@documentation-robotics/cli 0.2.0 → 0.3.0

package/dist/core/staging-area.js.map

@@ -1,7 +1,7 @@
 {
   "version": 3,
   "sources": ["../../src/core/staging-area.ts"],
-  "sourcesContent": ["/**\n * StagingAreaManager - Manages staged changesets and interception logic\n *\n * Provides:\n * - Changeset lifecycle management (create, load, list, delete)\n * - Staging operations (stage, unstage, discard)\n * - Commit operations with drift detection and validation\n * - Base snapshot tracking for drift detection\n */\n\nimport path from \"path\";\nimport ansis from \"ansis\";\nimport { StagedChangesetStorage } from \"./staged-changeset-storage.js\";\nimport { BaseSnapshotManager } from \"./base-snapshot-manager.js\";\nimport { Changeset, StagedChange } from \"./changeset.js\";\nimport { ChangesetValidator } from \"./changeset-validator.js\";\nimport { fileExists } from \"../utils/file-io.js\";\nimport type { Model } from \"./model.js\";\nimport type { VirtualProjectionEngine } from \"./virtual-projection.js\";\nimport { createSha256Hash } from \"../types/index.js\";\nimport type { BackupManifest } from \"../types/index.js\";\nimport { getErrorMessage } from \"../utils/errors.js\";\nimport { Layer } from \"./layer.js\";\nimport { isValidLayerName } from \"./layers.js\";\nimport {\n  isTelemetryEnabled,\n  startSpan,\n  startActiveSpan,\n  endSpan,\n  emitLog,\n  SeverityNumber,\n} from \"../telemetry/index.js\";\nimport { ModelReportOrchestrator } from \"../reports/model-report-orchestrator.js\";\n\n/**\n * Options for commit operation\n */\nexport interface CommitOptions {\n  force?: boolean; // Ignore drift warnings\n  validate?: boolean; // Run validation (default: true)\n  dryRun?: boolean; // Preview without applying\n}\n\n/**\n * Drift report for change detection\n *\n * NOTE: Detects whether the base model has drifted (changed) since the changeset was created.\n * Current implementation only identifies that drift occurred (isDrifted flag).\n * Element-level change tracking is not implemented; detailed diff detection would require\n * storing complete snapshot data, not just hashes.\n */\nexport interface DriftReport {\n  isDrifted: boolean;\n  baseSnapshotId: string;\n  currentSnapshotId: string;\n  warnings: string[];\n}\n\n/**\n * Result of commit operation\n */\nexport interface CommitResult {\n  changeset: string;\n  committed: number;\n  skipped?: number;\n  skippedDetails?: string[];\n  failed: number;\n  validation: {\n    passed: boolean;\n    errors: string[];\n  };\n  driftWarning?: DriftReport;\n}\n\n/**\n * StagingAreaManager provides changeset and staging operations\n */\nexport class StagingAreaManager {\n  private storage: StagedChangesetStorage;\n  private snapshotManager: BaseSnapshotManager;\n  private validator: ChangesetValidator;\n  private projectionEngine: VirtualProjectionEngine | null = null;\n  private rootPath: string;\n  private model: Model | null = null;\n\n  constructor(rootPath: string, model?: Model) {\n    this.rootPath = rootPath;\n    this.model = model || null;\n    this.storage = new StagedChangesetStorage(rootPath);\n    this.snapshotManager = new BaseSnapshotManager();\n    this.validator = new ChangesetValidator(rootPath);\n    this.projectionEngine = null; // Lazy loaded on first call to getProjectionEngine()\n  }\n\n  /**\n   * Validate changeset ID format and content\n   * Ensures ID is safe and provides early validation before file operations\n   *\n   * Validation rules:\n   * - Must be a non-empty string\n   * - Cannot contain path separators (.., /, \\)\n   * - Cannot contain special characters (<>:\"|?*)\n   * - During storage, the ID will be normalized: lowercase, spaces\u2192hyphens, non-alphanumeric\u2192stripped\n   *\n   * @param changesetId - The changeset ID to validate\n   * @throws Error if ID contains invalid characters or structure\n   */\n  private validateChangesetId(changesetId: string): void {\n    if (!changesetId || typeof changesetId !== \"string\") {\n      throw new Error(\"Changeset ID must be a non-empty string\");\n    }\n\n    if (changesetId.trim() === \"\") {\n      throw new Error(\"Changeset ID cannot be empty or whitespace-only\");\n    }\n\n    // Check for path traversal attempts\n    if (changesetId.includes(\"..\") || changesetId.includes(\"/\") || changesetId.includes(\"\\\\\")) {\n      throw new Error(\"Changeset ID cannot contain path separators or traversal sequences (..)\");\n    }\n\n    // Check for special characters that could cause issues\n    // Note: sanitizeId() will normalize the ID by converting to lowercase, replacing spaces with hyphens,\n    // and removing all non-alphanumeric characters (except hyphens)\n    if (/[<>:\"|?*]/.test(changesetId)) {\n      throw new Error(\n        'Changeset ID contains invalid special characters (<>:\"|?*). ' +\n          \"Only alphanumeric characters and hyphens are preserved. \" +\n          \"Spaces are converted to hyphens, and other characters are removed during storage.\"\n      );\n    }\n  }\n\n  /**\n   * Get or create projection engine instance (lazy initialization).\n   * Deferred initialization avoids circular dependency issues at module load time.\n   * @returns VirtualProjectionEngine instance for computing merged model views\n   */\n  private async getProjectionEngine(): Promise<VirtualProjectionEngine> {\n    if (!this.projectionEngine) {\n      const { VirtualProjectionEngine } = await import(\"./virtual-projection.js\");\n      this.projectionEngine = new VirtualProjectionEngine(this.rootPath);\n    }\n    return this.projectionEngine;\n  }\n\n  /**\n   * Create a new staged changeset\n   */\n  async create(name: string, description?: string): Promise<Changeset> {\n    if (!this.model) {\n      throw new Error(\"Model required for creating changesets\");\n    }\n    const id = this.generateChangesetId();\n    const baseSnapshotId = await this.snapshotManager.captureSnapshot(this.model);\n\n    const changeset = await this.storage.create(id, name, description, baseSnapshotId);\n    changeset.id = id;\n\n    // Mark as 'staged' so it can accept changes immediately\n    changeset.markStaged();\n    await this.storage.save(changeset);\n\n    return changeset;\n  }\n\n  /**\n   * Load a changeset by name or ID\n   */\n  async load(name: string): Promise<Changeset | null> {\n    // Try loading directly as ID first\n    let changeset = await this.storage.load(name);\n    if (changeset) {\n      return changeset;\n    }\n\n    // If not found by ID, search by name in all changesets\n    const all = await this.storage.list();\n    return all.find((cs) => cs.name === name) || null;\n  }\n\n  /**\n   * List all staged changesets\n   */\n  async list(): Promise<Changeset[]> {\n    return this.storage.list();\n  }\n\n  /**\n   * Delete a changeset\n   * If the changeset being deleted is the currently active changeset,\n   * this method will also clear the active changeset marker.\n   */\n  async delete(name: string): Promise<void> {\n    const changeset = await this.load(name);\n    if (!changeset) {\n      throw new Error(`Changeset '${name}' not found`);\n    }\n\n    if (!changeset.id) {\n      throw new Error(`Changeset '${name}' has no ID and cannot be deleted`);\n    }\n\n    // Check if this changeset is the active one and clear it if so\n    const activeChangeset = await this.getActive();\n    if (activeChangeset && activeChangeset.id === changeset.id) {\n      await this.clearActive();\n    }\n\n    await this.storage.delete(changeset.id);\n  }\n\n  /**\n   * Stage a change in the changeset.\n   * Records the change in the staging area without applying to the base model.\n   * The changeset must be in 'staged' status to accept new changes.\n   *\n   * @param changesetId - ID of the changeset to stage the change in\n   * @param change - The change to stage (type, elementId, layerName, before/after snapshots)\n   * @throws Error if changeset ID is invalid, changeset not found, or not in 'staged' status\n   */\n  async stage(changesetId: string, change: Omit<StagedChange, \"sequenceNumber\">): Promise<void> {\n    this.validateChangesetId(changesetId);\n\n    const changeset = await this.load(changesetId);\n    if (!changeset) {\n      throw new Error(`Changeset '${changesetId}' not found`);\n    }\n\n    // Only allow staging when status is 'staged' (not 'committed' or 'discarded')\n    if (changeset.status !== \"staged\") {\n      throw new Error(\n        `Cannot stage changes on changeset with status '${changeset.status}'. ` +\n          `Changeset must have status 'staged' to accept new changes.`\n      );\n    }\n\n    const stagedChange: Omit<StagedChange, \"sequenceNumber\"> = {\n      ...change,\n      timestamp: change.timestamp || new Date().toISOString(),\n    };\n\n    await this.storage.addChange(changesetId, stagedChange);\n\n    // Invalidate projection cache for this layer\n    const engine = await this.getProjectionEngine();\n    engine.invalidateOnStage(changesetId, change.layerName);\n  }\n\n  /**\n   * Unstage a specific element from the changeset.\n   * Removes all changes associated with the element.\n   * The changeset must be in 'staged' status.\n   *\n   * @param changesetId - ID of the changeset to unstage from\n   * @param elementId - ID of the element to remove all changes for\n   * @throws Error if changeset ID is invalid, changeset not found, or not in 'staged' status\n   */\n  async unstage(changesetId: string, elementId: string): Promise<void> {\n    this.validateChangesetId(changesetId);\n\n    const changeset = await this.load(changesetId);\n    if (!changeset) {\n      throw new Error(`Changeset '${changesetId}' not found`);\n    }\n\n    if (changeset.status !== \"staged\") {\n      throw new Error(\n        `Cannot unstage changes on changeset with status '${changeset.status}'. ` +\n          `Changeset must have status 'staged'.`\n      );\n    }\n\n    // Remove the element's changes and resequence remaining changes\n    await this.storage.removeChange(changesetId, elementId);\n\n    // Invalidate projection cache for the removed element's layers\n    const engine = await this.getProjectionEngine();\n    await engine.invalidateOnUnstage(changesetId, elementId);\n  }\n\n  /**\n   * Discard all changes in the changeset.\n   * Clears all staged changes and marks the changeset as 'discarded'.\n   * This operation is irreversible for the changeset but does not affect the base model.\n   *\n   * @param changesetId - ID of the changeset to discard\n   * @throws Error if changeset ID is invalid or changeset not found\n   */\n  async discard(changesetId: string): Promise<void> {\n    this.validateChangesetId(changesetId);\n\n    const changeset = await this.load(changesetId);\n    if (!changeset) {\n      throw new Error(`Changeset '${changesetId}' not found`);\n    }\n\n    // Clear all staged changes and update status\n    changeset.changes = [];\n    changeset.status = \"discarded\";\n    // Note: stats are auto-computed from changes array (will be 0/0/0 after clearing)\n    changeset.updateModified();\n\n    await this.storage.save(changeset);\n\n    // Invalidate all projection cache entries for this changeset\n    const engine = await this.getProjectionEngine();\n    engine.invalidateOnDiscard(changesetId);\n  }\n\n  /**\n   * Capture a base snapshot of the current model state for drift detection.\n   * Stores a hash of the model that can be compared later to detect changes.\n   *\n   * @param changesetId - ID of the changeset to capture snapshot for\n   * @returns SHA256 hash of the current model state\n   * @throws Error if changeset not found or model not available\n   */\n  async captureBaseSnapshot(changesetId: string): Promise<string> {\n    this.validateChangesetId(changesetId);\n\n    if (!this.model) {\n      throw new Error(\"Model required for capturing base snapshot\");\n    }\n    const changeset = await this.load(changesetId);\n    if (!changeset) {\n      throw new Error(`Changeset '${changesetId}' not found`);\n    }\n\n    const snapshotId = await this.snapshotManager.captureSnapshot(this.model);\n    changeset.baseSnapshot = snapshotId;\n    changeset.updateModified();\n    await this.storage.save(changeset);\n\n    return snapshotId;\n  }\n\n  /**\n   * Detect drift by comparing base snapshot hash to current model state.\n   * Identifies whether the base model has changed since the changeset was created.\n   *\n   * @param changesetId - ID of the changeset to check for drift\n   * @returns DriftReport with isDrifted flag, snapshot hashes, and warnings\n   * @throws Error if changeset ID is invalid, changeset not found, or model not available\n   *\n   * @remarks\n   * Drift detection uses hash-based comparison of the entire model snapshot.\n   * Element-level change tracking is not implemented - only the isDrifted flag\n   * indicates if the model has changed. Detailed diff detection would require\n   * storing complete snapshot data, not just hashes.\n   * Returns isDrifted=false and warnings if no base snapshot was captured.\n   */\n  async detectDrift(changesetId: string): Promise<DriftReport> {\n    this.validateChangesetId(changesetId);\n\n    if (!this.model) {\n      throw new Error(\"Model required for drift detection\");\n    }\n    const changeset = await this.load(changesetId);\n    if (!changeset) {\n      throw new Error(`Changeset '${changesetId}' not found`);\n    }\n\n    if (!changeset.baseSnapshot) {\n      return {\n        isDrifted: false,\n        baseSnapshotId: \"unknown\",\n        currentSnapshotId: \"unknown\",\n        warnings: [\"No base snapshot available for drift detection\"],\n      };\n    }\n\n    // Capture current model snapshot to compare against base\n    const currentSnapshotId = await this.snapshotManager.captureSnapshot(this.model);\n\n    // Compare snapshot hashes to detect drift\n    // isDrifted=true indicates base model has changed since changeset creation\n    const isDrifted = changeset.baseSnapshot !== currentSnapshotId;\n\n    const warnings: string[] = [];\n\n    if (isDrifted) {\n      warnings.push(\n        `Model has drifted since changeset creation (base snapshot hash differs from current)`\n      );\n    }\n\n    return {\n      isDrifted,\n      baseSnapshotId: changeset.baseSnapshot,\n      currentSnapshotId: currentSnapshotId,\n      warnings,\n    };\n  }\n\n  /**\n   * Commit a changeset to the base model with atomic guarantee.\n   * Applies all staged changes and persists them to the base model.\n   *\n   * Implements atomic commit with the following steps:\n   * 1. Detect drift in base model (fail unless force=true)\n   * 2. Validate projected model (schema, references, semantics)\n   * 3. Create backup of current model state\n   * 4. Apply all changes in sequence order\n   * 5. Save all modified layers to disk\n   * 6. Update changeset status and manifest history\n   * 7. Cleanup backup on success, restore on failure\n   *\n   * @param model - The model to commit changes to\n   * @param changesetId - ID of the changeset to commit\n   * @param options - Commit options (force, validate, dryRun)\n   * @returns CommitResult with count of committed/failed changes and validation status\n   * @throws Error if validation fails, drift detected without --force, or commit fails\n   *\n   * @remarks\n   * Validation errors always block commit (force flag does not override).\n   * Drift warnings can be bypassed with --force flag.\n   * Dry-run mode performs all checks but does not persist changes.\n   * On commit failure, model state is restored from backup; rollback failure triggers CRITICAL error.\n   */\n  async commit(\n    model: Model,\n    changesetId: string,\n    options: CommitOptions = {}\n  ): Promise<CommitResult> {\n    return startActiveSpan(\"staging.commit\", async (span) => {\n      this.validateChangesetId(changesetId);\n\n      const changeset = await this.load(changesetId);\n      if (!changeset) {\n        throw new Error(`Changeset '${changesetId}' not found`);\n      }\n\n      (span as any).setAttribute(\"changeset.name\", changeset.name);\n      (span as any).setAttribute(\"changeset.changeCount\", changeset.changes.length);\n\n      const isDryRun = options.dryRun === true;\n      const shouldValidate = options.validate !== false;\n\n      // Step 1: Detect drift and throw if drifted without --force\n      const driftSpan = isTelemetryEnabled ? startSpan(\"staging.detectDrift\") : null;\n      const drift = await this.detectDrift(changesetId);\n      if (isTelemetryEnabled && driftSpan) {\n        (driftSpan as any).setAttribute(\"drift.detected\", drift.isDrifted);\n        (driftSpan as any).setAttribute(\"drift.baseSnapshotId\", drift.baseSnapshotId);\n        (driftSpan as any).setAttribute(\"drift.currentSnapshotId\", drift.currentSnapshotId);\n        (driftSpan as any).setStatus({ code: 0 });\n      }\n      endSpan(driftSpan);\n\n      if (drift.isDrifted) {\n        (span as any).setAttribute(\"commit.driftDetected\", true);\n        if (options.force) {\n          emitLog(SeverityNumber.WARN, \"Drift detected but overridden with --force\", {\n            \"drift.baseSnapshot\": drift.baseSnapshotId,\n            \"drift.currentSnapshot\": drift.currentSnapshotId,\n          });\n        } else {\n          emitLog(SeverityNumber.ERROR, \"Drift detected, commit blocked\", {\n            \"drift.baseSnapshot\": drift.baseSnapshotId,\n            \"drift.currentSnapshot\": drift.currentSnapshotId,\n          });\n          throw new Error(\n            `Base model has drifted since changeset creation. ` + `Use --force to commit anyway.`\n          );\n        }\n      }\n\n      const result: CommitResult = {\n        changeset: changeset.name,\n        committed: 0,\n        skipped: 0,\n        skippedDetails: [],\n        failed: 0,\n        validation: {\n          passed: true,\n          errors: [],\n        },\n      };\n\n      // Step 2: Validate against projected model (force cannot override validation)\n      if (shouldValidate) {\n        await startActiveSpan(\"staging.validate\", async (validationSpan) => {\n          const validation = await this.validator.validateChangeset(model, changesetId);\n\n          (validationSpan as any).setAttribute(\"validation.passed\", validation.isValid());\n          (validationSpan as any).setAttribute(\"validation.errorCount\", validation.errors.length);\n          (validationSpan as any).setStatus({ code: 0 });\n\n          if (!validation.isValid()) {\n            result.validation.passed = false;\n            result.validation.errors = validation.errors.map((e) => e.message);\n\n            emitLog(SeverityNumber.ERROR, \"Validation failed\", {\n              \"validation.errorCount\": result.validation.errors.length,\n              \"validation.errors\": result.validation.errors.slice(0, 10), // First 10 errors\n            });\n\n            throw new Error(\n              `Validation failed with ${result.validation.errors.length} error(s):\\n` +\n                result.validation.errors.map((e) => `  - ${e}`).join(\"\\n\") +\n                `\\n\\nFix these validation errors before committing.`\n            );\n          }\n        });\n      }\n\n      // Step 3: Dry run early exit (before making any changes)\n      if (isDryRun) {\n        result.committed = changeset.changes.length;\n        if (drift.isDrifted) {\n          result.driftWarning = drift;\n        }\n        return result;\n      }\n\n      // Step 4: Backup model state for atomic rollback\n      let backup: string;\n      try {\n        backup = await this.backupModel(model);\n      } catch (backupError) {\n        // Backup creation failed - cannot proceed safely\n        throw new Error(\n          `Failed to create backup before commit. No changes have been applied. ` +\n            `${backupError instanceof Error ? backupError.message : String(backupError)}`\n        );\n      }\n\n      // Step 5: Apply all changes sequentially by sequence number\n      const sortedChanges = [...(changeset.changes as StagedChange[])].sort(\n        (a, b) => a.sequenceNumber - b.sequenceNumber\n      );\n\n      try {\n        const applySpan = isTelemetryEnabled\n          ? startSpan(\"staging.apply\", {\n              \"apply.changeCount\": changeset.changes.length,\n            })\n          : null;\n\n        try {\n          for (const change of sortedChanges) {\n            try {\n              // Use getBaseLayer() so commit operates on the actual mutable base layer,\n              // not a projected clone. getLayer() would return a projected (read-only clone)\n              // which cannot be persisted via saveLayer().\n              let layer = await model.getBaseLayer(change.layerName);\n              if (!layer) {\n                // Layer directory doesn't exist yet \u2014 this changeset introduces\n                // the first elements for this layer. Create an empty layer and\n                // register it so saveLayer() will create the directory on disk.\n                layer = new Layer(change.layerName);\n                model.addLayer(layer);\n              }\n\n              if (change.type === \"relationship-add\" && change.after) {\n                // Relationship-add: the relationship was already injected into model.relationships\n                // during Model.load() for transparent read-path visibility. Here we just need\n                // saveRelationships() to persist it. Skip adding if it already exists.\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                const existing = model.relationships.find(rel.source, rel.target, rel.predicate);\n                if (existing.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                result.committed++;\n                continue;\n              }\n\n              if (change.type === \"relationship-delete\" && change.before) {\n                // Relationship-delete: the relationship was already removed from model.relationships\n                // during Model.load(). Just ensure it's gone and count it.\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                result.committed++;\n                continue;\n              }\n\n              if (change.type === \"add\" && change.after) {\n                const { Element } = await import(\"./element.js\");\n                const elementData = change.after as Record<string, unknown>;\n                const elementId = elementData.id as string;\n\n                // Check if element already exists using the UUID from elementData\n                const elements = layer.listElements();\n                const elementExists = elements.some((e) => e.id === elementId);\n\n                if (!elementExists) {\n                  // Pass the entire elementData to Element constructor - it already has all fields from toJSON()\n                  const element = new Element(elementData);\n                  layer.addElement(element);\n                  result.committed++;\n                } else {\n                  result.skipped = (result.skipped ?? 0) + 1;\n                  result.skippedDetails = result.skippedDetails ?? [];\n                  result.skippedDetails.push(\n                    `'${elementId}' in '${change.layerName}' already exists \u2014 deduplicated`\n                  );\n                  emitLog(SeverityNumber.WARN, \"Element deduplicated during commit\", {\n                    \"change.elementId\": change.elementId,\n                    \"change.layer\": change.layerName,\n                  });\n                }\n              } else if (change.type === \"update\" && change.after) {\n                const element = layer.getElement(change.elementId);\n                if (element) {\n                  const elementData = change.after as Record<string, unknown>;\n                  Object.assign(element, elementData);\n                  // Persist the mutation back to the underlying graph node.\n                  // getElement() returns a new wrapper each time, so Object.assign\n                  // alone is discarded; updateElement() writes through to the graph.\n                  layer.updateElement(element);\n                  result.committed++;\n                } else {\n                  result.failed++;\n                  result.validation.passed = false;\n                  result.validation.errors.push(\n                    `Cannot update '${change.elementId}' in '${change.layerName}': element not found in base model`\n                  );\n                }\n              } else if (change.type === \"delete\") {\n                const element = layer.getElement(change.elementId);\n                if (element) {\n                  layer.deleteElement(element.path || element.id);\n                  result.committed++;\n                } else {\n                  // Element was already removed \u2014 count as skipped, not failed\n                  result.skipped = (result.skipped ?? 0) + 1;\n                  result.skippedDetails = result.skippedDetails ?? [];\n                  result.skippedDetails.push(\n                    `'${change.elementId}' in '${change.layerName}' not found \u2014 already deleted`\n                  );\n                }\n              } else {\n                // Handles: unknown change types, and known types with missing payloads\n                // (e.g. \"add\" with no change.after, \"relationship-add\" with no change.after).\n                result.failed++;\n                result.validation.passed = false;\n                result.validation.errors.push(\n                  `Cannot apply change '${change.type}' for '${change.elementId}': missing payload or unrecognised type`\n                );\n              }\n            } catch (error) {\n              result.failed++;\n              result.validation.passed = false;\n              result.validation.errors.push(\n                `Failed to apply change to ${change.elementId}: ${getErrorMessage(error)}`\n              );\n\n              emitLog(SeverityNumber.ERROR, \"Failed to apply change\", {\n                \"change.elementId\": change.elementId,\n                \"change.type\": change.type,\n                \"change.layer\": change.layerName,\n                \"error.message\": getErrorMessage(error),\n              });\n\n              throw new Error(\n                `Atomic commit failed at change ${sortedChanges.indexOf(change) + 1}/${sortedChanges.length}: ` +\n                  `${getErrorMessage(error)}`\n              );\n            }\n          }\n\n          if (isTelemetryEnabled && applySpan) {\n            (applySpan as any).setAttribute(\"apply.committed\", result.committed);\n            (applySpan as any).setAttribute(\"apply.failed\", result.failed);\n            (applySpan as any).setStatus({ code: 0 });\n          }\n        } finally {\n          endSpan(applySpan);\n        }\n\n        // Step 6: Save all modified layers and relationships atomically\n        const modifiedLayers = new Set<string>();\n        let hasRelationshipChanges = false;\n        for (const change of sortedChanges) {\n          if (change.type === \"relationship-add\" || change.type === \"relationship-delete\") {\n            hasRelationshipChanges = true;\n          } else {\n            modifiedLayers.add(change.layerName);\n          }\n        }\n\n        for (const layerName of modifiedLayers) {\n          try {\n            await model.saveLayer(layerName);\n          } catch (error) {\n            throw new Error(\n              `Failed to save layer '${layerName}': ${getErrorMessage(error)}`\n            );\n          }\n        }\n\n        // Persist staged relationship changes to relationships.yaml\n        if (hasRelationshipChanges) {\n          try {\n            await model.saveRelationships();\n          } catch (error) {\n            throw new Error(\n              `Failed to save relationships after commit: ${getErrorMessage(error)}`\n            );\n          }\n        }\n\n        // Step 7: Update changeset status to committed ONLY AFTER successful saves\n        changeset.status = \"committed\";\n        changeset.updateModified();\n\n        try {\n          await this.storage.save(changeset);\n        } catch (error) {\n          // Changeset status is critical metadata - must be persisted with model changes\n          throw new Error(\n            `Failed to save changeset status after commit: ${getErrorMessage(error)}. ` +\n              `This is a critical error that requires rollback to maintain consistency between model state and changeset metadata.`\n          );\n        }\n\n        // Step 8: Add changeset to manifest history\n        if (!model.manifest.changeset_history) {\n          model.manifest.changeset_history = [];\n        }\n        model.manifest.changeset_history.push({\n          name: changeset.name,\n          committed_at: new Date().toISOString(),\n          action: \"committed\",\n        });\n\n        // Step 9: Save manifest with updated changeset history\n        try {\n          await model.saveManifest();\n        } catch (manifestError) {\n          // Manifest save failed - this is CRITICAL and will trigger rollback\n          // Don't log here - let the rollback handler provide comprehensive error output\n          throw new Error(\n            `Failed to save manifest with changeset history: ${manifestError instanceof Error ? manifestError.message : String(manifestError)}. ` +\n              `Model will be rolled back to maintain consistency.`\n          );\n        }\n\n        // Step 9.5: Regenerate reports for all layers modified by this changeset\n        try {\n          const orchestrator = new ModelReportOrchestrator(model, model.rootPath);\n          const affectedLayers = new Set<string>();\n          for (const change of sortedChanges) {\n            if (isValidLayerName(change.layerName)) {\n              for (const layer of orchestrator.computeAffectedLayers(change.layerName)) {\n                affectedLayers.add(layer);\n              }\n            }\n          }\n          await orchestrator.regenerate(affectedLayers);\n        } catch (error) {\n          emitLog(\n            SeverityNumber.WARN,\n            \"Failed to regenerate layer reports after changeset commit\",\n            {\n              \"changeset.id\": changesetId,\n              \"changeset.name\": changeset.name,\n              \"changeset.changeCount\": sortedChanges.length,\n              \"error.message\": getErrorMessage(error),\n            }\n          );\n        }\n\n        // Step 10: Clean up backup directory after successful commit\n        // Note: cleanupBackup handles its own errors and logs them with ERROR severity\n        await this.cleanupBackup(backup);\n\n        (span as any).setAttribute(\"commit.success\", true);\n        (span as any).setAttribute(\"commit.committed\", result.committed);\n        if (drift.isDrifted) {\n          (span as any).setAttribute(\"commit.driftOverridden\", true);\n        }\n        (span as any).setStatus({ code: 0 });\n\n        return result;\n      } catch (commitError) {\n        // Attempt rollback on any failure - restore from backup\n        let rollbackSucceeded = false;\n        let rollbackError: Error | null = null;\n\n        const rollbackSpan = isTelemetryEnabled ? startSpan(\"staging.rollback\") : null;\n\n        try {\n          emitLog(SeverityNumber.WARN, \"Commit failed, attempting rollback\", {\n            \"commit.error\":\n              commitError instanceof Error ? commitError.message : String(commitError),\n          });\n\n          await this.restoreModel(model, backup);\n          rollbackSucceeded = true;\n\n          if (isTelemetryEnabled && rollbackSpan) {\n            (rollbackSpan as any).setAttribute(\"rollback.success\", true);\n            (rollbackSpan as any).setStatus({ code: 0 });\n          }\n\n          emitLog(SeverityNumber.INFO, \"Rollback succeeded, model restored\", {\n            \"backup.path\": backup,\n          });\n        } catch (err) {\n          rollbackError = err instanceof Error ? err : new Error(String(err));\n\n          if (isTelemetryEnabled && rollbackSpan) {\n            (rollbackSpan as any).setAttribute(\"rollback.success\", false);\n            (rollbackSpan as any).recordException(rollbackError);\n            (rollbackSpan as any).setStatus({ code: 2, message: rollbackError.message });\n          }\n\n          emitLog(SeverityNumber.ERROR, \"Rollback failed, model may be corrupted\", {\n            \"rollback.error\": rollbackError.message,\n            \"backup.path\": backup,\n          });\n        } finally {\n          endSpan(rollbackSpan);\n        }\n\n        // CRITICAL: Validate backup integrity BEFORE suggesting manual restoration\n        let backupHealth: { isValid: boolean; filesChecked: number; errors: string[] };\n        let backupValidationError: string | null = null;\n        let validationProcessFailed = false;\n\n        try {\n          backupHealth = await this.validateBackupIntegrity(backup);\n        } catch (validationErr) {\n          validationProcessFailed = true;\n          backupValidationError =\n            validationErr instanceof Error ? validationErr.message : String(validationErr);\n          backupHealth = {\n            isValid: false,\n            filesChecked: 0,\n            errors: [\n              `Validation process failed: ${backupValidationError}`,\n              `This indicates a critical issue with the backup infrastructure, not the backup content.`,\n              `Contact support before attempting manual restoration.`,\n            ],\n          };\n        }\n\n        // Build comprehensive error message\n        let compositeMessage: string;\n        const suggestions: string[] = [];\n\n        if (rollbackSucceeded) {\n          // Rollback succeeded - throw original commit error\n          compositeMessage = `Commit failed but rollback succeeded. Model restored to pre-commit state.\\n\\n`;\n          compositeMessage += `Error during commit:\\n`;\n          compositeMessage += `  ${commitError instanceof Error ? commitError.message : String(commitError)}\\n\\n`;\n          compositeMessage += `Backup location (for reference): ${backup}`;\n\n          // Clean up backup after successful rollback\n          // Note: cleanupBackup handles its own errors and logs them with ERROR severity\n          await this.cleanupBackup(backup);\n\n          (span as any).setAttribute(\"commit.success\", false);\n          (span as any).setAttribute(\"commit.rollbackSuccess\", true);\n          (span as any).recordException(commitError as Error);\n          (span as any).setStatus({\n            code: 2,\n            message: commitError instanceof Error ? commitError.message : String(commitError),\n          });\n\n          throw new Error(compositeMessage);\n        } else {\n          // Rollback failed - model may be corrupted\n          compositeMessage =\n            `Commit failed AND rollback failed. Model may be in corrupted state.\\n` +\n            `\\n` +\n            `Original commit error:\\n` +\n            `  ${commitError instanceof Error ? commitError.message : String(commitError)}\\n` +\n            `\\n` +\n            `Rollback error:\\n` +\n            `  ${rollbackError ? rollbackError.message : \"Unknown error\"}\\n` +\n            `\\n` +\n            `Backup location: ${backup}\\n`;\n\n          // Add backup health status (always show header for consistency with tests)\n          compositeMessage += `Backup integrity check:\\n`;\n          if (validationProcessFailed) {\n            compositeMessage += `  \u2717 Backup integrity issues found:\\n`;\n            compositeMessage += `    - Validation process failed: ${backupValidationError}\\n`;\n            compositeMessage += `\\n\u26A0 CRITICAL: Backup validation process crashed.\\n`;\n            compositeMessage += `This indicates a system-level issue (filesystem, memory, permissions).\\n`;\n            compositeMessage += `DO NOT attempt manual restoration until this is resolved.\\n`;\n          } else if (backupHealth.isValid) {\n            compositeMessage += `  \u2713 Backup is valid (${backupHealth.filesChecked} files checked)\\n`;\n          } else {\n            compositeMessage += `  \u2717 Backup integrity issues found:\\n`;\n            for (const error of backupHealth.errors) {\n              compositeMessage += `    - ${error}\\n`;\n            }\n          }\n\n          compositeMessage += `\\n`;\n\n          if (backupHealth.isValid) {\n            suggestions.push(\n              `Backup is valid. Manually restore from backup: ${backup}`,\n              `Copy manifest.json/manifest.yaml from backup to ${path.join(model.rootPath, \"documentation-robotics\")}`,\n              `Copy layer files from ${path.join(backup, \"layers\")} to ${path.join(model.rootPath, \"documentation-robotics\", \"layers\")}`,\n              `Run 'dr validate' after manual restoration`,\n              `Contact support if issue persists`\n            );\n          } else {\n            suggestions.push(\n              `\u26A0 Backup integrity is compromised. Do NOT use this backup for recovery.`,\n              `Check if backup files exist at: ${backup}`,\n              `Verify disk space and file permissions`,\n              `Contact support immediately - manual data recovery may be required`,\n              `Do not attempt manual restoration with a corrupted backup`\n            );\n          }\n\n          compositeMessage += `Manual recovery may be required.`;\n\n          (span as any).setAttribute(\"commit.success\", false);\n          (span as any).setAttribute(\"commit.rollbackSuccess\", false);\n          (span as any).recordException(commitError as Error);\n          (span as any).setStatus({ code: 2, message: \"Commit and rollback both failed\" });\n\n          const { CLIError } = await import(\"../utils/errors.js\");\n          throw new CLIError(compositeMessage, 1, suggestions);\n        }\n      }\n    }, {\n      \"changeset.id\": changesetId,\n      \"commit.validate\": options.validate !== false,\n      \"commit.force\": options.force === true,\n      \"commit.dryRun\": options.dryRun === true,\n    });\n  }\n\n  /**\n   * Check if a changeset is currently active.\n   * Active changesets intercept mutations to stage changes instead of applying to base model.\n   *\n   * @param changesetId - ID of the changeset to check\n   * @returns true if changeset is marked as active, false otherwise\n   * @throws Error if changeset ID is invalid\n   */\n  async isActive(changesetId: string): Promise<boolean> {\n    this.validateChangesetId(changesetId);\n\n    const activePath = path.join(this.rootPath, \"documentation-robotics\", \"changesets\", \".active\");\n    if (!(await fileExists(activePath))) {\n      return false;\n    }\n\n    const { readFile } = await import(\"../utils/file-io.js\");\n    const activeId = await readFile(activePath);\n    return activeId.trim() === changesetId;\n  }\n\n  /**\n   * Activate a changeset to intercept model mutations.\n   * Marks the changeset as active and transitions status to 'staged'.\n   * Only one changeset can be active at a time.\n   *\n   * @param changesetId - ID of the changeset to activate\n   * @throws Error if changeset ID is invalid or changeset not found\n   *\n   * @remarks\n   * When a changeset is active, add/update/delete commands will stage changes\n   * instead of applying them directly to the base model.\n   */\n  async setActive(changesetId: string): Promise<void> {\n    this.validateChangesetId(changesetId);\n\n    const changeset = await this.load(changesetId);\n    if (!changeset) {\n      throw new Error(`Changeset '${changesetId}' not found`);\n    }\n\n    // Transition to 'staged' status to enable interception\n    if (changeset.status !== \"staged\") {\n      changeset.markStaged();\n      await this.storage.save(changeset);\n    }\n\n    const { writeFile, ensureDir } = await import(\"../utils/file-io.js\");\n    const changesetDir = path.join(this.rootPath, \"documentation-robotics\", \"changesets\");\n    await ensureDir(changesetDir);\n\n    const activePath = path.join(changesetDir, \".active\");\n    // Write the actual changeset ID (not the user-provided name)\n    if (!changeset.id) {\n      throw new Error(`Changeset has no ID, cannot activate`);\n    }\n    await writeFile(activePath, changeset.id);\n  }\n\n  /**\n   * Clear the active changeset marker.\n   * Allows a new changeset to be activated or model mutations to proceed normally.\n   */\n  async clearActive(): Promise<void> {\n    const { writeFile } = await import(\"../utils/file-io.js\");\n    const activePath = path.join(this.rootPath, \"documentation-robotics\", \"changesets\", \".active\");\n\n    if (await fileExists(activePath)) {\n      await writeFile(activePath, \"\");\n    }\n  }\n\n  /**\n   * Get the currently active changeset.\n   * Returns null if no changeset is active.\n   *\n   * @returns The active changeset or null if none is active\n   */\n  async getActive(): Promise<Changeset | null> {\n    const activePath = path.join(this.rootPath, \"documentation-robotics\", \"changesets\", \".active\");\n\n    if (!(await fileExists(activePath))) {\n      return null;\n    }\n\n    const { readFile } = await import(\"../utils/file-io.js\");\n    const activeId = await readFile(activePath);\n    const id = activeId.trim();\n\n    if (!id) {\n      return null;\n    }\n\n    return this.storage.load(id);\n  }\n\n  /**\n   * Get the ID of the active changeset without loading the full changeset object.\n   * Useful for status display and quick active changeset checks.\n   *\n   * @returns The active changeset ID or null if no active changeset exists\n   */\n  async getActiveId(): Promise<string | null> {\n    const activePath = path.join(this.rootPath, \"documentation-robotics\", \"changesets\", \".active\");\n\n    if (!(await fileExists(activePath))) {\n      return null;\n    }\n\n    const { readFile } = await import(\"../utils/file-io.js\");\n    const activeId = await readFile(activePath);\n    const id = activeId.trim();\n\n    return id || null;\n  }\n\n  /**\n   * Apply a changeset to the base model.\n   * Alias for commit() to match legacy command terminology.\n   *\n   * @param model - The model to apply changes to\n   * @param changesetId - ID of the changeset to apply\n   * @param options - Commit options (force, validate, dryRun)\n   * @returns CommitResult with count of applied changes and validation status\n   * @throws Error if validation fails, drift detected without --force, or apply fails\n   *\n   * @remarks\n   * This method provides backward compatibility with changeset commands that use\n   * \"apply\" instead of \"commit\" terminology. All logic is delegated to commit().\n   */\n  async apply(\n    model: Model,\n    changesetId: string,\n    options: CommitOptions = {}\n  ): Promise<CommitResult> {\n    return this.commit(model, changesetId, options);\n  }\n\n  /**\n   * Revert a changeset without applying changes.\n   * Alias for discard() to match legacy command terminology.\n   *\n   * @param changesetId - ID of the changeset to revert\n   * @throws Error if changeset ID is invalid or changeset not found\n   *\n   * @remarks\n   * This method provides backward compatibility with changeset commands that use\n   * \"revert\" instead of \"discard\" terminology. All logic is delegated to discard().\n   */\n  async revert(changesetId: string): Promise<void> {\n    return this.discard(changesetId);\n  }\n\n  /**\n   * Backup the current model state for atomic rollback on commit failure.\n   * Creates a temporary backup directory with copies of all layer files and manifest.\n   * Validates backup completeness and calculates checksums for integrity verification.\n   *\n   * @param model - The model to backup\n   * @returns Path to the backup directory\n   * @throws Error if backup creation or validation fails\n   *\n   * @remarks\n   * Backup includes:\n   * - manifest.yaml or manifest.json\n   * - All layer YAML files\n   * - Backup manifest with checksums and metadata\n   * Backup is removed after successful commit; retained if commit fails for recovery.\n   */\n  private async backupModel(model: Model): Promise<string> {\n    const backupDir = path.join(\n      this.rootPath,\n      \"documentation-robotics\",\n      \".backups\",\n      `backup-${Date.now()}`\n    );\n\n    const { ensureDir, readFile, atomicWrite } = await import(\"../utils/file-io.js\");\n    const { createHash } = await import(\"crypto\");\n\n    await ensureDir(backupDir);\n\n    // Track what we're backing up for validation\n    // Use mutable array during construction, then make readonly when creating BackupManifest\n    const backupFiles: Array<{\n      path: string;\n      checksum: ReturnType<typeof createSha256Hash>;\n      size: number;\n    }> = [];\n    const timestamp = new Date().toISOString();\n\n    try {\n      // Backup manifest - try both .yaml and .json formats\n      let manifestPath = path.join(\n        model.rootPath,\n        \"documentation-robotics\",\n        \"model\",\n        \"manifest.yaml\"\n      );\n      if (!(await fileExists(manifestPath))) {\n        manifestPath = path.join(model.rootPath, \"documentation-robotics\", \"manifest.json\");\n      }\n      if (!(await fileExists(manifestPath))) {\n        throw new Error(\"Manifest file not found in expected locations\");\n      }\n\n      const manifestContent = await readFile(manifestPath);\n      const manifestChecksum = createSha256Hash(\n        createHash(\"sha256\").update(manifestContent).digest(\"hex\")\n      );\n      const manifestFilename = path.basename(manifestPath);\n\n      await atomicWrite(path.join(backupDir, manifestFilename), manifestContent);\n      backupFiles.push({\n        path: manifestFilename,\n        checksum: manifestChecksum,\n        size: manifestContent.length,\n      });\n\n      // Backup all layers - handle multiple YAML files per layer\n      const layersDir = path.join(backupDir, \"layers\");\n      await ensureDir(layersDir);\n\n      const fs = await import(\"fs/promises\");\n\n      for (const layer of model.layers.values()) {\n        const layerBackupDir = path.join(layersDir, layer.name);\n        await ensureDir(layerBackupDir);\n\n        // Find the layer directory in the model\n        const layerDirPath = await this.findLayerDirectory(model.rootPath, layer.name);\n        if (!layerDirPath) {\n          continue;\n        }\n\n        // Backup all YAML files in the layer directory\n        const files = await fs.readdir(layerDirPath);\n        for (const file of files) {\n          if (file.endsWith(\".yaml\") || file.endsWith(\".yml\")) {\n            const filePath = path.join(layerDirPath, file);\n            const fileContent = await readFile(filePath);\n            const fileChecksum = createSha256Hash(\n              createHash(\"sha256\").update(fileContent).digest(\"hex\")\n            );\n\n            await atomicWrite(path.join(layerBackupDir, file), fileContent);\n            backupFiles.push({\n              path: `layers/${layer.name}/${file}`,\n              checksum: fileChecksum,\n              size: fileContent.length,\n            });\n          }\n        }\n      }\n\n      // Create the final immutable BackupManifest\n      const backupManifest: BackupManifest = {\n        files: backupFiles as ReadonlyArray<(typeof backupFiles)[0]>,\n        timestamp,\n      };\n\n      // Write backup manifest for validation\n      await atomicWrite(\n        path.join(backupDir, \".backup-manifest.json\"),\n        JSON.stringify(backupManifest, null, 2)\n      );\n\n      // Validate backup completeness\n      await this.validateBackup(backupDir, backupManifest);\n\n      return backupDir;\n    } catch (error) {\n      // Clean up incomplete backup with detailed error handling\n      const cleanupError = await this.forceRemoveBackupDir(backupDir);\n\n      if (cleanupError) {\n        // This is CRITICAL - orphaned backups accumulate\n        throw new Error(\n          `Backup creation failed AND cleanup failed.\\n` +\n            `Original error: ${getErrorMessage(error)}\\n` +\n            `Cleanup error: ${cleanupError}\\n\\n` +\n            `Orphaned backup directory: ${backupDir}\\n` +\n            `This directory will accumulate and consume disk space.\\n\\n` +\n            `REQUIRED ACTIONS:\\n` +\n            `  1. Manually remove: rm -rf \"${backupDir}\"\\n` +\n            `  2. Check disk space: df -h\\n` +\n            `  3. Check permissions: ls -la \"${path.dirname(backupDir)}\"\\n\\n` +\n            `Cannot proceed with commit until this is resolved.`\n        );\n      }\n\n      throw new Error(\n        `Failed to create backup: ${getErrorMessage(error)}`\n      );\n    }\n  }\n\n  /**\n   * Validate backup completeness and file integrity.\n   * Verifies that all files in the manifest exist in the backup directory\n   * with matching checksums and sizes.\n   *\n   * @param backupDir - Path to the backup directory\n   * @param manifest - Backup manifest with file list and checksums\n   * @throws Error if any file is missing, checksum mismatches, or size differs\n   */\n  private async validateBackup(backupDir: string, manifest: BackupManifest): Promise<void> {\n    const { readFile, fileExists } = await import(\"../utils/file-io.js\");\n    const { createHash } = await import(\"crypto\");\n\n    for (const file of manifest.files) {\n      const backupFilePath = path.join(backupDir, file.path);\n\n      // Verify file exists\n      if (!(await fileExists(backupFilePath))) {\n        throw new Error(`Backup validation failed: ${file.path} not found in backup`);\n      }\n\n      // Verify checksum matches\n      const content = await readFile(backupFilePath);\n      const checksum = createHash(\"sha256\").update(content).digest(\"hex\");\n\n      if (checksum !== file.checksum) {\n        throw new Error(\n          `Backup validation failed: ${file.path} checksum mismatch (expected ${file.checksum}, got ${checksum})`\n        );\n      }\n\n      // Verify size matches\n      if (content.length !== file.size) {\n        throw new Error(\n          `Backup validation failed: ${file.path} size mismatch (expected ${file.size}, got ${content.length})`\n        );\n      }\n    }\n  }\n\n  /**\n   * Validate backup integrity by checking manifest and file checksums.\n   * This is called before suggesting manual restoration to ensure the backup is usable.\n   * @param backupDir - Path to the backup directory\n   * @returns Promise resolving to backup health status or throwing error with details\n   * @throws Error with details about any integrity issues found\n   */\n  async validateBackupIntegrity(backupDir: string): Promise<{\n    isValid: boolean;\n    filesChecked: number;\n    errors: string[];\n  }> {\n    const { readFile, fileExists } = await import(\"../utils/file-io.js\");\n    const { createHash } = await import(\"crypto\");\n\n    const errors: string[] = [];\n    let filesChecked = 0;\n\n    try {\n      // Check if backup directory exists\n      if (!(await fileExists(backupDir))) {\n        throw new Error(`Backup directory not found: ${backupDir}`);\n      }\n\n      // Load and validate backup manifest\n      const manifestPath = path.join(backupDir, \".backup-manifest.json\");\n      if (!(await fileExists(manifestPath))) {\n        throw new Error(`Backup manifest not found at ${manifestPath}`);\n      }\n\n      // Read manifest content first (can throw for parse errors)\n      let rawManifest;\n      try {\n        const manifestContent = await readFile(manifestPath);\n        if (!manifestContent || manifestContent.length === 0) {\n          throw new Error(\"Backup manifest is empty\");\n        }\n        rawManifest = JSON.parse(manifestContent.toString());\n      } catch (err) {\n        // JSON parse errors should throw - these are critical errors\n        throw new Error(\n          `Failed to read backup manifest: ${err instanceof Error ? err.message : String(err)}`\n        );\n      }\n\n      // Validate manifest structure (can throw for missing required arrays)\n      if (!rawManifest || typeof rawManifest !== \"object\") {\n        throw new Error(\"Backup manifest must be an object\");\n      }\n\n      if (!rawManifest.files || !Array.isArray(rawManifest.files)) {\n        throw new Error(\"Backup manifest must have a files array\");\n      }\n\n      // Validate each file entry in the manifest and collect errors gracefully\n      for (let index = 0; index < rawManifest.files.length; index++) {\n        const file = rawManifest.files[index];\n        filesChecked++;\n\n        // Validate file entry structure\n        if (!file || typeof file !== \"object\") {\n          errors.push(`Backup manifest file entry ${index} must be an object`);\n          continue;\n        }\n\n        if (typeof file.path !== \"string\" || !file.path) {\n          errors.push(`Backup manifest file entry ${index} must have a non-empty path string`);\n          continue;\n        }\n\n        // Validate required metadata fields - these are validation errors, not critical\n        if (typeof file.checksum !== \"string\") {\n          errors.push(`Backup manifest file entry ${index} must have a checksum string`);\n          continue;\n        }\n\n        if (typeof file.size !== \"number\" || file.size < 0) {\n          errors.push(`Backup manifest file entry ${index} must have a non-negative size number`);\n          continue;\n        }\n\n        // File validation: check file exists and integrity\n        const backupFilePath = path.join(backupDir, file.path);\n\n        // Check file exists\n        if (!(await fileExists(backupFilePath))) {\n          errors.push(`Missing: ${file.path}`);\n          continue;\n        }\n\n        // Check checksum\n        try {\n          const content = await readFile(backupFilePath);\n          const checksum = createHash(\"sha256\").update(content).digest(\"hex\");\n\n          if (checksum !== file.checksum) {\n            errors.push(\n              `Checksum mismatch: ${file.path} (expected ${file.checksum}, got ${checksum})`\n            );\n            continue;\n          }\n\n          // Check size\n          if (content.length !== file.size) {\n            errors.push(\n              `Size mismatch: ${file.path} (expected ${file.size}, got ${content.length})`\n            );\n          }\n        } catch (err) {\n          errors.push(\n            `Failed to validate: ${file.path} (${err instanceof Error ? err.message : String(err)})`\n          );\n        }\n      }\n\n      return {\n        isValid: errors.length === 0,\n        filesChecked,\n        errors,\n      };\n    } catch (err) {\n      throw new Error(\n        `Backup integrity check failed: ${err instanceof Error ? err.message : String(err)}`\n      );\n    }\n  }\n\n  /**\n   * Clean up a backup directory after successful commit.\n   * Removes the backup directory and all its contents to prevent disk space accumulation.\n   *\n   * @param backupDir - Path to the backup directory to remove\n   *\n   * @remarks\n   * Failures during cleanup are logged with ERROR severity but do not throw.\n   * Successful commits should not fail due to cleanup errors, but users need to\n   * know about cleanup failures to avoid disk space accumulation.\n   * Includes actionable guidance for common failure scenarios.\n   */\n  private async cleanupBackup(backupDir: string): Promise<void> {\n    try {\n      const { rm } = await import(\"node:fs/promises\");\n      await rm(backupDir, { recursive: true, force: true });\n    } catch (error) {\n      // Log cleanup failures with ERROR severity - these mask real problems\n      const errorMsg = getErrorMessage(error);\n      const errorCode = (error as NodeJS.ErrnoException)?.code;\n\n      let suggestions = \"\";\n\n      // Handle ENOENT specially - backup already deleted is not an error\n      if (errorCode === \"ENOENT\") {\n        // Backup was already deleted - directory removal goal is achieved\n        return;\n      }\n\n      // ENOSPC is CRITICAL - orphaned backups will accumulate and fill disk\n      if (errorCode === \"ENOSPC\") {\n        throw new Error(\n          `Backup cleanup failed due to disk full.\\n` +\n            `Original error: ${errorMsg}\\n\\n` +\n            `Orphaned backup directory: ${backupDir}\\n` +\n            `This directory will accumulate and consume disk space.\\n\\n` +\n            `REQUIRED ACTIONS:\\n` +\n            `  1. Manually remove: rm -rf \"${backupDir}\"\\n` +\n            `  2. Free up disk space: df -h\\n` +\n            `  3. Check disk usage: du -sh ${path.dirname(backupDir)}/*\\n\\n` +\n            `Cannot proceed with future commits until disk space is freed.`\n        );\n      }\n\n      // Provide specific guidance based on error type\n      if (errorCode === \"EACCES\") {\n        suggestions =\n          \"\\n\\n[PERMISSION ERROR] Cannot delete backup directory.\\n\" +\n          `Directory: ${backupDir}\\n` +\n          \"Check file permissions or try manual cleanup:\\n\" +\n          `sudo rm -rf \"${backupDir}\"`;\n      } else {\n        suggestions =\n          \"\\n\\n[ACTION REQUIRED] Backup cleanup failed due to file system error.\\n\" +\n          `Directory: ${backupDir}\\n` +\n          `Manual cleanup: rm -rf \"${backupDir}\"\\n` +\n          \"Note: Backup directories accumulate over time and can fill disk space.\";\n      }\n\n      console.error(\n        `[ERROR] Failed to clean up backup directory after commit: ${errorMsg}` + suggestions\n      );\n    }\n  }\n\n  /**\n   * Force remove a backup directory with enhanced error handling.\n   * Attempts multiple strategies to ensure removal even with permission issues.\n   *\n   * @param backupDir - Path to the backup directory to remove\n   * @returns Error message if removal failed, null if successful\n   *\n   * @remarks\n   * This is used during backup creation failures to ensure cleanup of partial state.\n   * Returns error details instead of throwing so caller can log and continue.\n   */\n  private async forceRemoveBackupDir(backupDir: string): Promise<string | null> {\n    const fs = await import(\"fs/promises\");\n\n    try {\n      // Try standard removal first\n      await fs.rm(backupDir, { recursive: true, force: true });\n      return null;\n    } catch (error) {\n      // If standard removal fails, try more aggressive approach\n      try {\n        // Accumulate removal failures for detailed error reporting\n        const removalFailures: Array<{ path: string; error: string }> = [];\n\n        // List directory contents and try to remove each item\n        const entries = await fs.readdir(backupDir, { withFileTypes: true });\n        for (const entry of entries) {\n          const fullPath = path.join(backupDir, entry.name);\n          try {\n            if (entry.isDirectory()) {\n              await fs.rm(fullPath, { recursive: true, force: true });\n            } else {\n              await fs.unlink(fullPath);\n            }\n          } catch (itemError) {\n            removalFailures.push({\n              path: fullPath,\n              error: itemError instanceof Error ? itemError.message : String(itemError),\n            });\n          }\n        }\n\n        // Try to remove the directory itself\n        try {\n          await fs.rmdir(backupDir);\n          return null;\n        } catch {\n          // Directory may not be empty due to removal failures\n          if (removalFailures.length > 0) {\n            const failureDetails = removalFailures\n              .map((f) => `  - ${f.path}: ${f.error}`)\n              .join(\"\\n\");\n\n            return (\n              `Could not remove ${removalFailures.length} items from backup directory:\\n` +\n              failureDetails +\n              `\\n\\nManual cleanup required: rm -rf \"${backupDir}\"`\n            );\n          }\n\n          return `Could not remove directory ${backupDir} - may contain leftover files`;\n        }\n      } catch (aggressiveError) {\n        return `Backup cleanup failed: ${aggressiveError instanceof Error ? aggressiveError.message : String(aggressiveError)}`;\n      }\n    }\n  }\n\n  /**\n   * Restore model state from backup after failed commit.\n   * Restores manifest first (critical), then all layer files with defensive error handling.\n   * Provides detailed reporting of restoration progress and failures.\n   *\n   * @param model - The model to restore\n   * @param backupDir - Path to the backup directory\n   * @throws Error with detailed restoration summary if restoration fails\n   *\n   * @remarks\n   * Restoration strategy:\n   * 1. Restore manifest first (critical for model integrity)\n   * 2. Restore all layer files with per-file error handling\n   * 3. Continue restoring remaining files even if some fail\n   * 4. Throw detailed error if critical files fail to restore\n   * Both manifest and layer restoration failures are critical and will throw errors.\n   */\n  private async restoreModel(model: Model, backupDir: string): Promise<void> {\n    const { readFile, fileExists, atomicWrite } = await import(\"../utils/file-io.js\");\n\n    const restoredFiles: string[] = [];\n    const failedFiles: Array<{ path: string; error: string; isCritical: boolean }> = [];\n    const criticalLayers = new Set<string>(); // Track critical layer failures\n\n    try {\n      // Restore manifest first (most critical) - try both .yaml and .json\n      let backupManifestFile = path.join(backupDir, \"manifest.yaml\");\n      let manifestDestPath = path.join(\n        model.rootPath,\n        \"documentation-robotics\",\n        \"model\",\n        \"manifest.yaml\"\n      );\n\n      if (!(await fileExists(backupManifestFile))) {\n        backupManifestFile = path.join(backupDir, \"manifest.json\");\n        manifestDestPath = path.join(model.rootPath, \"documentation-robotics\", \"manifest.json\");\n      }\n\n      try {\n        if (!(await fileExists(backupManifestFile))) {\n          throw new Error(\"Backup manifest file not found (tried .yaml and .json)\");\n        }\n\n        const manifestContent = await readFile(backupManifestFile);\n        await atomicWrite(manifestDestPath, manifestContent);\n        restoredFiles.push(path.basename(backupManifestFile));\n      } catch (error) {\n        failedFiles.push({\n          path: path.basename(backupManifestFile),\n          error: getErrorMessage(error),\n          isCritical: true,\n        });\n        // Manifest is critical - throw immediately\n        throw new Error(\n          `Failed to restore ${path.basename(backupManifestFile)}: ${getErrorMessage(error)}`\n        );\n      }\n\n      // Restore all layer files with defensive error handling\n      const backupLayersDir = path.join(backupDir, \"layers\");\n      const fs = await import(\"fs/promises\");\n\n      for (const layer of model.layers.values()) {\n        const backupLayerDir = path.join(backupLayersDir, layer.name);\n\n        try {\n          if (!(await fileExists(backupLayerDir))) {\n            // CRITICAL: Layer directory missing in backup - this is a data loss scenario\n            const errorMsg = `Layer '${layer.name}' not found in backup (backup incomplete or corrupted)`;\n            failedFiles.push({\n              path: `layers/${layer.name}`,\n              error: errorMsg,\n              isCritical: true,\n            });\n            criticalLayers.add(layer.name);\n            continue;\n          }\n\n          // Find the correct destination directory for this layer\n          const layerDirPath = await this.findLayerDirectory(model.rootPath, layer.name);\n\n          if (!layerDirPath) {\n            // CRITICAL: Cannot find destination for layer - filesystem issue or permission problem\n            const errorMsg = `Destination directory not found for layer '${layer.name}' (permissions issue or directory structure changed)`;\n            failedFiles.push({\n              path: `layers/${layer.name}`,\n              error: errorMsg,\n              isCritical: true,\n            });\n            criticalLayers.add(layer.name);\n            continue;\n          }\n\n          // Restore all YAML files from backup\n          const backupFiles = await fs.readdir(backupLayerDir);\n          let filesRestoredInLayer = 0;\n\n          for (const file of backupFiles) {\n            if (file.endsWith(\".yaml\") || file.endsWith(\".yml\")) {\n              const backupFilePath = path.join(backupLayerDir, file);\n              const destFilePath = path.join(layerDirPath, file);\n              try {\n                const fileContent = await readFile(backupFilePath);\n                await atomicWrite(destFilePath, fileContent);\n                restoredFiles.push(`layers/${layer.name}/${file}`);\n                filesRestoredInLayer++;\n              } catch (fileError) {\n                // Individual file restoration failure - still critical for data integrity\n                const errorMsg = fileError instanceof Error ? fileError.message : String(fileError);\n\n                // Log immediately with ERROR severity\n                console.error(ansis.red(`\u2717 Failed to restore ${layer.name}/${file}: ${errorMsg}`));\n\n                failedFiles.push({\n                  path: `layers/${layer.name}/${file}`,\n                  error: errorMsg,\n                  isCritical: true,\n                });\n                criticalLayers.add(layer.name);\n              }\n            }\n          }\n        } catch (error) {\n          // Unexpected error during layer restoration - treat as critical\n          const errorMessage = getErrorMessage(error);\n          failedFiles.push({\n            path: `layers/${layer.name}`,\n            error: errorMessage,\n            isCritical: true,\n          });\n          criticalLayers.add(layer.name);\n        }\n      }\n\n      // Reload model layers to reflect restored state\n      model.layers.clear();\n\n      // CRITICAL: If any critical layers failed to restore, throw error immediately\n      if (criticalLayers.size > 0) {\n        const failedLayersList = Array.from(criticalLayers).join(\", \");\n        const detailedErrors = failedFiles.map((f) => `  - ${f.path}: ${f.error}`).join(\"\\n\");\n\n        const errorSummary =\n          `Model restoration FAILED - ${failedFiles.length} critical layer(s) could not be restored:\\n` +\n          `  Failed layers: ${failedLayersList}\\n` +\n          `\\n` +\n          `Detailed errors:\\n${detailedErrors}\\n` +\n          `\\n` +\n          `Successfully restored: ${restoredFiles.length} files\\n` +\n          `Failed to restore: ${failedFiles.length} files\\n` +\n          `\\n` +\n          `Possible causes:\\n` +\n          `  1. Backup directory corrupted or incomplete\\n` +\n          `  2. Insufficient permissions to write to model directory\\n` +\n          `  3. Disk full during restoration\\n` +\n          `  4. Layer directory structure changed since backup\\n` +\n          `\\n` +\n          `Backup location: ${backupDir}\\n` +\n          `\\n` +\n          `ACTION REQUIRED: Manually restore from backup or contact support.`;\n\n        throw new Error(errorSummary);\n      }\n    } catch (error) {\n      // Critical failure during restore\n      const errorMessage = getErrorMessage(error);\n      const summary =\n        `Model restoration failed: ${errorMessage}\\n` +\n        `\\n` +\n        `Restoration progress:\\n` +\n        `  Successfully restored: ${restoredFiles.length} files\\n` +\n        `  Failed to restore: ${failedFiles.length} files (all critical)\\n` +\n        `\\n` +\n        `Restored files:\\n${restoredFiles.map((f) => `  \u2713 ${f}`).join(\"\\n\")}\\n` +\n        `\\n` +\n        `Failed files:\\n${failedFiles.map((f) => `  ${f.isCritical ? \"\u2717 [CRITICAL]\" : \"\u26A0 [WARNING]\"} ${f.path}: ${f.error}`).join(\"\\n\")}\\n` +\n        `\\n` +\n        `Backup location: ${backupDir}`;\n\n      throw new Error(summary);\n    }\n  }\n\n  /**\n   * Find the directory path for a layer in the model.\n   * Uses same discovery logic as Model.loadLayer to locate layer directories.\n   * Handles naming convention: `{PREFIX}_{layerName}` where PREFIX is numeric (01_motivation, etc).\n   *\n   * @param rootPath - Root path of the model\n   * @param layerName - Name of the layer to find\n   * @returns Path to the layer directory or null if not found\n   */\n  private async findLayerDirectory(rootPath: string, layerName: string): Promise<string | null> {\n    const fs = await import(\"fs/promises\");\n    const modelDir = path.join(rootPath, \"documentation-robotics\", \"model\");\n\n    try {\n      const entries = await fs.readdir(modelDir, { withFileTypes: true });\n      const layerDir = entries.find(\n        (e) =>\n          e.isDirectory() && e.name.match(/^\\d{2}_/) && e.name.replace(/^\\d{2}_/, \"\") === layerName\n      );\n\n      if (layerDir) {\n        return path.join(modelDir, layerDir.name);\n      }\n\n      // Layer directory legitimately not found\n      return null;\n    } catch (error) {\n      const errorCode = (error as NodeJS.ErrnoException)?.code;\n\n      if (errorCode === \"ENOENT\") {\n        // Model directory doesn't exist - this might be OK during restore\n        return null;\n      }\n\n      // All other errors are CRITICAL during restore operations\n      throw new Error(\n        `Cannot access model directory for layer '${layerName}': ${getErrorMessage(error)}\\n` +\n          `Location: ${modelDir}\\n` +\n          `Error code: ${errorCode}\\n` +\n          `This indicates a filesystem or permissions issue. Check:\\n` +\n          `  1. Directory permissions: ls -la ${path.dirname(modelDir)}\\n` +\n          `  2. Disk health: df -h\\n` +\n          `  3. Filesystem errors: dmesg | tail`\n      );\n    }\n  }\n\n  /**\n   * Generate a unique changeset ID.\n   * Combines timestamp and random suffix to ensure uniqueness across concurrent operations.\n   *\n   * @returns A unique changeset ID in format `changeset-{timestamp}-{random}`\n   */\n  private generateChangesetId(): string {\n    return `changeset-${Date.now()}-${Math.random().toString(36).substr(2, 9)}`;\n  }\n}\n"],
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+  "sourcesContent": ["/**\n * StagingAreaManager - Manages staged changesets and interception logic\n *\n * Provides:\n * - Changeset lifecycle management (create, load, list, delete)\n * - Staging operations (stage, unstage, discard)\n * - Commit operations with drift detection and validation\n * - Base snapshot tracking for drift detection\n */\n\nimport path from \"path\";\nimport ansis from \"ansis\";\nimport { StagedChangesetStorage } from \"./staged-changeset-storage.js\";\nimport { BaseSnapshotManager } from \"./base-snapshot-manager.js\";\nimport { Changeset, StagedChange, withSequenceNumbers } from \"./changeset.js\";\nimport { ChangesetValidator } from \"./changeset-validator.js\";\nimport { fileExists } from \"../utils/file-io.js\";\nimport type { Model } from \"./model.js\";\nimport type { VirtualProjectionEngine } from \"./virtual-projection.js\";\nimport { createSha256Hash } from \"../types/index.js\";\nimport type { BackupManifest } from \"../types/index.js\";\nimport { getErrorMessage } from \"../utils/errors.js\";\nimport { Layer } from \"./layer.js\";\nimport { canonicalStagedSnapshot } from \"./staged-source-reference.js\";\nimport { elementIdentifiers } from \"./relationships.js\";\nimport { isValidLayerName } from \"./layers.js\";\nimport {\n  isTelemetryEnabled,\n  startSpan,\n  startActiveSpan,\n  endSpan,\n  emitLog,\n  SeverityNumber,\n} from \"../telemetry/index.js\";\nimport { ModelReportOrchestrator } from \"../reports/model-report-orchestrator.js\";\n\n/**\n * Options for commit operation\n */\nexport interface CommitOptions {\n  force?: boolean; // Ignore drift warnings\n  validate?: boolean; // Run validation (default: true)\n  dryRun?: boolean; // Preview without applying\n}\n\n/**\n * Drift report for change detection\n *\n * NOTE: Detects whether the base model has drifted (changed) since the changeset was created.\n * Current implementation only identifies that drift occurred (isDrifted flag).\n * Element-level change tracking is not implemented; detailed diff detection would require\n * storing complete snapshot data, not just hashes.\n */\nexport interface DriftReport {\n  isDrifted: boolean;\n  baseSnapshotId: string;\n  currentSnapshotId: string;\n  warnings: string[];\n}\n\n/**\n * Result of commit operation\n */\nexport interface CommitResult {\n  changeset: string;\n  committed: number;\n  skipped?: number;\n  skippedDetails?: string[];\n  failed: number;\n  validation: {\n    passed: boolean;\n    errors: string[];\n    /** Whether validation ran (false when the caller passed validate: false). */\n    ran?: boolean;\n    /**\n     * Errors the base model already had that the changeset leaves in place. They are\n     * reported, not blocking: commit judges the change, not the base.\n     */\n    preExistingErrors?: number;\n    /** A sample of the pre-existing errors' messages (first 10). */\n    preExistingSample?: string[];\n    /** Set when the base model could not be validated, so every error blocked. */\n    baseValidationFailure?: string;\n  };\n  driftWarning?: DriftReport;\n}\n\n/**\n * StagingAreaManager provides changeset and staging operations\n */\nexport class StagingAreaManager {\n  private storage: StagedChangesetStorage;\n  private snapshotManager: BaseSnapshotManager;\n  private validator: ChangesetValidator;\n  private projectionEngine: VirtualProjectionEngine | null = null;\n  private rootPath: string;\n  private model: Model | null = null;\n\n  constructor(rootPath: string, model?: Model) {\n    this.rootPath = rootPath;\n    this.model = model || null;\n    this.storage = new StagedChangesetStorage(rootPath);\n    this.snapshotManager = new BaseSnapshotManager();\n    this.validator = new ChangesetValidator(rootPath);\n    this.projectionEngine = null; // Lazy loaded on first call to getProjectionEngine()\n  }\n\n  /**\n   * Validate changeset ID format and content\n   * Ensures ID is safe and provides early validation before file operations\n   *\n   * Validation rules:\n   * - Must be a non-empty string\n   * - Cannot contain path separators (.., /, \\)\n   * - Cannot contain special characters (<>:\"|?*)\n   * - During storage, the ID will be normalized: lowercase, spaces\u2192hyphens, non-alphanumeric\u2192stripped\n   *\n   * @param changesetId - The changeset ID to validate\n   * @throws Error if ID contains invalid characters or structure\n   */\n  private validateChangesetId(changesetId: string): void {\n    if (!changesetId || typeof changesetId !== \"string\") {\n      throw new Error(\"Changeset ID must be a non-empty string\");\n    }\n\n    if (changesetId.trim() === \"\") {\n      throw new Error(\"Changeset ID cannot be empty or whitespace-only\");\n    }\n\n    // Check for path traversal attempts\n    if (changesetId.includes(\"..\") || changesetId.includes(\"/\") || changesetId.includes(\"\\\\\")) {\n      throw new Error(\"Changeset ID cannot contain path separators or traversal sequences (..)\");\n    }\n\n    // Check for special characters that could cause issues\n    // Note: sanitizeId() will normalize the ID by converting to lowercase, replacing spaces with hyphens,\n    // and removing all non-alphanumeric characters (except hyphens)\n    if (/[<>:\"|?*]/.test(changesetId)) {\n      throw new Error(\n        'Changeset ID contains invalid special characters (<>:\"|?*). ' +\n          \"Only alphanumeric characters and hyphens are preserved. \" +\n          \"Spaces are converted to hyphens, and other characters are removed during storage.\"\n      );\n    }\n  }\n\n  /**\n   * Get or create projection engine instance (lazy initialization).\n   * Deferred initialization avoids circular dependency issues at module load time.\n   * @returns VirtualProjectionEngine instance for computing merged model views\n   */\n  private async getProjectionEngine(): Promise<VirtualProjectionEngine> {\n    // Share the model's engine when there is one: its cache is the one `model.getLayer()`\n    // reads, so staging must invalidate that cache, not a private copy. Otherwise a model\n    // held across calls (the MCP server's) serves pre-stage layers until the cache expires.\n    if (!this.projectionEngine && typeof this.model?.getVirtualProjectionEngine === \"function\") {\n      this.projectionEngine = this.model.getVirtualProjectionEngine();\n    }\n    if (!this.projectionEngine) {\n      const { VirtualProjectionEngine } = await import(\"./virtual-projection.js\");\n      this.projectionEngine = new VirtualProjectionEngine(this.rootPath);\n    }\n    return this.projectionEngine;\n  }\n\n  /**\n   * Create a new staged changeset\n   */\n  async create(name: string, description?: string): Promise<Changeset> {\n    if (!this.model) {\n      throw new Error(\"Model required for creating changesets\");\n    }\n    const id = this.generateChangesetId();\n    const baseSnapshotId = await this.snapshotManager.captureSnapshot(this.model);\n\n    const changeset = await this.storage.create(id, name, description, baseSnapshotId);\n    changeset.id = id;\n\n    // Mark as 'staged' so it can accept changes immediately\n    changeset.markStaged();\n    await this.storage.save(changeset);\n\n    // Record which elements and relationships the base has now, so verify and brief can tell what\n    // predates the plan. Optional: without it they fall back and say so, so a failure is reported,\n    // not fatal.\n    try {\n      const { captureBaseIndex, writeBaseIndex } = await import(\"./changeset-base-index.js\");\n      await writeBaseIndex(this.rootPath, changeset.id, await captureBaseIndex(this.model));\n    } catch (error) {\n      console.warn(\n        `Warning: could not record the base index for changeset '${name}': ${getErrorMessage(error)}. ` +\n          \"Verify and brief will fall back to what they can tell without it.\"\n      );\n    }\n\n    return changeset;\n  }\n\n  /**\n   * Load a changeset by name or ID\n   */\n  async load(name: string): Promise<Changeset | null> {\n    // Try loading directly as ID first\n    let changeset = await this.storage.load(name);\n    if (changeset) {\n      return changeset;\n    }\n\n    // If not found by ID, search by name in all changesets\n    const all = await this.storage.list();\n    return all.find((cs) => cs.name === name) || null;\n  }\n\n  /**\n   * List all staged changesets\n   */\n  async list(): Promise<Changeset[]> {\n    return this.storage.list();\n  }\n\n  /**\n   * Delete a changeset\n   * If the changeset being deleted is the currently active changeset,\n   * this method will also clear the active changeset marker.\n   */\n  async delete(name: string): Promise<void> {\n    const changeset = await this.load(name);\n    if (!changeset) {\n      throw new Error(`Changeset '${name}' not found`);\n    }\n\n    if (!changeset.id) {\n      throw new Error(`Changeset '${name}' has no ID and cannot be deleted`);\n    }\n\n    // Check if this changeset is the active one and clear it if so\n    const activeChangeset = await this.getActive();\n    if (activeChangeset && activeChangeset.id === changeset.id) {\n      await this.clearActive();\n    }\n\n    await this.storage.delete(changeset.id);\n  }\n\n  /**\n   * Rename a changeset and/or change its description (its stated intent). Staged changes,\n   * status and the active marker are untouched. Names stay unique: renaming to a name another\n   * changeset already has is refused.\n   *\n   * @param nameOrId - Changeset ID or current name\n   * @param patch - Fields to change; an empty description clears it\n   * @throws Error if the changeset is not found, or the new name is taken\n   */\n  async update(nameOrId: string, patch: { name?: string; description?: string }): Promise<Changeset> {\n    const changeset = await this.load(nameOrId);\n    if (!changeset || !changeset.id) {\n      throw new Error(`Changeset '${nameOrId}' not found`);\n    }\n    if (patch.name !== undefined) {\n      const name = patch.name.trim();\n      if (!name) {\n        throw new Error(\"Changeset name cannot be empty\");\n      }\n      const clash = (await this.storage.list()).find((cs) => cs.name === name && cs.id !== changeset.id);\n      if (clash) {\n        throw new Error(`Another changeset (${clash.id}) is already named '${name}'`);\n      }\n      patch = { ...patch, name };\n    }\n    return this.storage.updateMetadata(changeset.id, patch);\n  }\n\n  /**\n   * Stage a change in the changeset.\n   * Records the change in the staging area without applying to the base model.\n   * The changeset must be in 'staged' status to accept new changes.\n   *\n   * @param changesetId - ID of the changeset to stage the change in\n   * @param change - The change to stage (type, elementId, layerName, before/after snapshots)\n   * @throws Error if changeset ID is invalid, changeset not found, or not in 'staged' status\n   */\n  async stage(changesetId: string, change: Omit<StagedChange, \"sequenceNumber\">): Promise<void> {\n    this.validateChangesetId(changesetId);\n\n    const changeset = await this.load(changesetId);\n    if (!changeset) {\n      throw new Error(`Changeset '${changesetId}' not found`);\n    }\n\n    // Only allow staging when status is 'staged' (not 'committed' or 'discarded')\n    if (changeset.status !== \"staged\") {\n      throw new Error(\n        `Cannot stage changes on changeset with status '${changeset.status}'. ` +\n          `Changeset must have status 'staged' to accept new changes.`\n      );\n    }\n\n    const stagedChange: Omit<StagedChange, \"sequenceNumber\"> = {\n      ...change,\n      timestamp: change.timestamp || new Date().toISOString(),\n    };\n\n    await this.storage.addChange(changesetId, stagedChange);\n\n    // A model held across calls (the MCP server's) lists its layers from what was staged when it\n    // loaded: tell it about an element change in a layer it may not have, so lookups find it.\n    if (!change.type.startsWith(\"relationship-\") && typeof this.model?.noteStagedLayer === \"function\") {\n      this.model.noteStagedLayer(changesetId, change.layerName);\n    }\n\n    // Invalidate projection cache for this layer\n    const engine = await this.getProjectionEngine();\n    engine.invalidateOnStage(changesetId, change.layerName);\n  }\n\n  /**\n   * Rewrite a staged change in place, keeping its sequence number: e.g. to fold an update of an\n   * element into the changeset's add of it. The changeset must be in 'staged' status.\n   *\n   * @param elementId - The key (`elementId`) of the change to rewrite\n   * @throws Error if the changeset is not found, not staged, or has no change with that key\n   */\n  async restage(\n    changesetId: string,\n    elementId: string,\n    change: Omit<StagedChange, \"sequenceNumber\">\n  ): Promise<void> {\n    this.validateChangesetId(changesetId);\n\n    const changeset = await this.load(changesetId);\n    if (!changeset) {\n      throw new Error(`Changeset '${changesetId}' not found`);\n    }\n    if (changeset.status !== \"staged\") {\n      throw new Error(\n        `Cannot change staged changes on changeset with status '${changeset.status}'. ` +\n          `Changeset must have status 'staged'.`\n      );\n    }\n\n    await this.storage.updateChange(changesetId, elementId, {\n      ...change,\n      timestamp: change.timestamp || new Date().toISOString(),\n    });\n\n    const engine = await this.getProjectionEngine();\n    engine.invalidateOnStage(changesetId, change.layerName);\n  }\n\n  /**\n   * Unstage a specific element from the changeset.\n   * Removes all changes associated with the element.\n   * The changeset must be in 'staged' status.\n   *\n   * @param changesetId - ID of the changeset to unstage from\n   * @param elementId - ID of the element to remove all changes for\n   * @throws Error if changeset ID is invalid, changeset not found, or not in 'staged' status\n   */\n  async unstage(changesetId: string, elementId: string): Promise<void> {\n    this.validateChangesetId(changesetId);\n\n    const changeset = await this.load(changesetId);\n    if (!changeset) {\n      throw new Error(`Changeset '${changesetId}' not found`);\n    }\n\n    if (changeset.status !== \"staged\") {\n      throw new Error(\n        `Cannot unstage changes on changeset with status '${changeset.status}'. ` +\n          `Changeset must have status 'staged'.`\n      );\n    }\n\n    // Remove the element's changes and resequence remaining changes\n    await this.storage.removeChange(changesetId, elementId);\n\n    // Invalidate projection cache for the removed element's layers\n    const engine = await this.getProjectionEngine();\n    await engine.invalidateOnUnstage(changesetId, elementId);\n  }\n\n  /**\n   * Discard all changes in the changeset.\n   * Clears all staged changes and marks the changeset as 'discarded'.\n   * This operation is irreversible for the changeset but does not affect the base model.\n   *\n   * @param changesetId - ID of the changeset to discard\n   * @throws Error if changeset ID is invalid or changeset not found\n   */\n  async discard(changesetId: string): Promise<void> {\n    this.validateChangesetId(changesetId);\n\n    const changeset = await this.load(changesetId);\n    if (!changeset) {\n      throw new Error(`Changeset '${changesetId}' not found`);\n    }\n\n    // Clear all staged changes and update status\n    changeset.changes = [];\n    // Discard is for good: the unstage tombstones go with the changes.\n    changeset.unstaged = [];\n    changeset.status = \"discarded\";\n    // Note: stats are auto-computed from changes array (will be 0/0/0 after clearing)\n    changeset.updateModified();\n\n    await this.storage.save(changeset);\n\n    // Invalidate all projection cache entries for this changeset\n    const engine = await this.getProjectionEngine();\n    engine.invalidateOnDiscard(changesetId);\n  }\n\n  /**\n   * Capture a base snapshot of the current model state for drift detection.\n   * Stores a hash of the model that can be compared later to detect changes.\n   *\n   * @param changesetId - ID of the changeset to capture snapshot for\n   * @returns SHA256 hash of the current model state\n   * @throws Error if changeset not found or model not available\n   */\n  async captureBaseSnapshot(changesetId: string): Promise<string> {\n    this.validateChangesetId(changesetId);\n\n    if (!this.model) {\n      throw new Error(\"Model required for capturing base snapshot\");\n    }\n    const changeset = await this.load(changesetId);\n    if (!changeset) {\n      throw new Error(`Changeset '${changesetId}' not found`);\n    }\n\n    const snapshotId = await this.snapshotManager.captureSnapshot(this.model);\n    changeset.baseSnapshot = snapshotId;\n    changeset.updateModified();\n    await this.storage.save(changeset);\n\n    return snapshotId;\n  }\n\n  /**\n   * Detect drift by comparing base snapshot hash to current model state.\n   * Identifies whether the base model has changed since the changeset was created.\n   *\n   * @param changesetId - ID of the changeset to check for drift\n   * @returns DriftReport with isDrifted flag, snapshot hashes, and warnings\n   * @throws Error if changeset ID is invalid, changeset not found, or model not available\n   *\n   * @remarks\n   * Drift detection uses hash-based comparison of the entire model snapshot.\n   * Element-level change tracking is not implemented - only the isDrifted flag\n   * indicates if the model has changed. Detailed diff detection would require\n   * storing complete snapshot data, not just hashes.\n   * Returns isDrifted=false and warnings if no base snapshot was captured.\n   */\n  async detectDrift(changesetId: string): Promise<DriftReport> {\n    this.validateChangesetId(changesetId);\n\n    if (!this.model) {\n      throw new Error(\"Model required for drift detection\");\n    }\n    const changeset = await this.load(changesetId);\n    if (!changeset) {\n      throw new Error(`Changeset '${changesetId}' not found`);\n    }\n\n    if (!changeset.baseSnapshot) {\n      return {\n        isDrifted: false,\n        baseSnapshotId: \"unknown\",\n        currentSnapshotId: \"unknown\",\n        warnings: [\"No base snapshot available for drift detection\"],\n      };\n    }\n\n    // Capture current model snapshot to compare against base\n    const currentSnapshotId = await this.snapshotManager.captureSnapshot(this.model);\n\n    // Compare snapshot hashes to detect drift\n    // isDrifted=true indicates base model has changed since changeset creation\n    const isDrifted = changeset.baseSnapshot !== currentSnapshotId;\n\n    const warnings: string[] = [];\n\n    if (isDrifted) {\n      warnings.push(\n        `Model has drifted since changeset creation (base snapshot hash differs from current)`\n      );\n    }\n\n    return {\n      isDrifted,\n      baseSnapshotId: changeset.baseSnapshot,\n      currentSnapshotId: currentSnapshotId,\n      warnings,\n    };\n  }\n\n  /**\n   * Commit a changeset to the base model with atomic guarantee.\n   * Applies all staged changes and persists them to the base model.\n   *\n   * Implements atomic commit with the following steps:\n   * 1. Detect drift in base model (fail unless force=true)\n   * 2. Validate projected model (schema, references, semantics)\n   * 3. Create backup of current model state\n   * 4. Apply all changes in sequence order\n   * 5. Save all modified layers to disk\n   * 6. Update changeset status and manifest history\n   * 7. Cleanup backup on success, restore on failure\n   *\n   * @param model - The model to commit changes to\n   * @param changesetId - ID of the changeset to commit\n   * @param options - Commit options (force, validate, dryRun)\n   * @returns CommitResult with count of committed/failed changes and validation status\n   * @throws Error if validation fails, drift detected without --force, or commit fails\n   *\n   * @remarks\n   * Validation errors always block commit (force flag does not override).\n   * Drift warnings can be bypassed with --force flag.\n   * Dry-run mode performs all checks but does not persist changes.\n   * On commit failure, model state is restored from backup; rollback failure triggers CRITICAL error.\n   */\n  async commit(\n    model: Model,\n    changesetId: string,\n    options: CommitOptions = {}\n  ): Promise<CommitResult> {\n    return startActiveSpan(\"staging.commit\", async (span) => {\n      this.validateChangesetId(changesetId);\n\n      const changeset = await this.load(changesetId);\n      if (!changeset) {\n        throw new Error(`Changeset '${changesetId}' not found`);\n      }\n\n      (span as any).setAttribute(\"changeset.name\", changeset.name);\n      (span as any).setAttribute(\"changeset.changeCount\", changeset.changes.length);\n\n      const isDryRun = options.dryRun === true;\n      const shouldValidate = options.validate !== false;\n\n      // Step 1: Detect drift and throw if drifted without --force\n      const driftSpan = isTelemetryEnabled ? startSpan(\"staging.detectDrift\") : null;\n      const drift = await this.detectDrift(changesetId);\n      if (isTelemetryEnabled && driftSpan) {\n        (driftSpan as any).setAttribute(\"drift.detected\", drift.isDrifted);\n        (driftSpan as any).setAttribute(\"drift.baseSnapshotId\", drift.baseSnapshotId);\n        (driftSpan as any).setAttribute(\"drift.currentSnapshotId\", drift.currentSnapshotId);\n        (driftSpan as any).setStatus({ code: 0 });\n      }\n      endSpan(driftSpan);\n\n      if (drift.isDrifted) {\n        (span as any).setAttribute(\"commit.driftDetected\", true);\n        if (options.force) {\n          emitLog(SeverityNumber.WARN, \"Drift detected but overridden with --force\", {\n            \"drift.baseSnapshot\": drift.baseSnapshotId,\n            \"drift.currentSnapshot\": drift.currentSnapshotId,\n          });\n        } else {\n          emitLog(SeverityNumber.ERROR, \"Drift detected, commit blocked\", {\n            \"drift.baseSnapshot\": drift.baseSnapshotId,\n            \"drift.currentSnapshot\": drift.currentSnapshotId,\n          });\n          throw new Error(\n            `Base model has drifted since changeset creation. ` + `Use --force to commit anyway.`\n          );\n        }\n      }\n\n      const result: CommitResult = {\n        changeset: changeset.name,\n        committed: 0,\n        skipped: 0,\n        skippedDetails: [],\n        failed: 0,\n        validation: {\n          passed: true,\n          errors: [],\n          ran: shouldValidate,\n        },\n      };\n\n      // Step 2: Validate the change (force cannot override validation). Only errors the\n      // changeset introduces block; errors already in the base model are counted and\n      // reported, so a model with old problems can still take a change.\n      if (shouldValidate) {\n        await startActiveSpan(\"staging.validate\", async (validationSpan) => {\n          const report = await this.validator.validateChangesetReport(model, changesetId);\n          const validation = report.result;\n          result.validation.preExistingErrors = report.preExistingErrors.length;\n          if (report.preExistingErrors.length > 0) {\n            result.validation.preExistingSample = report.preExistingErrors\n              .slice(0, 10)\n              .map((e) => e.message);\n            emitLog(SeverityNumber.WARN, \"Pre-existing validation errors not counted against the changeset\", {\n              \"validation.preExistingErrorCount\": report.preExistingErrors.length,\n            });\n          }\n          if (report.baseValidationFailure) {\n            result.validation.baseValidationFailure = report.baseValidationFailure;\n            emitLog(SeverityNumber.WARN, \"Base model could not be validated; every error counts\", {\n              \"validation.baseValidationFailure\": report.baseValidationFailure,\n            });\n          }\n\n          (validationSpan as any).setAttribute(\"validation.passed\", validation.isValid());\n          (validationSpan as any).setAttribute(\"validation.errorCount\", validation.errors.length);\n          (validationSpan as any).setAttribute(\n            \"validation.preExistingErrorCount\",\n            report.preExistingErrors.length\n          );\n          (validationSpan as any).setStatus({ code: 0 });\n\n          if (!validation.isValid()) {\n            result.validation.passed = false;\n            result.validation.errors = validation.errors.map((e) => e.message);\n\n            emitLog(SeverityNumber.ERROR, \"Validation failed\", {\n              \"validation.errorCount\": result.validation.errors.length,\n              \"validation.errors\": result.validation.errors.slice(0, 10), // First 10 errors\n            });\n\n            const notes: string[] = [];\n            if (report.preExistingErrors.length > 0) {\n              notes.push(\n                `${report.preExistingErrors.length} pre-existing error(s) in the base model were not counted against this changeset.`\n              );\n            }\n            if (report.baseValidationFailure) {\n              notes.push(\n                `The base model could not be validated (${report.baseValidationFailure}), so every error was counted.`\n              );\n            }\n            throw new Error(\n              `Validation failed with ${result.validation.errors.length} error(s) introduced by this changeset:\\n` +\n                result.validation.errors.map((e) => `  - ${e}`).join(\"\\n\") +\n                (notes.length > 0 ? `\\n\\n${notes.join(\"\\n\")}` : \"\") +\n                `\\n\\nFix these validation errors before committing, or skip validation with --no-validate.`\n            );\n          }\n        });\n      }\n\n      // Step 3: Dry run early exit (before making any changes)\n      if (isDryRun) {\n        result.committed = changeset.changes.length;\n        if (drift.isDrifted) {\n          result.driftWarning = drift;\n        }\n        return result;\n      }\n\n      // Step 4: Backup model state for atomic rollback\n      let backup: string;\n      try {\n        backup = await this.backupModel(model);\n      } catch (backupError) {\n        // Backup creation failed - cannot proceed safely\n        throw new Error(\n          `Failed to create backup before commit. No changes have been applied. ` +\n            `${backupError instanceof Error ? backupError.message : String(backupError)}`\n        );\n      }\n\n      // Step 5: Apply all changes sequentially by sequence number (numbers may have gaps where\n      // changes were unstaged; unstage tombstones are never applied)\n      const sortedChanges = withSequenceNumbers(changeset.changes).sort(\n        (a, b) => a.sequenceNumber - b.sequenceNumber\n      );\n      // Set when applying an element delete removed rows from relationships.yaml\n      let relationshipsPurged = false;\n\n      try {\n        const applySpan = isTelemetryEnabled\n          ? startSpan(\"staging.apply\", {\n              \"apply.changeCount\": changeset.changes.length,\n            })\n          : null;\n\n        try {\n          for (const change of sortedChanges) {\n            try {\n              // Use getBaseLayer() so commit operates on the actual mutable base layer,\n              // not a projected clone. getLayer() would return a projected (read-only clone)\n              // which cannot be persisted via saveLayer().\n              let layer = await model.getBaseLayer(change.layerName);\n              if (!layer) {\n                // Layer directory doesn't exist yet \u2014 this changeset introduces\n                // the first elements for this layer. Create an empty layer and\n                // register it so saveLayer() will create the directory on disk.\n                layer = new Layer(change.layerName);\n                model.addLayer(layer);\n              }\n\n              if (change.type === \"relationship-add\" && change.after) {\n                // Relationship-add: the relationship was already injected into model.relationships\n                // during Model.load() for transparent read-path visibility. Here we just need\n                // saveRelationships() to persist it. Skip adding if it already exists.\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                const existing = model.relationships.find(rel.source, rel.target, rel.predicate);\n                if (existing.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                result.committed++;\n                continue;\n              }\n\n              if (change.type === \"relationship-delete\" && change.before) {\n                // Relationship-delete: the relationship was already removed from model.relationships\n                // during Model.load(). Just ensure it's gone and count it.\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                result.committed++;\n                continue;\n              }\n\n              if (change.type === \"add\" && change.after) {\n                const { Element } = await import(\"./element.js\");\n                const elementData = change.after as Record<string, unknown>;\n                const elementId = elementData.id as string;\n\n                // Check if element already exists using the UUID from elementData\n                const elements = layer.listElements();\n                const elementExists = elements.some((e) => e.id === elementId);\n\n                if (!elementExists) {\n                  // Pass the entire elementData to Element constructor - it already has all fields from toJSON()\n                  const element = new Element(canonicalStagedSnapshot(elementData).data);\n                  layer.addElement(element);\n                  result.committed++;\n                } else {\n                  result.skipped = (result.skipped ?? 0) + 1;\n                  result.skippedDetails = result.skippedDetails ?? [];\n                  result.skippedDetails.push(\n                    `'${elementId}' in '${change.layerName}' already exists \u2014 deduplicated`\n                  );\n                  emitLog(SeverityNumber.WARN, \"Element deduplicated during commit\", {\n                    \"change.elementId\": change.elementId,\n                    \"change.layer\": change.layerName,\n                  });\n                }\n              } else if (change.type === \"update\" && change.after) {\n                const element = layer.getElement(change.elementId);\n                if (element) {\n                  const { data: elementData, sourceReference } = canonicalStagedSnapshot(\n                    change.after as Record<string, unknown>\n                  );\n                  Object.assign(element, elementData);\n                  if (sourceReference.present) element.setSourceReference(sourceReference.value);\n                  // Persist the mutation back to the underlying graph node.\n                  // getElement() returns a new wrapper each time, so Object.assign\n                  // alone is discarded; updateElement() writes through to the graph.\n                  layer.updateElement(element);\n                  result.committed++;\n                } else {\n                  result.failed++;\n                  result.validation.passed = false;\n                  result.validation.errors.push(\n                    `Cannot update '${change.elementId}' in '${change.layerName}': element not found in base model`\n                  );\n                }\n              } else if (change.type === \"delete\") {\n                const element = layer.getElement(change.elementId);\n                // Purge relationships that name the element by UUID or by path.\n                // Deletes staged before relationship purging existed carry no\n                // relationship-delete changes, so this is the safety net at commit.\n                const before = (change.before ?? {}) as { id?: unknown; path?: unknown };\n                const purged = model.relationships.deleteForElement(\n                  elementIdentifiers(element ?? before, before.id as string | undefined,\n                    before.path as string | undefined, change.elementId)\n                );\n                if (purged > 0) {\n                  relationshipsPurged = true;\n                }\n                if (element) {\n                  layer.deleteElement(element.path || element.id);\n                  result.committed++;\n                } else {\n                  // Element was already removed \u2014 count as skipped, not failed\n                  result.skipped = (result.skipped ?? 0) + 1;\n                  result.skippedDetails = result.skippedDetails ?? [];\n                  result.skippedDetails.push(\n                    `'${change.elementId}' in '${change.layerName}' not found \u2014 already deleted`\n                  );\n                }\n              } else {\n                // Handles: unknown change types, and known types with missing payloads\n                // (e.g. \"add\" with no change.after, \"relationship-add\" with no change.after).\n                result.failed++;\n                result.validation.passed = false;\n                result.validation.errors.push(\n                  `Cannot apply change '${change.type}' for '${change.elementId}': missing payload or unrecognised type`\n                );\n              }\n            } catch (error) {\n              result.failed++;\n              result.validation.passed = false;\n              result.validation.errors.push(\n                `Failed to apply change to ${change.elementId}: ${getErrorMessage(error)}`\n              );\n\n              emitLog(SeverityNumber.ERROR, \"Failed to apply change\", {\n                \"change.elementId\": change.elementId,\n                \"change.type\": change.type,\n                \"change.layer\": change.layerName,\n                \"error.message\": getErrorMessage(error),\n              });\n\n              throw new Error(\n                `Atomic commit failed at change ${sortedChanges.indexOf(change) + 1}/${sortedChanges.length}: ` +\n                  `${getErrorMessage(error)}`\n              );\n            }\n          }\n\n          if (isTelemetryEnabled && applySpan) {\n            (applySpan as any).setAttribute(\"apply.committed\", result.committed);\n            (applySpan as any).setAttribute(\"apply.failed\", result.failed);\n            (applySpan as any).setStatus({ code: 0 });\n          }\n        } finally {\n          endSpan(applySpan);\n        }\n\n        // Step 6: Save all modified layers and relationships atomically\n        const modifiedLayers = new Set<string>();\n        let hasRelationshipChanges = false;\n        for (const change of sortedChanges) {\n          if (change.type === \"relationship-add\" || change.type === \"relationship-delete\") {\n            hasRelationshipChanges = true;\n          } else {\n            modifiedLayers.add(change.layerName);\n          }\n        }\n\n        for (const layerName of modifiedLayers) {\n          try {\n            await model.saveLayer(layerName);\n          } catch (error) {\n            throw new Error(\n              `Failed to save layer '${layerName}': ${getErrorMessage(error)}`\n            );\n          }\n        }\n\n        // Persist staged relationship changes to relationships.yaml\n        if (hasRelationshipChanges || relationshipsPurged) {\n          try {\n            await model.saveRelationships();\n          } catch (error) {\n            throw new Error(\n              `Failed to save relationships after commit: ${getErrorMessage(error)}`\n            );\n          }\n        }\n\n        // Step 7: Update changeset status to committed ONLY AFTER successful saves\n        changeset.status = \"committed\";\n        changeset.updateModified();\n\n        try {\n          await this.storage.save(changeset);\n        } catch (error) {\n          // Changeset status is critical metadata - must be persisted with model changes\n          throw new Error(\n            `Failed to save changeset status after commit: ${getErrorMessage(error)}. ` +\n              `This is a critical error that requires rollback to maintain consistency between model state and changeset metadata.`\n          );\n        }\n\n        // Step 8: Add changeset to manifest history\n        if (!model.manifest.changeset_history) {\n          model.manifest.changeset_history = [];\n        }\n        model.manifest.changeset_history.push({\n          name: changeset.name,\n          committed_at: new Date().toISOString(),\n          action: \"committed\",\n        });\n\n        // Step 9: Save manifest with updated changeset history\n        try {\n          await model.saveManifest();\n        } catch (manifestError) {\n          // Manifest save failed - this is CRITICAL and will trigger rollback\n          // Don't log here - let the rollback handler provide comprehensive error output\n          throw new Error(\n            `Failed to save manifest with changeset history: ${manifestError instanceof Error ? manifestError.message : String(manifestError)}. ` +\n              `Model will be rolled back to maintain consistency.`\n          );\n        }\n\n        // Step 9.5: Regenerate reports for all layers modified by this changeset\n        try {\n          const orchestrator = new ModelReportOrchestrator(model, model.rootPath);\n          const affectedLayers = new Set<string>();\n          for (const change of sortedChanges) {\n            if (isValidLayerName(change.layerName)) {\n              for (const layer of orchestrator.computeAffectedLayers(change.layerName)) {\n                affectedLayers.add(layer);\n              }\n            }\n          }\n          await orchestrator.regenerate(affectedLayers);\n        } catch (error) {\n          emitLog(\n            SeverityNumber.WARN,\n            \"Failed to regenerate layer reports after changeset commit\",\n            {\n              \"changeset.id\": changesetId,\n              \"changeset.name\": changeset.name,\n              \"changeset.changeCount\": sortedChanges.length,\n              \"error.message\": getErrorMessage(error),\n            }\n          );\n        }\n\n        // Step 10: Clean up backup directory after successful commit\n        // Note: cleanupBackup handles its own errors and logs them with ERROR severity\n        await this.cleanupBackup(backup);\n\n        (span as any).setAttribute(\"commit.success\", true);\n        (span as any).setAttribute(\"commit.committed\", result.committed);\n        if (drift.isDrifted) {\n          (span as any).setAttribute(\"commit.driftOverridden\", true);\n        }\n        (span as any).setStatus({ code: 0 });\n\n        return result;\n      } catch (commitError) {\n        // Attempt rollback on any failure - restore from backup\n        let rollbackSucceeded = false;\n        let rollbackError: Error | null = null;\n\n        const rollbackSpan = isTelemetryEnabled ? startSpan(\"staging.rollback\") : null;\n\n        try {\n          emitLog(SeverityNumber.WARN, \"Commit failed, attempting rollback\", {\n            \"commit.error\":\n              commitError instanceof Error ? commitError.message : String(commitError),\n          });\n\n          await this.restoreModel(model, backup);\n          rollbackSucceeded = true;\n\n          if (isTelemetryEnabled && rollbackSpan) {\n            (rollbackSpan as any).setAttribute(\"rollback.success\", true);\n            (rollbackSpan as any).setStatus({ code: 0 });\n          }\n\n          emitLog(SeverityNumber.INFO, \"Rollback succeeded, model restored\", {\n            \"backup.path\": backup,\n          });\n        } catch (err) {\n          rollbackError = err instanceof Error ? err : new Error(String(err));\n\n          if (isTelemetryEnabled && rollbackSpan) {\n            (rollbackSpan as any).setAttribute(\"rollback.success\", false);\n            (rollbackSpan as any).recordException(rollbackError);\n            (rollbackSpan as any).setStatus({ code: 2, message: rollbackError.message });\n          }\n\n          emitLog(SeverityNumber.ERROR, \"Rollback failed, model may be corrupted\", {\n            \"rollback.error\": rollbackError.message,\n            \"backup.path\": backup,\n          });\n        } finally {\n          endSpan(rollbackSpan);\n        }\n\n        // CRITICAL: Validate backup integrity BEFORE suggesting manual restoration\n        let backupHealth: { isValid: boolean; filesChecked: number; errors: string[] };\n        let backupValidationError: string | null = null;\n        let validationProcessFailed = false;\n\n        try {\n          backupHealth = await this.validateBackupIntegrity(backup);\n        } catch (validationErr) {\n          validationProcessFailed = true;\n          backupValidationError =\n            validationErr instanceof Error ? validationErr.message : String(validationErr);\n          backupHealth = {\n            isValid: false,\n            filesChecked: 0,\n            errors: [\n              `Validation process failed: ${backupValidationError}`,\n              `This indicates a critical issue with the backup infrastructure, not the backup content.`,\n              `Contact support before attempting manual restoration.`,\n            ],\n          };\n        }\n\n        // Build comprehensive error message\n        let compositeMessage: string;\n        const suggestions: string[] = [];\n\n        if (rollbackSucceeded) {\n          // Rollback succeeded - throw original commit error\n          compositeMessage = `Commit failed but rollback succeeded. Model restored to pre-commit state.\\n\\n`;\n          compositeMessage += `Error during commit:\\n`;\n          compositeMessage += `  ${commitError instanceof Error ? commitError.message : String(commitError)}\\n\\n`;\n          compositeMessage += `Backup location (for reference): ${backup}`;\n\n          // Clean up backup after successful rollback\n          // Note: cleanupBackup handles its own errors and logs them with ERROR severity\n          await this.cleanupBackup(backup);\n\n          (span as any).setAttribute(\"commit.success\", false);\n          (span as any).setAttribute(\"commit.rollbackSuccess\", true);\n          (span as any).recordException(commitError as Error);\n          (span as any).setStatus({\n            code: 2,\n            message: commitError instanceof Error ? commitError.message : String(commitError),\n          });\n\n          throw new Error(compositeMessage);\n        } else {\n          // Rollback failed - model may be corrupted\n          compositeMessage =\n            `Commit failed AND rollback failed. Model may be in corrupted state.\\n` +\n            `\\n` +\n            `Original commit error:\\n` +\n            `  ${commitError instanceof Error ? commitError.message : String(commitError)}\\n` +\n            `\\n` +\n            `Rollback error:\\n` +\n            `  ${rollbackError ? rollbackError.message : \"Unknown error\"}\\n` +\n            `\\n` +\n            `Backup location: ${backup}\\n`;\n\n          // Add backup health status (always show header for consistency with tests)\n          compositeMessage += `Backup integrity check:\\n`;\n          if (validationProcessFailed) {\n            compositeMessage += `  \u2717 Backup integrity issues found:\\n`;\n            compositeMessage += `    - Validation process failed: ${backupValidationError}\\n`;\n            compositeMessage += `\\n\u26A0 CRITICAL: Backup validation process crashed.\\n`;\n            compositeMessage += `This indicates a system-level issue (filesystem, memory, permissions).\\n`;\n            compositeMessage += `DO NOT attempt manual restoration until this is resolved.\\n`;\n          } else if (backupHealth.isValid) {\n            compositeMessage += `  \u2713 Backup is valid (${backupHealth.filesChecked} files checked)\\n`;\n          } else {\n            compositeMessage += `  \u2717 Backup integrity issues found:\\n`;\n            for (const error of backupHealth.errors) {\n              compositeMessage += `    - ${error}\\n`;\n            }\n          }\n\n          compositeMessage += `\\n`;\n\n          if (backupHealth.isValid) {\n            suggestions.push(\n              `Backup is valid. Manually restore from backup: ${backup}`,\n              `Copy manifest.json/manifest.yaml from backup to ${path.join(model.rootPath, \"documentation-robotics\")}`,\n              `Copy layer files from ${path.join(backup, \"layers\")} to ${path.join(model.rootPath, \"documentation-robotics\", \"layers\")}`,\n              `Run 'dr validate' after manual restoration`,\n              `Contact support if issue persists`\n            );\n          } else {\n            suggestions.push(\n              `\u26A0 Backup integrity is compromised. Do NOT use this backup for recovery.`,\n              `Check if backup files exist at: ${backup}`,\n              `Verify disk space and file permissions`,\n              `Contact support immediately - manual data recovery may be required`,\n              `Do not attempt manual restoration with a corrupted backup`\n            );\n          }\n\n          compositeMessage += `Manual recovery may be required.`;\n\n          (span as any).setAttribute(\"commit.success\", false);\n          (span as any).setAttribute(\"commit.rollbackSuccess\", false);\n          (span as any).recordException(commitError as Error);\n          (span as any).setStatus({ code: 2, message: \"Commit and rollback both failed\" });\n\n          const { CLIError } = await import(\"../utils/errors.js\");\n          throw new CLIError(compositeMessage, 1, suggestions);\n        }\n      }\n    }, {\n      \"changeset.id\": changesetId,\n      \"commit.validate\": options.validate !== false,\n      \"commit.force\": options.force === true,\n      \"commit.dryRun\": options.dryRun === true,\n    });\n  }\n\n  /**\n   * Check if a changeset is currently active.\n   * Active changesets intercept mutations to stage changes instead of applying to base model.\n   *\n   * @param changesetId - ID of the changeset to check\n   * @returns true if changeset is marked as active, false otherwise\n   * @throws Error if changeset ID is invalid\n   */\n  async isActive(changesetId: string): Promise<boolean> {\n    this.validateChangesetId(changesetId);\n\n    const activePath = path.join(this.rootPath, \"documentation-robotics\", \"changesets\", \".active\");\n    if (!(await fileExists(activePath))) {\n      return false;\n    }\n\n    const { readFile } = await import(\"../utils/file-io.js\");\n    const activeId = await readFile(activePath);\n    return activeId.trim() === changesetId;\n  }\n\n  /**\n   * Activate a changeset to intercept model mutations.\n   * Marks the changeset as active and transitions status to 'staged'.\n   * Only one changeset can be active at a time.\n   *\n   * @param changesetId - ID of the changeset to activate\n   * @throws Error if changeset ID is invalid or changeset not found\n   *\n   * @remarks\n   * When a changeset is active, add/update/delete commands will stage changes\n   * instead of applying them directly to the base model.\n   */\n  async setActive(changesetId: string): Promise<void> {\n    this.validateChangesetId(changesetId);\n\n    const changeset = await this.load(changesetId);\n    if (!changeset) {\n      throw new Error(`Changeset '${changesetId}' not found`);\n    }\n\n    // Transition to 'staged' status to enable interception\n    if (changeset.status !== \"staged\") {\n      changeset.markStaged();\n      await this.storage.save(changeset);\n    }\n\n    const { writeFile, ensureDir } = await import(\"../utils/file-io.js\");\n    const changesetDir = path.join(this.rootPath, \"documentation-robotics\", \"changesets\");\n    await ensureDir(changesetDir);\n\n    const activePath = path.join(changesetDir, \".active\");\n    // Write the actual changeset ID (not the user-provided name)\n    if (!changeset.id) {\n      throw new Error(`Changeset has no ID, cannot activate`);\n    }\n    await writeFile(activePath, changeset.id);\n  }\n\n  /**\n   * Clear the active changeset marker.\n   * Allows a new changeset to be activated or model mutations to proceed normally.\n   */\n  async clearActive(): Promise<void> {\n    const { writeFile } = await import(\"../utils/file-io.js\");\n    const activePath = path.join(this.rootPath, \"documentation-robotics\", \"changesets\", \".active\");\n\n    if (await fileExists(activePath)) {\n      await writeFile(activePath, \"\");\n    }\n  }\n\n  /**\n   * Get the currently active changeset.\n   * Returns null if no changeset is active.\n   *\n   * @returns The active changeset or null if none is active\n   */\n  async getActive(): Promise<Changeset | null> {\n    const activePath = path.join(this.rootPath, \"documentation-robotics\", \"changesets\", \".active\");\n\n    if (!(await fileExists(activePath))) {\n      return null;\n    }\n\n    const { readFile } = await import(\"../utils/file-io.js\");\n    const activeId = await readFile(activePath);\n    const id = activeId.trim();\n\n    if (!id) {\n      return null;\n    }\n\n    return this.storage.load(id);\n  }\n\n  /**\n   * Get the ID of the active changeset without loading the full changeset object.\n   * Useful for status display and quick active changeset checks.\n   *\n   * @returns The active changeset ID or null if no active changeset exists\n   */\n  async getActiveId(): Promise<string | null> {\n    const activePath = path.join(this.rootPath, \"documentation-robotics\", \"changesets\", \".active\");\n\n    if (!(await fileExists(activePath))) {\n      return null;\n    }\n\n    const { readFile } = await import(\"../utils/file-io.js\");\n    const activeId = await readFile(activePath);\n    const id = activeId.trim();\n\n    return id || null;\n  }\n\n  /**\n   * Apply a changeset to the base model.\n   * Alias for commit() to match legacy command terminology.\n   *\n   * @param model - The model to apply changes to\n   * @param changesetId - ID of the changeset to apply\n   * @param options - Commit options (force, validate, dryRun)\n   * @returns CommitResult with count of applied changes and validation status\n   * @throws Error if validation fails, drift detected without --force, or apply fails\n   *\n   * @remarks\n   * This method provides backward compatibility with changeset commands that use\n   * \"apply\" instead of \"commit\" terminology. All logic is delegated to commit().\n   */\n  async apply(\n    model: Model,\n    changesetId: string,\n    options: CommitOptions = {}\n  ): Promise<CommitResult> {\n    return this.commit(model, changesetId, options);\n  }\n\n  /**\n   * Revert a changeset without applying changes.\n   * Alias for discard() to match legacy command terminology.\n   *\n   * @param changesetId - ID of the changeset to revert\n   * @throws Error if changeset ID is invalid or changeset not found\n   *\n   * @remarks\n   * This method provides backward compatibility with changeset commands that use\n   * \"revert\" instead of \"discard\" terminology. All logic is delegated to discard().\n   */\n  async revert(changesetId: string): Promise<void> {\n    return this.discard(changesetId);\n  }\n\n  /**\n   * Backup the current model state for atomic rollback on commit failure.\n   * Creates a temporary backup directory with copies of all layer files and manifest.\n   * Validates backup completeness and calculates checksums for integrity verification.\n   *\n   * @param model - The model to backup\n   * @returns Path to the backup directory\n   * @throws Error if backup creation or validation fails\n   *\n   * @remarks\n   * Backup includes:\n   * - manifest.yaml or manifest.json\n   * - All layer YAML files\n   * - Backup manifest with checksums and metadata\n   * Backup is removed after successful commit; retained if commit fails for recovery.\n   */\n  private async backupModel(model: Model): Promise<string> {\n    const backupDir = path.join(\n      this.rootPath,\n      \"documentation-robotics\",\n      \".backups\",\n      `backup-${Date.now()}`\n    );\n\n    const { ensureDir, readFile, atomicWrite } = await import(\"../utils/file-io.js\");\n    const { createHash } = await import(\"crypto\");\n\n    await ensureDir(backupDir);\n\n    // Track what we're backing up for validation\n    // Use mutable array during construction, then make readonly when creating BackupManifest\n    const backupFiles: Array<{\n      path: string;\n      checksum: ReturnType<typeof createSha256Hash>;\n      size: number;\n    }> = [];\n    const timestamp = new Date().toISOString();\n\n    try {\n      // Backup manifest - try both .yaml and .json formats\n      let manifestPath = path.join(\n        model.rootPath,\n        \"documentation-robotics\",\n        \"model\",\n        \"manifest.yaml\"\n      );\n      if (!(await fileExists(manifestPath))) {\n        manifestPath = path.join(model.rootPath, \"documentation-robotics\", \"manifest.json\");\n      }\n      if (!(await fileExists(manifestPath))) {\n        throw new Error(\"Manifest file not found in expected locations\");\n      }\n\n      const manifestContent = await readFile(manifestPath);\n      const manifestChecksum = createSha256Hash(\n        createHash(\"sha256\").update(manifestContent).digest(\"hex\")\n      );\n      const manifestFilename = path.basename(manifestPath);\n\n      await atomicWrite(path.join(backupDir, manifestFilename), manifestContent);\n      backupFiles.push({\n        path: manifestFilename,\n        checksum: manifestChecksum,\n        size: manifestContent.length,\n      });\n\n      // Backup all layers - handle multiple YAML files per layer\n      const layersDir = path.join(backupDir, \"layers\");\n      await ensureDir(layersDir);\n\n      const fs = await import(\"fs/promises\");\n\n      for (const layer of model.layers.values()) {\n        const layerBackupDir = path.join(layersDir, layer.name);\n        await ensureDir(layerBackupDir);\n\n        // Find the layer directory in the model\n        const layerDirPath = await this.findLayerDirectory(model.rootPath, layer.name);\n        if (!layerDirPath) {\n          continue;\n        }\n\n        // Backup all YAML files in the layer directory\n        const files = await fs.readdir(layerDirPath);\n        for (const file of files) {\n          if (file.endsWith(\".yaml\") || file.endsWith(\".yml\")) {\n            const filePath = path.join(layerDirPath, file);\n            const fileContent = await readFile(filePath);\n            const fileChecksum = createSha256Hash(\n              createHash(\"sha256\").update(fileContent).digest(\"hex\")\n            );\n\n            await atomicWrite(path.join(layerBackupDir, file), fileContent);\n            backupFiles.push({\n              path: `layers/${layer.name}/${file}`,\n              checksum: fileChecksum,\n              size: fileContent.length,\n            });\n          }\n        }\n      }\n\n      // Create the final immutable BackupManifest\n      const backupManifest: BackupManifest = {\n        files: backupFiles as ReadonlyArray<(typeof backupFiles)[0]>,\n        timestamp,\n      };\n\n      // Write backup manifest for validation\n      await atomicWrite(\n        path.join(backupDir, \".backup-manifest.json\"),\n        JSON.stringify(backupManifest, null, 2)\n      );\n\n      // Validate backup completeness\n      await this.validateBackup(backupDir, backupManifest);\n\n      return backupDir;\n    } catch (error) {\n      // Clean up incomplete backup with detailed error handling\n      const cleanupError = await this.forceRemoveBackupDir(backupDir);\n\n      if (cleanupError) {\n        // This is CRITICAL - orphaned backups accumulate\n        throw new Error(\n          `Backup creation failed AND cleanup failed.\\n` +\n            `Original error: ${getErrorMessage(error)}\\n` +\n            `Cleanup error: ${cleanupError}\\n\\n` +\n            `Orphaned backup directory: ${backupDir}\\n` +\n            `This directory will accumulate and consume disk space.\\n\\n` +\n            `REQUIRED ACTIONS:\\n` +\n            `  1. Manually remove: rm -rf \"${backupDir}\"\\n` +\n            `  2. Check disk space: df -h\\n` +\n            `  3. Check permissions: ls -la \"${path.dirname(backupDir)}\"\\n\\n` +\n            `Cannot proceed with commit until this is resolved.`\n        );\n      }\n\n      throw new Error(\n        `Failed to create backup: ${getErrorMessage(error)}`\n      );\n    }\n  }\n\n  /**\n   * Validate backup completeness and file integrity.\n   * Verifies that all files in the manifest exist in the backup directory\n   * with matching checksums and sizes.\n   *\n   * @param backupDir - Path to the backup directory\n   * @param manifest - Backup manifest with file list and checksums\n   * @throws Error if any file is missing, checksum mismatches, or size differs\n   */\n  private async validateBackup(backupDir: string, manifest: BackupManifest): Promise<void> {\n    const { readFile, fileExists } = await import(\"../utils/file-io.js\");\n    const { createHash } = await import(\"crypto\");\n\n    for (const file of manifest.files) {\n      const backupFilePath = path.join(backupDir, file.path);\n\n      // Verify file exists\n      if (!(await fileExists(backupFilePath))) {\n        throw new Error(`Backup validation failed: ${file.path} not found in backup`);\n      }\n\n      // Verify checksum matches\n      const content = await readFile(backupFilePath);\n      const checksum = createHash(\"sha256\").update(content).digest(\"hex\");\n\n      if (checksum !== file.checksum) {\n        throw new Error(\n          `Backup validation failed: ${file.path} checksum mismatch (expected ${file.checksum}, got ${checksum})`\n        );\n      }\n\n      // Verify size matches\n      if (content.length !== file.size) {\n        throw new Error(\n          `Backup validation failed: ${file.path} size mismatch (expected ${file.size}, got ${content.length})`\n        );\n      }\n    }\n  }\n\n  /**\n   * Validate backup integrity by checking manifest and file checksums.\n   * This is called before suggesting manual restoration to ensure the backup is usable.\n   * @param backupDir - Path to the backup directory\n   * @returns Promise resolving to backup health status or throwing error with details\n   * @throws Error with details about any integrity issues found\n   */\n  async validateBackupIntegrity(backupDir: string): Promise<{\n    isValid: boolean;\n    filesChecked: number;\n    errors: string[];\n  }> {\n    const { readFile, fileExists } = await import(\"../utils/file-io.js\");\n    const { createHash } = await import(\"crypto\");\n\n    const errors: string[] = [];\n    let filesChecked = 0;\n\n    try {\n      // Check if backup directory exists\n      if (!(await fileExists(backupDir))) {\n        throw new Error(`Backup directory not found: ${backupDir}`);\n      }\n\n      // Load and validate backup manifest\n      const manifestPath = path.join(backupDir, \".backup-manifest.json\");\n      if (!(await fileExists(manifestPath))) {\n        throw new Error(`Backup manifest not found at ${manifestPath}`);\n      }\n\n      // Read manifest content first (can throw for parse errors)\n      let rawManifest;\n      try {\n        const manifestContent = await readFile(manifestPath);\n        if (!manifestContent || manifestContent.length === 0) {\n          throw new Error(\"Backup manifest is empty\");\n        }\n        rawManifest = JSON.parse(manifestContent.toString());\n      } catch (err) {\n        // JSON parse errors should throw - these are critical errors\n        throw new Error(\n          `Failed to read backup manifest: ${err instanceof Error ? err.message : String(err)}`\n        );\n      }\n\n      // Validate manifest structure (can throw for missing required arrays)\n      if (!rawManifest || typeof rawManifest !== \"object\") {\n        throw new Error(\"Backup manifest must be an object\");\n      }\n\n      if (!rawManifest.files || !Array.isArray(rawManifest.files)) {\n        throw new Error(\"Backup manifest must have a files array\");\n      }\n\n      // Validate each file entry in the manifest and collect errors gracefully\n      for (let index = 0; index < rawManifest.files.length; index++) {\n        const file = rawManifest.files[index];\n        filesChecked++;\n\n        // Validate file entry structure\n        if (!file || typeof file !== \"object\") {\n          errors.push(`Backup manifest file entry ${index} must be an object`);\n          continue;\n        }\n\n        if (typeof file.path !== \"string\" || !file.path) {\n          errors.push(`Backup manifest file entry ${index} must have a non-empty path string`);\n          continue;\n        }\n\n        // Validate required metadata fields - these are validation errors, not critical\n        if (typeof file.checksum !== \"string\") {\n          errors.push(`Backup manifest file entry ${index} must have a checksum string`);\n          continue;\n        }\n\n        if (typeof file.size !== \"number\" || file.size < 0) {\n          errors.push(`Backup manifest file entry ${index} must have a non-negative size number`);\n          continue;\n        }\n\n        // File validation: check file exists and integrity\n        const backupFilePath = path.join(backupDir, file.path);\n\n        // Check file exists\n        if (!(await fileExists(backupFilePath))) {\n          errors.push(`Missing: ${file.path}`);\n          continue;\n        }\n\n        // Check checksum\n        try {\n          const content = await readFile(backupFilePath);\n          const checksum = createHash(\"sha256\").update(content).digest(\"hex\");\n\n          if (checksum !== file.checksum) {\n            errors.push(\n              `Checksum mismatch: ${file.path} (expected ${file.checksum}, got ${checksum})`\n            );\n            continue;\n          }\n\n          // Check size\n          if (content.length !== file.size) {\n            errors.push(\n              `Size mismatch: ${file.path} (expected ${file.size}, got ${content.length})`\n            );\n          }\n        } catch (err) {\n          errors.push(\n            `Failed to validate: ${file.path} (${err instanceof Error ? err.message : String(err)})`\n          );\n        }\n      }\n\n      return {\n        isValid: errors.length === 0,\n        filesChecked,\n        errors,\n      };\n    } catch (err) {\n      throw new Error(\n        `Backup integrity check failed: ${err instanceof Error ? err.message : String(err)}`\n      );\n    }\n  }\n\n  /**\n   * Clean up a backup directory after successful commit.\n   * Removes the backup directory and all its contents to prevent disk space accumulation.\n   *\n   * @param backupDir - Path to the backup directory to remove\n   *\n   * @remarks\n   * Failures during cleanup are logged with ERROR severity but do not throw.\n   * Successful commits should not fail due to cleanup errors, but users need to\n   * know about cleanup failures to avoid disk space accumulation.\n   * Includes actionable guidance for common failure scenarios.\n   */\n  private async cleanupBackup(backupDir: string): Promise<void> {\n    try {\n      const { rm } = await import(\"node:fs/promises\");\n      await rm(backupDir, { recursive: true, force: true });\n    } catch (error) {\n      // Log cleanup failures with ERROR severity - these mask real problems\n      const errorMsg = getErrorMessage(error);\n      const errorCode = (error as NodeJS.ErrnoException)?.code;\n\n      let suggestions = \"\";\n\n      // Handle ENOENT specially - backup already deleted is not an error\n      if (errorCode === \"ENOENT\") {\n        // Backup was already deleted - directory removal goal is achieved\n        return;\n      }\n\n      // ENOSPC is CRITICAL - orphaned backups will accumulate and fill disk\n      if (errorCode === \"ENOSPC\") {\n        throw new Error(\n          `Backup cleanup failed due to disk full.\\n` +\n            `Original error: ${errorMsg}\\n\\n` +\n            `Orphaned backup directory: ${backupDir}\\n` +\n            `This directory will accumulate and consume disk space.\\n\\n` +\n            `REQUIRED ACTIONS:\\n` +\n            `  1. Manually remove: rm -rf \"${backupDir}\"\\n` +\n            `  2. Free up disk space: df -h\\n` +\n            `  3. Check disk usage: du -sh ${path.dirname(backupDir)}/*\\n\\n` +\n            `Cannot proceed with future commits until disk space is freed.`\n        );\n      }\n\n      // Provide specific guidance based on error type\n      if (errorCode === \"EACCES\") {\n        suggestions =\n          \"\\n\\n[PERMISSION ERROR] Cannot delete backup directory.\\n\" +\n          `Directory: ${backupDir}\\n` +\n          \"Check file permissions or try manual cleanup:\\n\" +\n          `sudo rm -rf \"${backupDir}\"`;\n      } else {\n        suggestions =\n          \"\\n\\n[ACTION REQUIRED] Backup cleanup failed due to file system error.\\n\" +\n          `Directory: ${backupDir}\\n` +\n          `Manual cleanup: rm -rf \"${backupDir}\"\\n` +\n          \"Note: Backup directories accumulate over time and can fill disk space.\";\n      }\n\n      console.error(\n        `[ERROR] Failed to clean up backup directory after commit: ${errorMsg}` + suggestions\n      );\n    }\n  }\n\n  /**\n   * Force remove a backup directory with enhanced error handling.\n   * Attempts multiple strategies to ensure removal even with permission issues.\n   *\n   * @param backupDir - Path to the backup directory to remove\n   * @returns Error message if removal failed, null if successful\n   *\n   * @remarks\n   * This is used during backup creation failures to ensure cleanup of partial state.\n   * Returns error details instead of throwing so caller can log and continue.\n   */\n  private async forceRemoveBackupDir(backupDir: string): Promise<string | null> {\n    const fs = await import(\"fs/promises\");\n\n    try {\n      // Try standard removal first\n      await fs.rm(backupDir, { recursive: true, force: true });\n      return null;\n    } catch (error) {\n      // If standard removal fails, try more aggressive approach\n      try {\n        // Accumulate removal failures for detailed error reporting\n        const removalFailures: Array<{ path: string; error: string }> = [];\n\n        // List directory contents and try to remove each item\n        const entries = await fs.readdir(backupDir, { withFileTypes: true });\n        for (const entry of entries) {\n          const fullPath = path.join(backupDir, entry.name);\n          try {\n            if (entry.isDirectory()) {\n              await fs.rm(fullPath, { recursive: true, force: true });\n            } else {\n              await fs.unlink(fullPath);\n            }\n          } catch (itemError) {\n            removalFailures.push({\n              path: fullPath,\n              error: itemError instanceof Error ? itemError.message : String(itemError),\n            });\n          }\n        }\n\n        // Try to remove the directory itself\n        try {\n          await fs.rmdir(backupDir);\n          return null;\n        } catch {\n          // Directory may not be empty due to removal failures\n          if (removalFailures.length > 0) {\n            const failureDetails = removalFailures\n              .map((f) => `  - ${f.path}: ${f.error}`)\n              .join(\"\\n\");\n\n            return (\n              `Could not remove ${removalFailures.length} items from backup directory:\\n` +\n              failureDetails +\n              `\\n\\nManual cleanup required: rm -rf \"${backupDir}\"`\n            );\n          }\n\n          return `Could not remove directory ${backupDir} - may contain leftover files`;\n        }\n      } catch (aggressiveError) {\n        return `Backup cleanup failed: ${aggressiveError instanceof Error ? aggressiveError.message : String(aggressiveError)}`;\n      }\n    }\n  }\n\n  /**\n   * Restore model state from backup after failed commit.\n   * Restores manifest first (critical), then all layer files with defensive error handling.\n   * Provides detailed reporting of restoration progress and failures.\n   *\n   * @param model - The model to restore\n   * @param backupDir - Path to the backup directory\n   * @throws Error with detailed restoration summary if restoration fails\n   *\n   * @remarks\n   * Restoration strategy:\n   * 1. Restore manifest first (critical for model integrity)\n   * 2. Restore all layer files with per-file error handling\n   * 3. Continue restoring remaining files even if some fail\n   * 4. Throw detailed error if critical files fail to restore\n   * Both manifest and layer restoration failures are critical and will throw errors.\n   */\n  private async restoreModel(model: Model, backupDir: string): Promise<void> {\n    const { readFile, fileExists, atomicWrite } = await import(\"../utils/file-io.js\");\n\n    const restoredFiles: string[] = [];\n    const failedFiles: Array<{ path: string; error: string; isCritical: boolean }> = [];\n    const criticalLayers = new Set<string>(); // Track critical layer failures\n\n    try {\n      // Restore manifest first (most critical) - try both .yaml and .json\n      let backupManifestFile = path.join(backupDir, \"manifest.yaml\");\n      let manifestDestPath = path.join(\n        model.rootPath,\n        \"documentation-robotics\",\n        \"model\",\n        \"manifest.yaml\"\n      );\n\n      if (!(await fileExists(backupManifestFile))) {\n        backupManifestFile = path.join(backupDir, \"manifest.json\");\n        manifestDestPath = path.join(model.rootPath, \"documentation-robotics\", \"manifest.json\");\n      }\n\n      try {\n        if (!(await fileExists(backupManifestFile))) {\n          throw new Error(\"Backup manifest file not found (tried .yaml and .json)\");\n        }\n\n        const manifestContent = await readFile(backupManifestFile);\n        await atomicWrite(manifestDestPath, manifestContent);\n        restoredFiles.push(path.basename(backupManifestFile));\n      } catch (error) {\n        failedFiles.push({\n          path: path.basename(backupManifestFile),\n          error: getErrorMessage(error),\n          isCritical: true,\n        });\n        // Manifest is critical - throw immediately\n        throw new Error(\n          `Failed to restore ${path.basename(backupManifestFile)}: ${getErrorMessage(error)}`\n        );\n      }\n\n      // Restore all layer files with defensive error handling\n      const backupLayersDir = path.join(backupDir, \"layers\");\n      const fs = await import(\"fs/promises\");\n\n      for (const layer of model.layers.values()) {\n        const backupLayerDir = path.join(backupLayersDir, layer.name);\n\n        try {\n          if (!(await fileExists(backupLayerDir))) {\n            // CRITICAL: Layer directory missing in backup - this is a data loss scenario\n            const errorMsg = `Layer '${layer.name}' not found in backup (backup incomplete or corrupted)`;\n            failedFiles.push({\n              path: `layers/${layer.name}`,\n              error: errorMsg,\n              isCritical: true,\n            });\n            criticalLayers.add(layer.name);\n            continue;\n          }\n\n          // Find the correct destination directory for this layer\n          const layerDirPath = await this.findLayerDirectory(model.rootPath, layer.name);\n\n          if (!layerDirPath) {\n            // CRITICAL: Cannot find destination for layer - filesystem issue or permission problem\n            const errorMsg = `Destination directory not found for layer '${layer.name}' (permissions issue or directory structure changed)`;\n            failedFiles.push({\n              path: `layers/${layer.name}`,\n              error: errorMsg,\n              isCritical: true,\n            });\n            criticalLayers.add(layer.name);\n            continue;\n          }\n\n          // Restore all YAML files from backup\n          const backupFiles = await fs.readdir(backupLayerDir);\n          let filesRestoredInLayer = 0;\n\n          for (const file of backupFiles) {\n            if (file.endsWith(\".yaml\") || file.endsWith(\".yml\")) {\n              const backupFilePath = path.join(backupLayerDir, file);\n              const destFilePath = path.join(layerDirPath, file);\n              try {\n                const fileContent = await readFile(backupFilePath);\n                await atomicWrite(destFilePath, fileContent);\n                restoredFiles.push(`layers/${layer.name}/${file}`);\n                filesRestoredInLayer++;\n              } catch (fileError) {\n                // Individual file restoration failure - still critical for data integrity\n                const errorMsg = fileError instanceof Error ? fileError.message : String(fileError);\n\n                // Log immediately with ERROR severity\n                console.error(ansis.red(`\u2717 Failed to restore ${layer.name}/${file}: ${errorMsg}`));\n\n                failedFiles.push({\n                  path: `layers/${layer.name}/${file}`,\n                  error: errorMsg,\n                  isCritical: true,\n                });\n                criticalLayers.add(layer.name);\n              }\n            }\n          }\n        } catch (error) {\n          // Unexpected error during layer restoration - treat as critical\n          const errorMessage = getErrorMessage(error);\n          failedFiles.push({\n            path: `layers/${layer.name}`,\n            error: errorMessage,\n            isCritical: true,\n          });\n          criticalLayers.add(layer.name);\n        }\n      }\n\n      // Reload model layers to reflect restored state\n      model.layers.clear();\n\n      // CRITICAL: If any critical layers failed to restore, throw error immediately\n      if (criticalLayers.size > 0) {\n        const failedLayersList = Array.from(criticalLayers).join(\", \");\n        const detailedErrors = failedFiles.map((f) => `  - ${f.path}: ${f.error}`).join(\"\\n\");\n\n        const errorSummary =\n          `Model restoration FAILED - ${failedFiles.length} critical layer(s) could not be restored:\\n` +\n          `  Failed layers: ${failedLayersList}\\n` +\n          `\\n` +\n          `Detailed errors:\\n${detailedErrors}\\n` +\n          `\\n` +\n          `Successfully restored: ${restoredFiles.length} files\\n` +\n          `Failed to restore: ${failedFiles.length} files\\n` +\n          `\\n` +\n          `Possible causes:\\n` +\n          `  1. Backup directory corrupted or incomplete\\n` +\n          `  2. Insufficient permissions to write to model directory\\n` +\n          `  3. Disk full during restoration\\n` +\n          `  4. Layer directory structure changed since backup\\n` +\n          `\\n` +\n          `Backup location: ${backupDir}\\n` +\n          `\\n` +\n          `ACTION REQUIRED: Manually restore from backup or contact support.`;\n\n        throw new Error(errorSummary);\n      }\n    } catch (error) {\n      // Critical failure during restore\n      const errorMessage = getErrorMessage(error);\n      const summary =\n        `Model restoration failed: ${errorMessage}\\n` +\n        `\\n` +\n        `Restoration progress:\\n` +\n        `  Successfully restored: ${restoredFiles.length} files\\n` +\n        `  Failed to restore: ${failedFiles.length} files (all critical)\\n` +\n        `\\n` +\n        `Restored files:\\n${restoredFiles.map((f) => `  \u2713 ${f}`).join(\"\\n\")}\\n` +\n        `\\n` +\n        `Failed files:\\n${failedFiles.map((f) => `  ${f.isCritical ? \"\u2717 [CRITICAL]\" : \"\u26A0 [WARNING]\"} ${f.path}: ${f.error}`).join(\"\\n\")}\\n` +\n        `\\n` +\n        `Backup location: ${backupDir}`;\n\n      throw new Error(summary);\n    }\n  }\n\n  /**\n   * Find the directory path for a layer in the model.\n   * Uses same discovery logic as Model.loadLayer to locate layer directories.\n   * Handles naming convention: `{PREFIX}_{layerName}` where PREFIX is numeric (01_motivation, etc).\n   *\n   * @param rootPath - Root path of the model\n   * @param layerName - Name of the layer to find\n   * @returns Path to the layer directory or null if not found\n   */\n  private async findLayerDirectory(rootPath: string, layerName: string): Promise<string | null> {\n    const fs = await import(\"fs/promises\");\n    const modelDir = path.join(rootPath, \"documentation-robotics\", \"model\");\n\n    try {\n      const entries = await fs.readdir(modelDir, { withFileTypes: true });\n      const layerDir = entries.find(\n        (e) =>\n          e.isDirectory() && e.name.match(/^\\d{2}_/) && e.name.replace(/^\\d{2}_/, \"\") === layerName\n      );\n\n      if (layerDir) {\n        return path.join(modelDir, layerDir.name);\n      }\n\n      // Layer directory legitimately not found\n      return null;\n    } catch (error) {\n      const errorCode = (error as NodeJS.ErrnoException)?.code;\n\n      if (errorCode === \"ENOENT\") {\n        // Model directory doesn't exist - this might be OK during restore\n        return null;\n      }\n\n      // All other errors are CRITICAL during restore operations\n      throw new Error(\n        `Cannot access model directory for layer '${layerName}': ${getErrorMessage(error)}\\n` +\n          `Location: ${modelDir}\\n` +\n          `Error code: ${errorCode}\\n` +\n          `This indicates a filesystem or permissions issue. Check:\\n` +\n          `  1. Directory permissions: ls -la ${path.dirname(modelDir)}\\n` +\n          `  2. Disk health: df -h\\n` +\n          `  3. Filesystem errors: dmesg | tail`\n      );\n    }\n  }\n\n  /**\n   * Generate a unique changeset ID.\n   * Combines timestamp and random suffix to ensure uniqueness across concurrent operations.\n   *\n   * @returns A unique changeset ID in format `changeset-{timestamp}-{random}`\n   */\n  private generateChangesetId(): string {\n    return `changeset-${Date.now()}-${Math.random().toString(36).substr(2, 9)}`;\n  }\n}\n"],
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   "names": ["fileExists"]
 }

package/dist/core/virtual-projection.js

@@ -1,5 +1,7 @@
+import { readStagedSourceReference, stagedSourceReference } from "./staged-source-reference.js";
 import { Layer as LayerClass } from "./layer.js";
 import { Element as ElementClass } from "./element.js";
+import { withSequenceNumbers } from "./changeset.js";
 import { StagedChangesetStorage } from "./staged-changeset-storage.js";
 class VirtualProjectionEngine {
   stagingAreaManager;
@@ -60,7 +62,10 @@ class VirtualProjectionEngine {
         },
         references: Array.isArray(projectedData.references) ? projectedData.references : baseElement.references,
         relationships: Array.isArray(projectedData.relationships) ? projectedData.relationships : baseElement.relationships,
-        source_reference: baseElement.source_reference,
+        source_reference: (() => {
+          const staged = readStagedSourceReference(projectedData);
+          return staged.present ? staged.value : baseElement.source_reference;
+        })(),
         metadata: baseElement.metadata
       };
       return new ElementClass(mergedData);
@@ -76,7 +81,7 @@ class VirtualProjectionEngine {
         attributes: typeof projectedData.attributes == "object" ? projectedData.attributes : {},
         references: Array.isArray(projectedData.references) ? projectedData.references : [],
         relationships: Array.isArray(projectedData.relationships) ? projectedData.relationships : [],
-        source_reference: projectedData.source_reference,
+        source_reference: stagedSourceReference(projectedData),
         metadata: projectedData.metadata,
         layer: lastChange.layerName
       });
@@ -112,7 +117,7 @@ class VirtualProjectionEngine {
     const baseLayer = await baseModel.getBaseLayer(layerName), projectedLayer = baseLayer ? this.cloneLayer(baseLayer) : new LayerClass(layerName), changeset = await this.stagingAreaManager.load(changesetId);
     if (!changeset)
       throw new Error(`Changeset '${changesetId}' not found`);
-    const layerChanges = changeset.changes.filter((c) => c.layerName === layerName).sort((a, b) => a.sequenceNumber - b.sequenceNumber);
+    const layerChanges = withSequenceNumbers(changeset.changes).filter((c) => c.layerName === layerName).sort((a, b) => a.sequenceNumber - b.sequenceNumber);
     for (const change of layerChanges)
       switch (change.type) {
         case "add":
@@ -128,7 +133,7 @@ class VirtualProjectionEngine {
               attributes: typeof change.after.attributes == "object" ? change.after.attributes : {},
               references: Array.isArray(change.after.references) ? change.after.references : [],
               relationships: Array.isArray(change.after.relationships) ? change.after.relationships : [],
-              source_reference: change.after.source_reference,
+              source_reference: stagedSourceReference(change.after),
               metadata: change.after.metadata,
               layer: layerName
             });
@@ -154,7 +159,10 @@ class VirtualProjectionEngine {
                 references: Array.isArray(change.after.references) ? change.after.references : existing.references,
                 relationships: Array.isArray(change.after.relationships) ? change.after.relationships : existing.relationships,
                 layer: layerName,
-                source_reference: existing.source_reference,
+                source_reference: (() => {
+                  const staged = readStagedSourceReference(change.after);
+                  return staged.present ? staged.value : existing.source_reference;
+                })(),
                 metadata: existing.metadata
               });
               projectedLayer.updateElement(updatedElement);