequence number, and each removed change is kept as a tombstone.
+   *
+   * Uses file locking to prevent concurrent modification race conditions
+   *
+   * @throws {Error} If lock acquisition, changeset load, save, or lock release fails
+   */
+  async removeChanges(id, elementIds) {
+    const keys = new Set(elementIds), changesetPath = this.getChangesetPath(id), lock = new FileLock(changesetPath);
     try {
       await lock.withLock(async () => {
         const changeset = await this.load(id);
         if (!changeset)
           throw new Error(`Changeset '${id}' not found`);
-        const filtered = changeset.changes.filter((c) => c.elementId !== elementId);
-        changeset.changes = filtered.map((c, idx) => ({
-          ...c,
-          sequenceNumber: idx
-        })), changeset.updateModified(), await this.save(changeset);
+        const numbered = withSequenceNumbers(changeset.changes), removed = numbered.filter((c) => keys.has(c.elementId));
+        if (changeset.changes = numbered.filter((c) => !keys.has(c.elementId)), removed.length > 0) {
+          const removedAt = nextSequenceNumber({ ...changeset, changes: numbered });
+          changeset.lastSequence = removedAt, addTombstones(changeset, removed.map((c, index) => ({
+            sequence: sequenceOf(c, index),
+            removedAt,
+            change: compactChange(c)
+          })));
+        }
+        changeset.updateModified(), await this.save(changeset);
       });
     } catch (error) {
       const errorMessage = getErrorMessage(error);
@@ -239,11 +331,14 @@ Changeset path: ${changesetPath}`);
         const index = changeset.changes.findIndex((c) => c.elementId === elementId);
         if (index === -1)
           throw new Error(`No change for element '${elementId}' in changeset '${id}'`);
-        const existing = changeset.changes[index];
-        changeset.changes[index] = {
+        changeset.changes = withSequenceNumbers(changeset.changes, nextSequenceNumber(changeset));
+        const existing = changeset.changes[index], rewrittenAt = nextSequenceNumber(changeset);
+        changeset.lastSequence = rewrittenAt, addTombstones(changeset, [
+          { sequence: existing.sequenceNumber, removedAt: rewrittenAt, change: compactChange(existing), rewritten: !0 }
+        ]), changeset.changes[index] = {
           ...existing,
           ...updated,
-          sequenceNumber: existing.sequenceNumber ?? index
+          sequenceNumber: existing.sequenceNumber
         }, changeset.updateModified(), await this.save(changeset);
       });
     } catch (error) {
@@ -252,9 +347,40 @@ Changeset path: ${changesetPath}`);
 Changeset path: ${changesetPath}`);
     }
   }
+  /**
+   * Change a changeset's name and/or description in place, under the changeset's file lock so a
+   * concurrent stage cannot be lost. Staged changes are untouched.
+   *
+   * @returns The updated changeset
+   * @throws {Error} If the changeset is not found, or on lock or I/O failure
+   */
+  async updateMetadata(id, patch) {
+    return new FileLock(this.getChangesetPath(id)).withLock(async () => {
+      const changeset = await this.load(id);
+      if (!changeset)
+        throw new Error(`Changeset '${id}' not found`);
+      return patch.name !== void 0 && (changeset.name = patch.name), patch.description !== void 0 && (changeset.description = patch.description || void 0), changeset.updateModified(), await this.save(changeset), changeset;
+    });
+  }
   /**
    * Get the storage path for a changeset
    */
+  /**
+   * Remove every file in the changeset's directory except metadata.yaml and changes.yaml (and
+   * dotfiles such as a lock): e.g. the base index, once the changeset is discarded and nothing
+   * reads it again.
+   *
+   * @returns The names of the files removed
+   */
+  async removeSideFiles(id) {
+    const changesetPath = this.getChangesetPath(id);
+    if (!await fileExists(changesetPath))
+      return [];
+    const keep = /* @__PURE__ */ new Set(["metadata.yaml", "changes.yaml"]), removed = [];
+    for (const entry of await readdir(changesetPath, { withFileTypes: !0 }))
+      keep.has(entry.name) || entry.name.startsWith(".") || !entry.isFile() || (await rm(path.join(changesetPath, entry.name), { force: !0 }), removed.push(entry.name));
+    return removed;
+  }
   getChangesetPath(id) {
     const sanitizedId = this.sanitizeId(id);
     return path.join(this.changesetsDir, sanitizedId);
@@ -277,6 +403,7 @@ Changeset path: ${changesetPath}`);
   }
 }
 export {
+  MAX_UNSTAGED_TOMBSTONES,
   StagedChangesetStorage
 };
 //# sourceMappingURL=staged-changeset-storage.js.map