@documentation-robotics/cli 0.1.10 → 0.1.11

package/dist/cli.js

@@ -32,6 +32,7 @@ import { reportsCommands } from "./commands/reports.js";
 import { auditCommand } from "./commands/audit.js";
 import { auditDiffCommand } from "./commands/audit-diff.js";
 import { auditSnapshotsCommand } from "./commands/audit-snapshots.js";
+import { repairAttributeCollisionCommand } from "./commands/repair.js";
 import { initTelemetry, startActiveSpan, shutdownTelemetry } from "./telemetry/index.js";
 import { installConsoleInterceptor } from "./telemetry/console-interceptor.js";
 import { getErrorMessage } from "./utils/errors.js";
@@ -47,7 +48,7 @@ async function extractExitCode(error) {
   }
   return 1;
 }
-const cliVersion = "0.1.10", program = new Command();
+const cliVersion = "0.1.11", program = new Command();
 (process.argv.includes("--version") || process.argv.includes("-V")) && (process.argv = ["node", "dr", "version"]), program.name("dr").description("Documentation Robotics CLI - Architecture Model Management").option("-v, --verbose", "Enable verbose output").option("--debug", "Enable debug mode").exitOverride().showSuggestionAfterError().hook("preAction", async (thisCommand) => {
   const options = thisCommand.opts();
   setGlobalOptions({
@@ -215,7 +216,22 @@ Actions:
 Examples:
   $ dr audit:snapshots list
   $ dr audit:snapshots delete --id 20260220-100000
-  $ dr audit:snapshots clear`).action((action, options) => auditSnapshotsCommand({ ...options, action }));
+  $ dr audit:snapshots clear`).action((action, options) => auditSnapshotsCommand({ ...options, action })), program.command("repair:attribute-collision").description(`Find and best-effort-recover model data lost to a fixed bug where saveLayer() stripped "source"/"x-source-reference" attributes from every element, even when a node type's schema declared one as a real (sometimes required) attribute`).option("--apply", "Restore recoverable values found in changeset history (default: report only)").option("--format <format>", "Output format: text (default), json").option("--output <path>", "Write the report to a file instead of stdout").addHelpText("after", `
+This repairs damage from a fixed bug in Model.saveLayer(): a hardcoded, type-blind "internal
+fields" blocklist unconditionally stripped any attribute literally named "source" or
+"x-source-reference" from every element's attributes before writing YAML, regardless of whether
+the element's own schema declared it as a real domain attribute. 41 of 191 node schemas across 8
+layers do (3 mark it required, meaning affected elements fail validation today).
+
+Recovery is best-effort: values can only be restored if they still exist in changeset history
+(committing a changeset does not delete it). Elements with no recoverable value are always
+reported, never fabricated \u2014 you'll need to re-supply those manually with
+"dr update <id> --attributes '{...}'".
+
+Examples:
+  $ dr repair:attribute-collision                    # Report only \u2014 no changes made
+  $ dr repair:attribute-collision --apply             # Restore every recoverable value
+  $ dr repair:attribute-collision --format json --output report.json`).action((options) => repairAttributeCollisionCommand(options));
 const relationshipGroup = program.command("relationship").description("Relationship operations");
 relationshipCommands(relationshipGroup);
 const elementGroup = program.command("element").description("Element operations");

package/dist/cli.js.map

@@ -1,7 +1,7 @@
 {
   "version": 3,
   "sources": ["../src/cli.ts"],
-  "sourcesContent": ["#!/usr/bin/env node\n\n/**\n * Documentation Robotics CLI - Bun Implementation\n * Entry point for the command-line interface\n *\n * Instrumented with OpenTelemetry to create root spans for command execution.\n * Telemetry is controlled by the TELEMETRY_ENABLED build-time constant.\n */\n\nimport { Command, CommanderError } from \"commander\";\nimport { setGlobalOptions } from \"./utils/globals.js\";\nimport { initCommand } from \"./commands/init.js\";\nimport { addCommand } from \"./commands/add.js\";\nimport { updateCommand } from \"./commands/update.js\";\nimport { deleteCommand } from \"./commands/delete.js\";\nimport { showCommand } from \"./commands/show.js\";\nimport { listCommand } from \"./commands/list.js\";\nimport { searchCommand } from \"./commands/search.js\";\nimport { validateCommand } from \"./commands/validate.js\";\nimport { infoCommand } from \"./commands/info.js\";\nimport { relationshipCommands } from \"./commands/relationship.js\";\nimport { elementCommands } from \"./commands/element.js\";\nimport { schemaCommands } from \"./commands/schema.js\";\nimport { catalogCommands } from \"./commands/catalog.js\";\nimport { docsCommands } from \"./commands/docs.js\";\nimport { traceCommand } from \"./commands/trace.js\";\nimport { exportCommand } from \"./commands/export.js\";\nimport { importCommand } from \"./commands/import.js\";\nimport { chatCommand } from \"./commands/chat.js\";\nimport { upgradeCommand } from \"./commands/upgrade.js\";\nimport { conformanceCommand } from \"./commands/conformance.js\";\nimport { changesetCommands } from \"./commands/changeset.js\";\nimport { claudeCommands } from \"./commands/claude.js\";\nimport { copilotCommands } from \"./commands/copilot.js\";\nimport { analyzerCommands } from \"./commands/analyzer.js\";\nimport { versionCommand } from \"./commands/version.js\";\nimport { statsCommand } from \"./commands/stats.js\";\nimport { reportCommand } from \"./commands/report.js\";\nimport { reportsCommands } from \"./commands/reports.js\";\nimport { auditCommand } from \"./commands/audit.js\";\nimport { auditDiffCommand } from \"./commands/audit-diff.js\";\nimport { auditSnapshotsCommand } from \"./commands/audit-snapshots.js\";\nimport { initTelemetry, startActiveSpan, shutdownTelemetry } from \"./telemetry/index.js\";\nimport { installConsoleInterceptor } from \"./telemetry/console-interceptor.js\";\nimport { getErrorMessage } from \"./utils/errors.js\";\n\n// Declare TELEMETRY_ENABLED as a build-time constant (substituted by esbuild)\n// Provide runtime fallback when not running through esbuild\ndeclare const TELEMETRY_ENABLED: boolean;\nconst isTelemetryEnabled = typeof TELEMETRY_ENABLED !== \"undefined\" ? TELEMETRY_ENABLED : false;\n\n// Commands that require console interceptor for telemetry logging\nconst CONSOLE_LOGGING_COMMANDS = new Set(['chat', 'validate', 'import', 'export']);\n\n/**\n * Extract exit code from an error object.\n * Handles CLIError instances and duck-typed objects with exitCode property.\n */\nasync function extractExitCode(error: unknown): Promise<number> {\n  const { CLIError } = await import(\"./utils/errors.js\");\n\n  if (error instanceof CLIError) {\n    return error.exitCode;\n  }\n\n  // Commander's own errors (--help, unknown commands, etc.) carry exitCode as\n  // expected control flow \u2014 handle them directly without duck-typing.\n  if (error instanceof CommanderError) {\n    return error.exitCode;\n  }\n\n  // Fallback for duck-typing (handles bundling/module issues)\n  if (error && typeof error === \"object\" && \"exitCode\" in error) {\n    const errorObj = error as any;\n    if (typeof errorObj.exitCode === \"number\") {\n      // Validate this looks like a CLIError before accepting\n      if (errorObj.name === \"CLIError\" || errorObj.message) {\n        if (process.argv.includes(\"--debug\")) {\n          console.warn(\n            \"[DEBUG] Using duck-typed error object as fallback - this may indicate a module loading issue\"\n          );\n        }\n        return errorObj.exitCode;\n      }\n    }\n  }\n\n  return 1;\n}\n\n// Declare build-time constant (substituted by esbuild)\ndeclare const CLI_VERSION: string;\nconst cliVersion = typeof CLI_VERSION !== \"undefined\" ? CLI_VERSION : \"0.1.3\";\n\nconst program = new Command();\n\n// Handle --version and -V flags by redirecting to version command\n// This ensures they go through the telemetry wrapper\nif (process.argv.includes(\"--version\") || process.argv.includes(\"-V\")) {\n  process.argv = [\"node\", \"dr\", \"version\"];\n}\n\nprogram\n  .name(\"dr\")\n  .description(\"Documentation Robotics CLI - Architecture Model Management\")\n  .option(\"-v, --verbose\", \"Enable verbose output\")\n  .option(\"--debug\", \"Enable debug mode\")\n  .exitOverride() // Prevent Commander from calling process.exit() - we handle exit ourselves\n  .showSuggestionAfterError() // \"Did you mean X?\" on unknown commands/options\n  .hook(\"preAction\", async (thisCommand) => {\n    // Set up global state (verbose/debug flags)\n    const options = thisCommand.opts();\n    setGlobalOptions({\n      verbose: options.verbose as boolean | undefined,\n      debug: options.debug as boolean | undefined,\n    });\n  });\n\n// Model commands\nprogram\n  .command(\"init [name]\")\n  .description(\"Initialize a new architecture model\")\n  .option(\"--name <name>\", \"Model name (overrides positional argument)\")\n  .option(\"--author <author>\", \"Model author\")\n  .option(\"--description <desc>\", \"Model description\")\n  .addHelpText(\n    \"after\",\n    `\nExamples:\n  $ dr init\n  $ dr init claudetoreum\n  $ dr init \"Enterprise Architecture\" --author \"Team A\"\n  $ dr init --name \"My Project\" --description \"13-layer federated model\"`\n  )\n  .action((name, options) => initCommand({ ...options, name: options.name || name }));\n\nprogram\n  .command(\"add <layer> <type> <name>\")\n  .description(\"Add an element to a layer\")\n  .option(\"--name <name>\", \"Element display name (defaults to the name argument)\")\n  .option(\"--description <desc>\", \"Element description\")\n  .option(\"--attributes <json>\", \"Element type-specific attributes as JSON object\")\n  .option(\"--source-file <path>\", \"Source file path (relative from repository root)\")\n  .option(\"--source-symbol <name>\", \"Symbol name (class, function, variable) in source file\")\n  .option(\"--source-provenance <type>\", \"Provenance type: extracted, manual, inferred, generated\")\n  .option(\"--source-repo-remote <url>\", \"Git remote URL for repository context\")\n  .option(\"--source-repo-commit <sha>\", \"Git commit SHA (40 hex characters) for repository context\")\n  .addHelpText(\n    \"after\",\n    `\nExamples:\n  $ dr add business service \"Customer Management\"\n  $ dr add api operation \"Create Customer\" --attributes '{\"operationId\":\"createCustomer\",\"summary\":\"Create a customer\",\"tags\":\"customers\"}'\n  $ dr add application component \"Customer API\" --description \"REST API for customer operations\"\n  $ dr add security policy \"Auth Validator\" --source-file \"src/auth/validator.ts\" --source-symbol \"validateToken\" --source-provenance \"extracted\"\n\nNote: Element IDs are generated automatically in format {layer}.{type}.{kebab-name}`\n  )\n  .action(addCommand);\n\nprogram\n  .command(\"update <id>\")\n  .description(\"Update an element\")\n  .option(\"--name <name>\", \"New element name\")\n  .option(\"--description <desc>\", \"New description\")\n  .option(\"--type <new-type>\", \"Change element type (must be valid for the element's layer; incompatible attributes must be cleaned up manually)\")\n  .option(\"--attributes <json>\", \"Updated type-specific attributes (JSON)\")\n  .option(\"--source-file <path>\", \"Source file path (relative from repository root)\")\n  .option(\"--source-symbol <name>\", \"Symbol name (class, function, variable) in source file\")\n  .option(\"--source-provenance <type>\", \"Provenance type: extracted, manual, inferred, generated\")\n  .option(\"--source-repo-remote <url>\", \"Git remote URL for repository context\")\n  .option(\"--source-repo-commit <sha>\", \"Git commit SHA (40 hex characters) for repository context\")\n  .option(\"--clear-source-reference\", \"Remove source reference from element\")\n  .addHelpText(\n    \"after\",\n    `\nNote: Changes are written immediately to model files.\nTo track changes for review, activate a changeset first:\n  $ dr changeset activate my-changeset\n\nExamples:\n  $ dr update api-endpoint-create-customer --name \"Create Customer (v2)\"\n  $ dr update business-service-order --description \"Updated description\"\n  $ dr update application-applicationfunction-process-orders --type applicationservice\n  $ dr update security-policy-auth --source-file \"src/auth/policy.ts\" --source-provenance \"extracted\"`\n  )\n  .action(updateCommand);\n\nprogram\n  .command(\"delete <id>\")\n  .description(\"Delete an element\")\n  .option(\"--force\", \"Skip dependency checks (confirmation is also skipped in non-TTY environments)\")\n  .option(\"--cascade\", \"Remove dependent elements automatically\")\n  .option(\"--dry-run\", \"Show what would be removed without actually removing\")\n  .addHelpText(\n    \"after\",\n    `\nExamples:\n  $ dr delete api-endpoint-old-endpoint\n  $ dr delete api-endpoint-old-endpoint --force\n  $ dr delete api-endpoint-old-endpoint --cascade\n  $ dr delete api-endpoint-old-endpoint --dry-run\n  $ dr delete api-endpoint-old-endpoint --cascade --dry-run`\n  )\n  .action(deleteCommand);\n\nprogram\n  .command(\"show <id>\")\n  .description(\"Display element details\")\n  .option(\"--model <path>\", \"Path to model root (contains model/manifest.yaml)\")\n  .addHelpText(\n    \"after\",\n    `\nExamples:\n  $ dr show api-endpoint-create-customer\n  $ dr show business-service-order-mgmt`\n  )\n  .action((id, options) => showCommand(id, options));\n\nprogram\n  .command(\"list [layer]\")\n  .description(\"List elements in a layer (or all layers if omitted)\")\n  .option(\"--type <type>\", \"Filter by element type\")\n  .option(\"--json\", \"Output as JSON\")\n  .option(\"--model <path>\", \"Path to model root (contains model/manifest.yaml)\")\n  .addHelpText(\n    \"after\",\n    `\nExamples:\n  $ dr list\n  $ dr list api\n  $ dr list business --type businessservice\n  $ dr list api --json\n  $ dr list --json`\n  )\n  .action(listCommand);\n\nprogram\n  .command(\"search <query>\")\n  .description(\"Search for elements by name or ID\")\n  .option(\"--layer <layer>\", \"Limit search to specific layer\")\n  .option(\"--type <type>\", \"Filter by element type\")\n  .option(\n    \"--source-file <path>\",\n    \"Find elements referencing a source file (takes precedence over pattern matching)\"\n  )\n  .option(\"--json\", \"Output as JSON\")\n  .addHelpText(\n    \"after\",\n    `\nExamples:\n  $ dr search customer\n  $ dr search \"order processing\" --layer business\n  $ dr search create-* --type endpoint\n  $ dr search \"\" --source-file src/api/customer.ts`\n  )\n  .action(searchCommand);\n\nprogram\n  .command(\"validate\")\n  .description(\"Validate the architecture model\")\n  .option(\"--layers <layers...>\", \"Specific layers to validate\")\n  .option(\"--strict\", \"Treat warnings as errors\")\n  .option(\"--verbose\", \"Show detailed validation output with relationship breakdown\")\n  .option(\"--quiet\", \"Show minimal output\")\n  .option(\"--output <path>\", \"Export validation report to file (JSON or Markdown)\")\n  .option(\"--model <path>\", \"Path to model root (contains model/manifest.yaml)\")\n  .option(\"--orphans\", \"Show only orphaned elements grouped by layer with relationship suggestions\")\n  .option(\"--all\", \"Run all validations (default behavior)\")\n  .option(\"--markdown\", \"Validate markdown structure\")\n  .option(\"--schemas\", \"Validate JSON schemas\")\n  .option(\"--schema\", \"Validate JSON schemas (alias for --schemas)\")\n  .option(\"--relationships\", \"Validate relationships\")\n  .option(\"--structure\", \"Validate documentation structure\")\n  .option(\"--naming\", \"Validate naming conventions\")\n  .option(\"--references\", \"Validate cross-layer references\")\n  .addHelpText(\n    \"after\",\n    `\nExamples:\n  $ dr validate\n  $ dr validate --all --strict\n  $ dr validate --verbose\n  $ dr validate --quiet\n  $ dr validate --output report.json\n  $ dr validate --output report.md\n  $ dr validate --schemas\n  $ dr validate --relationships\n  $ dr validate --layers business api\n  $ dr validate --orphans\n  $ dr validate --orphans --output orphans.json`\n  )\n  .action(validateCommand);\n\nprogram\n  .command(\"export <format>\")\n  .description(\"Export the architecture model to various formats\")\n  .option(\"--output <path>\", \"Output file path (default: print to stdout)\")\n  .option(\"--layers <layers...>\", \"Specific layers to export\")\n  .option(\"--model <path>\", \"Path to model root directory or manifest.yaml file\")\n  .option(\"--include-sources\", \"Include source file paths in PlantUML diagrams as notes\")\n  .addHelpText(\n    \"after\",\n    `\nSupported formats:\n  archimate    Export to ArchiMate XML (layers 1, 2, 5, 6)\n  openapi      Export to OpenAPI 3.0 specification (layer 7)\n  jsonschema   Export to JSON Schema (layer 8)\n  plantuml     Export to PlantUML diagram\n  graphml      Export to GraphML (graph visualization)\n  markdown     Export to Markdown documentation\n\nExamples:\n  $ dr export archimate --output model.xml\n  $ dr export openapi --layers api\n  $ dr export plantuml --include-sources --output diagram.puml\n  $ dr export markdown --output docs/architecture.md`\n  )\n  .action(async (format, options) => {\n    await exportCommand({\n      format,\n      output: options.output,\n      layers: options.layers,\n      model: options.model,\n      includeSources: options.includeSources,\n    });\n  });\n\nprogram\n  .command(\"import <format>\")\n  .description(\"Import architecture model from various formats\")\n  .option(\"--input <path>\", \"Input file path (required)\", undefined)\n  .option(\"--model <path>\", \"Path to model root directory or manifest.yaml file\")\n  .option(\n    \"--merge-strategy <strategy>\",\n    \"How to handle existing elements: add, update, skip (default: add)\"\n  )\n  .addHelpText(\n    \"after\",\n    `\nSupported formats:\n  archimate    Import from ArchiMate XML (layers 1, 2, 5, 6)\n  openapi      Import from OpenAPI 3.0 specification (layer 7)\n\nExamples:\n  $ dr import archimate --input model.xml\n  $ dr import openapi --input api.json --merge-strategy add\n  $ dr import archimate --input model.xml --model ./myproject`\n  )\n  .action(async (format, options) => {\n    if (!options.input) {\n      console.error(\"Error: --input path is required\");\n      process.exit(1);\n    }\n    await importCommand({\n      format,\n      input: options.input,\n      model: options.model,\n      mergeStrategy: options.mergeStrategy as \"add\" | \"update\" | \"skip\" | undefined,\n    });\n  });\n\nprogram\n  .command(\"info\")\n  .description(\"Show model information\")\n  .option(\"--layer <layer>\", \"Show specific layer details\")\n  .option(\"--verbose\", \"Show detailed breakdown by element type\")\n  .addHelpText(\n    \"after\",\n    `\nExamples:\n  $ dr info\n  $ dr info --layer business\n  $ dr info --layer api --verbose`\n  )\n  .action(infoCommand);\n\nprogram\n  .command(\"stats\")\n  .description(\"Display model statistics and health metrics\")\n  .option(\"--model <path>\", \"Path to the model directory\")\n  .option(\"--format <format>\", \"Output format: text (default), json, markdown, compact\")\n  .option(\"--output <path>\", \"Output file path (auto-detects format from extension)\")\n  .option(\"--compact\", \"Show compact one-line summary\")\n  .option(\"--verbose\", \"Show detailed information\")\n  .addHelpText(\n    \"after\",\n    `\nOutput formats:\n  text       Full formatted statistics (default)\n  json       JSON output for automation\n  markdown   Markdown report format\n  compact    Single-line summary\n\nExamples:\n  $ dr stats                           # Show full statistics\n  $ dr stats --compact                 # Show one-line summary\n  $ dr stats --format json             # Output as JSON\n  $ dr stats --output stats.md         # Save as markdown file\n  $ dr stats --output stats.json       # Save as JSON file\n  $ dr stats --verbose                 # Show detailed information`\n  )\n  .action((options) => statsCommand(options));\n\nprogram\n  .command(\"report\")\n  .description(\"Generate comprehensive architecture reports\")\n  .option(\"--model <path>\", \"Path to the model directory\")\n  .option(\"--type <type>\", \"Report type: comprehensive (default), statistics, relationships, data-model, quality\")\n  .option(\"--format <format>\", \"Output format: text (default), json, markdown\")\n  .option(\"--output <path>\", \"Output file path (auto-detects format from extension)\")\n  .option(\"--verbose\", \"Show detailed information\")\n  .option(\"--include-data-model\", \"Include data model analysis (default: true)\")\n  .option(\"--include-quality\", \"Include quality metrics (default: true)\")\n  .addHelpText(\n    \"after\",\n    `\nReport types:\n  comprehensive  Full report with statistics, relationships, and data model (default)\n  statistics     Statistics and quality metrics\n  relationships  Relationship analysis and classification\n  data-model     Layer 8 data model analysis\n  quality        Quality metrics and recommendations\n\nOutput formats:\n  text       Full formatted report (default)\n  json       JSON output for automation\n  markdown   Markdown report format\n\nExamples:\n  $ dr report                                      # Show comprehensive report\n  $ dr report --type relationships                 # Show relationship analysis\n  $ dr report --format json                        # Output as JSON\n  $ dr report --output report.md                   # Save as markdown file\n  $ dr report --type data-model --output dm.md     # Data model report as markdown\n  $ dr report --verbose                            # Show detailed information`\n  )\n  .action((options) => reportCommand(options));\n\n// Reports subcommands (managed layer report files)\nconst reportsGroup = program.command(\"reports\").description(\"Manage architecture layer reports\");\nreportsCommands(reportsGroup);\n\n// Audit command - Relationship analysis\nprogram\n  .command(\"audit [layer]\")\n  .description(\"Analyze relationship coverage, gaps, duplicates, and balance\")\n  .option(\"--type <type>\", \"Audit type: relationships (default), nodes, all\")\n  .option(\"--format <format>\", \"Output format: text (default), json, markdown\")\n  .option(\"--output <path>\", \"Output file path (auto-detects format from extension)\")\n  .option(\"--verbose\", \"Show detailed analysis\")\n  .option(\"--save-snapshot\", \"Save audit report as snapshot for differential analysis\")\n  .addHelpText(\n    \"after\",\n    `\nAudit types:\n  relationships  Relationship coverage, gaps, duplicates, balance (default)\n  nodes          Node type usage distribution across model layers\n  all            Both relationship and node audits\n\nOutput formats:\n  text       Full formatted audit report (default)\n  json       JSON output for automation\n  markdown   Markdown audit report format\n\nExamples:\n  $ dr audit                           # Full relationship audit of all layers\n  $ dr audit security                  # Audit security layer only\n  $ dr audit --type nodes              # Node type distribution audit\n  $ dr audit --type all                # Combined relationship + node audit\n  $ dr audit --format json             # Output as JSON\n  $ dr audit --output audit.md         # Save as markdown file\n  $ dr audit --verbose                 # Show detailed analysis\n  $ dr audit --save-snapshot           # Save snapshot for later comparison\n  $ dr audit api --output api-audit.json  # API layer audit as JSON`\n  )\n  .action((layer, options) =>\n    auditCommand({ ...options, layer, verbose: options.verbose ?? program.opts().verbose }));\n\n// Audit diff command - Compare snapshots\nprogram\n  .command(\"audit:diff\")\n  .description(\"Compare before/after audit snapshots\")\n  .option(\"--before <id>\", \"Before snapshot ID or timestamp\")\n  .option(\"--after <id>\", \"After snapshot ID or timestamp\")\n  .option(\"--format <format>\", \"Output format: text (default), json, markdown\")\n  .option(\"--output <path>\", \"Output file path\")\n  .option(\"--verbose\", \"Show detailed comparison\")\n  .addHelpText(\n    \"after\",\n    `\nExamples:\n  $ dr audit:diff                                  # Compare latest two snapshots\n  $ dr audit:diff --before 20260220-100000 --after 20260220-150000\n  $ dr audit:diff --format markdown --output diff.md\n  $ dr audit:diff --verbose                        # Show detailed changes`\n  )\n  .action((options) => auditDiffCommand(options));\n\n// Audit snapshots command - Manage snapshots\nprogram\n  .command(\"audit:snapshots <action>\")\n  .description(\"Manage audit snapshots (list, delete, clear)\")\n  .option(\"--id <id>\", \"Snapshot ID (for delete action)\")\n  .addHelpText(\n    \"after\",\n    `\nActions:\n  list     List all available snapshots\n  delete   Delete a specific snapshot (requires --id)\n  clear    Delete all snapshots\n\nExamples:\n  $ dr audit:snapshots list\n  $ dr audit:snapshots delete --id 20260220-100000\n  $ dr audit:snapshots clear`\n  )\n  .action((action, options) => auditSnapshotsCommand({ ...options, action }));\n\n// Relationship subcommands\nconst relationshipGroup = program.command(\"relationship\").description(\"Relationship operations\");\nrelationshipCommands(relationshipGroup);\n\n// Element subcommands\nconst elementGroup = program.command(\"element\").description(\"Element operations\");\nelementCommands(elementGroup);\n\n// Schema introspection subcommands\nschemaCommands(program);\n\n// Catalog subcommands (modern relationship catalog)\ncatalogCommands(program);\n\n// Documentation subcommands (schema-driven generation)\ndocsCommands(program);\n\n// Dependency analysis commands\nprogram\n  .command(\"trace <elementId>\")\n  .description(\"Trace dependencies for an element\")\n  .option(\n    \"--direction <dir>\",\n    \"Trace direction: up (dependencies), down (dependents), both (default)\"\n  )\n  .option(\"--depth <num>\", \"Maximum traversal depth\")\n  .option(\"--metrics\", \"Show graph and element metrics\")\n  .option(\"--model <path>\", \"Path to model root (contains model/manifest.yaml)\")\n  .addHelpText(\n    \"after\",\n    `\nExamples:\n  $ dr trace api-endpoint-create-customer\n  $ dr trace business-service-order --direction down --metrics\n  $ dr trace application-component-api --depth 3`\n  )\n  .action(async (elementId, options) => {\n    await traceCommand(elementId, {\n      direction: options.direction as \"up\" | \"down\" | \"both\" | undefined,\n      depth: options.depth ? parseInt(options.depth) : undefined,\n      showMetrics: options.metrics,\n      model: options.model,\n    });\n  });\n\nprogram\n  .command(\"visualize\")\n  .description(\"Launch visualization server with WebSocket support\")\n  .option(\"--port <num>\", \"Server port (default: 8080)\")\n  .option(\"--no-browser\", \"Do not auto-open browser\")\n  .option(\"--no-auth\", \"Disable authentication (enabled by default)\")\n  .option(\"--token <token>\", \"Custom auth token (auto-generated by default)\")\n  .option(\"--with-danger\", \"Enable dangerous mode for chat (skip permissions)\")\n  .option(\n    \"--viewer-path <path>\",\n    \"Path to custom viewer build (e.g., ./dist/embedded/dr-viewer-bundle)\"\n  )\n  .addHelpText(\n    \"after\",\n    `\nExamples:\n  $ dr visualize\n  $ dr visualize --port 3000\n  $ dr visualize --no-browser\n  $ dr visualize --no-auth\n  $ dr visualize --token my-secret-token\n  $ dr visualize --with-danger\n  $ dr visualize --viewer-path ./dist/embedded/dr-viewer-bundle\n\nThe --with-danger flag enables dangerous mode for chat functionality:\n  - Claude Code: --dangerously-skip-permissions\n  - GitHub Copilot: --allow-all-tools\n\nThe --viewer-path option allows loading a local build of the web UI:\n  - Point to a directory containing index.html and supporting files\n  - Useful for developing custom viewers or using bundled distributions`\n  )\n  .action(async (options) => {\n    const { visualizeCommand } = await import(\"./commands/visualize.js\");\n    await visualizeCommand({\n      port: options.port,\n      noBrowser: options.browser === false, // Commander sets 'browser' to false when --no-browser is used\n      noAuth: options.auth === false, // Commander sets 'auth' to false when --no-auth is used\n      token: options.token,\n      withDanger: options.withDanger,\n      viewerPath: options.viewerPath,\n    });\n  });\n\n// AI Integration command\nprogram\n  .command(\"chat [client] [withDanger]\")\n  .description(\"Interactive chat with AI about the architecture model\")\n  .addHelpText(\n    \"after\",\n    `\nArguments:\n  client      Optional AI client to use: \"claude-code\" or \"github-copilot\"\n  withDanger  Enable dangerous mode: \"with-danger\"\n\nExamples:\n  $ dr chat                           # Auto-detect or use saved preference\n  $ dr chat claude-code               # Use Claude Code, save as preference\n  $ dr chat github-copilot            # Use GitHub Copilot, save as preference\n  $ dr chat with-danger               # Auto-detect with dangerous mode\n  $ dr chat claude-code with-danger   # Use Claude Code with dangerous mode\n  $ dr chat github-copilot with-danger # Use GitHub Copilot with dangerous mode\n\nDangerous mode enables:\n  - Claude Code: --dangerously-skip-permissions\n  - GitHub Copilot: --allow-all-tools\n\nThis launches an interactive chat interface where you can ask AI questions\nabout your architecture model. Supports Claude Code CLI and GitHub Copilot CLI.\n\nInstall instructions:\n  - Claude Code: https://claude.ai\n  - GitHub Copilot: gh extension install github/gh-copilot`\n  )\n  .action(async (client?: string, withDangerArg?: string) => {\n    // Parse arguments - handle both \"with-danger\" as first or second arg\n    let selectedClient: string | undefined;\n    let withDanger = false;\n\n    if (client === \"with-danger\") {\n      // Format: dr chat with-danger\n      withDanger = true;\n      selectedClient = undefined;\n    } else if (withDangerArg === \"with-danger\") {\n      // Format: dr chat <client> with-danger\n      withDanger = true;\n      selectedClient = client;\n    } else {\n      // Format: dr chat <client>\n      selectedClient = client;\n    }\n\n    await chatCommand(selectedClient, withDanger);\n  });\n\n// Advanced commands\nprogram\n  .command(\"version\")\n  .description(\"Show CLI and embedded spec version information\")\n  .addHelpText(\n    \"after\",\n    `\nExamples:\n  $ dr version`\n  )\n  .action(async () => {\n    await versionCommand();\n  });\n\nprogram\n  .command(\"upgrade\")\n  .description(\"Upgrade spec reference and migrate model to latest versions\")\n  .option(\"-y, --yes\", \"Automatically upgrade without prompting\")\n  .option(\"--dry-run\", \"Show what would be upgraded without making changes\")\n  .option(\"--force\", \"Force all upgrades regardless of current versions; skips migration validation\")\n  .addHelpText(\n    \"after\",\n    `\nExamples:\n  $ dr upgrade              # Scan, show plan, and prompt for upgrades\n  $ dr upgrade --dry-run    # Preview available upgrades\n  $ dr upgrade --yes        # Upgrade without prompting\n  $ dr upgrade --force      # Force all upgrades, ignoring version checks`\n  )\n  .action(async (options) => {\n    await upgradeCommand({\n      yes: options.yes,\n      dryRun: options.dryRun,\n      force: options.force,\n    });\n  });\n\nprogram\n  .command(\"conformance\")\n  .description(\"Check model conformance to layer specifications\")\n  .option(\"--layers <layers...>\", \"Specific layers to check\")\n  .option(\"--json\", \"Output as JSON\")\n  .option(\"--verbose\", \"Verbose output\")\n  .addHelpText(\n    \"after\",\n    `\nExamples:\n  $ dr conformance\n  $ dr conformance --layers business api application\n  $ dr conformance --json\n  $ dr conformance --verbose`\n  )\n  .action(async (options) => {\n    await conformanceCommand({\n      layers: options.layers,\n      json: options.json,\n      verbose: options.verbose ?? program.opts().verbose,\n    });\n  });\n\n// Changeset subcommands\nchangesetCommands(program);\n\n// Claude Code integration subcommands\nclaudeCommands(program);\n\n// GitHub Copilot integration subcommands\ncopilotCommands(program);\n\n// Analyzer integration subcommands\nanalyzerCommands(program);\n\n// Execute CLI with proper telemetry span wrapping\n// This creates a root span that all child spans will be linked to\n(async () => {\n  let exitCode = 0;\n  try {\n    if (isTelemetryEnabled) {\n      // Initialize telemetry before execution\n      await initTelemetry();\n\n      // Only install console interceptor for commands that need it\n      const commandName = process.argv[2] || \"unknown\";\n      if (CONSOLE_LOGGING_COMMANDS.has(commandName)) {\n        await installConsoleInterceptor();\n      }\n\n      const args = process.argv.slice(3).join(\" \");\n\n      // Wrap entire CLI execution in active span for proper context propagation\n      await startActiveSpan(\n        \"cli.execute\",\n        async (span) => {\n          // Attributes already set via options parameter - no duplicate setAttributes needed\n          try {\n            // Execute command - all child spans will now link to this root span\n            await program.parseAsync(process.argv);\n\n            // Set success status\n            span.setStatus({ code: 0 }); // SpanStatusCode.OK\n          } catch (error) {\n            // Record exception and set error status\n            // CommanderError with exitCode 0 is help text / unknown subcommand shown \u2014 not a real error\n            if (error instanceof CommanderError) {\n              if (error.exitCode === 0) {\n                span.setStatus({ code: 0 }); // SpanStatusCode.OK\n              } else {\n                span.recordException(error as Error);\n                span.setStatus({\n                  code: 2, // SpanStatusCode.ERROR\n                  message: error.message,\n                });\n              }\n            } else {\n              span.recordException(error as Error);\n              span.setStatus({\n                code: 2, // SpanStatusCode.ERROR\n                message: getErrorMessage(error),\n              });\n            }\n\n            // Print error message for CLIError instances\n            // Skip CommanderError \u2014 Commander already printed its own output (e.g. help text, unknown command)\n            const { CLIError } = await import(\"./utils/errors.js\");\n            if (error instanceof CommanderError) {\n              // Commander handled its own output; nothing to print\n            } else if (error instanceof CLIError) {\n              console.error(error.format());\n            } else if (error instanceof Error) {\n              console.error(error.message);\n            } else {\n              console.error(String(error));\n            }\n\n            // Extract exit code from CLIError if available\n            exitCode = await extractExitCode(error);\n            // Don't throw - let telemetry shutdown complete\n          }\n        },\n        {\n          \"cli.command\": commandName,\n          \"cli.args\": args,\n          \"cli.cwd\": process.cwd(),\n          \"cli.version\": cliVersion,\n        }\n      );\n\n      // Shutdown telemetry after execution completes\n      await shutdownTelemetry();\n\n      // Exit with exit code (keepAlive disabled in exporters prevents hanging)\n      process.exit(exitCode);\n    } else {\n      // No telemetry - just parse normally with error handling\n      try {\n        await program.parseAsync(process.argv);\n      } catch (error) {\n        // Extract exit code from CLIError if available\n        // Skip CommanderError \u2014 Commander already printed its own output (e.g. help text, unknown command)\n        const { CLIError } = await import(\"./utils/errors.js\");\n        if (error instanceof CommanderError) {\n          // Commander handled its own output; nothing to print\n        } else if (error instanceof CLIError) {\n          console.error(error.format());\n        } else {\n          // Unexpected exceptions need to be printed\n          if (error instanceof Error) {\n            console.error(error.message);\n          } else {\n            console.error(String(error));\n          }\n        }\n        const exitCodeFromError = await extractExitCode(error);\n        process.exit(exitCodeFromError);\n      }\n    }\n  } catch (error) {\n    // Error during telemetry init or shutdown\n    if (!isTelemetryEnabled) {\n      // No telemetry - exit immediately with error\n      process.exit(1);\n    }\n    // Telemetry enabled - try to shutdown before exit\n    await shutdownTelemetry();\n    process.exit(1);\n  }\n})();\n"],
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+  "sourcesContent": ["#!/usr/bin/env node\n\n/**\n * Documentation Robotics CLI - Bun Implementation\n * Entry point for the command-line interface\n *\n * Instrumented with OpenTelemetry to create root spans for command execution.\n * Telemetry is controlled by the TELEMETRY_ENABLED build-time constant.\n */\n\nimport { Command, CommanderError } from \"commander\";\nimport { setGlobalOptions } from \"./utils/globals.js\";\nimport { initCommand } from \"./commands/init.js\";\nimport { addCommand } from \"./commands/add.js\";\nimport { updateCommand } from \"./commands/update.js\";\nimport { deleteCommand } from \"./commands/delete.js\";\nimport { showCommand } from \"./commands/show.js\";\nimport { listCommand } from \"./commands/list.js\";\nimport { searchCommand } from \"./commands/search.js\";\nimport { validateCommand } from \"./commands/validate.js\";\nimport { infoCommand } from \"./commands/info.js\";\nimport { relationshipCommands } from \"./commands/relationship.js\";\nimport { elementCommands } from \"./commands/element.js\";\nimport { schemaCommands } from \"./commands/schema.js\";\nimport { catalogCommands } from \"./commands/catalog.js\";\nimport { docsCommands } from \"./commands/docs.js\";\nimport { traceCommand } from \"./commands/trace.js\";\nimport { exportCommand } from \"./commands/export.js\";\nimport { importCommand } from \"./commands/import.js\";\nimport { chatCommand } from \"./commands/chat.js\";\nimport { upgradeCommand } from \"./commands/upgrade.js\";\nimport { conformanceCommand } from \"./commands/conformance.js\";\nimport { changesetCommands } from \"./commands/changeset.js\";\nimport { claudeCommands } from \"./commands/claude.js\";\nimport { copilotCommands } from \"./commands/copilot.js\";\nimport { analyzerCommands } from \"./commands/analyzer.js\";\nimport { versionCommand } from \"./commands/version.js\";\nimport { statsCommand } from \"./commands/stats.js\";\nimport { reportCommand } from \"./commands/report.js\";\nimport { reportsCommands } from \"./commands/reports.js\";\nimport { auditCommand } from \"./commands/audit.js\";\nimport { auditDiffCommand } from \"./commands/audit-diff.js\";\nimport { auditSnapshotsCommand } from \"./commands/audit-snapshots.js\";\nimport { repairAttributeCollisionCommand } from \"./commands/repair.js\";\nimport { initTelemetry, startActiveSpan, shutdownTelemetry } from \"./telemetry/index.js\";\nimport { installConsoleInterceptor } from \"./telemetry/console-interceptor.js\";\nimport { getErrorMessage } from \"./utils/errors.js\";\n\n// Declare TELEMETRY_ENABLED as a build-time constant (substituted by esbuild)\n// Provide runtime fallback when not running through esbuild\ndeclare const TELEMETRY_ENABLED: boolean;\nconst isTelemetryEnabled = typeof TELEMETRY_ENABLED !== \"undefined\" ? TELEMETRY_ENABLED : false;\n\n// Commands that require console interceptor for telemetry logging\nconst CONSOLE_LOGGING_COMMANDS = new Set(['chat', 'validate', 'import', 'export']);\n\n/**\n * Extract exit code from an error object.\n * Handles CLIError instances and duck-typed objects with exitCode property.\n */\nasync function extractExitCode(error: unknown): Promise<number> {\n  const { CLIError } = await import(\"./utils/errors.js\");\n\n  if (error instanceof CLIError) {\n    return error.exitCode;\n  }\n\n  // Commander's own errors (--help, unknown commands, etc.) carry exitCode as\n  // expected control flow \u2014 handle them directly without duck-typing.\n  if (error instanceof CommanderError) {\n    return error.exitCode;\n  }\n\n  // Fallback for duck-typing (handles bundling/module issues)\n  if (error && typeof error === \"object\" && \"exitCode\" in error) {\n    const errorObj = error as any;\n    if (typeof errorObj.exitCode === \"number\") {\n      // Validate this looks like a CLIError before accepting\n      if (errorObj.name === \"CLIError\" || errorObj.message) {\n        if (process.argv.includes(\"--debug\")) {\n          console.warn(\n            \"[DEBUG] Using duck-typed error object as fallback - this may indicate a module loading issue\"\n          );\n        }\n        return errorObj.exitCode;\n      }\n    }\n  }\n\n  return 1;\n}\n\n// Declare build-time constant (substituted by esbuild)\ndeclare const CLI_VERSION: string;\nconst cliVersion = typeof CLI_VERSION !== \"undefined\" ? CLI_VERSION : \"0.1.3\";\n\nconst program = new Command();\n\n// Handle --version and -V flags by redirecting to version command\n// This ensures they go through the telemetry wrapper\nif (process.argv.includes(\"--version\") || process.argv.includes(\"-V\")) {\n  process.argv = [\"node\", \"dr\", \"version\"];\n}\n\nprogram\n  .name(\"dr\")\n  .description(\"Documentation Robotics CLI - Architecture Model Management\")\n  .option(\"-v, --verbose\", \"Enable verbose output\")\n  .option(\"--debug\", \"Enable debug mode\")\n  .exitOverride() // Prevent Commander from calling process.exit() - we handle exit ourselves\n  .showSuggestionAfterError() // \"Did you mean X?\" on unknown commands/options\n  .hook(\"preAction\", async (thisCommand) => {\n    // Set up global state (verbose/debug flags)\n    const options = thisCommand.opts();\n    setGlobalOptions({\n      verbose: options.verbose as boolean | undefined,\n      debug: options.debug as boolean | undefined,\n    });\n  });\n\n// Model commands\nprogram\n  .command(\"init [name]\")\n  .description(\"Initialize a new architecture model\")\n  .option(\"--name <name>\", \"Model name (overrides positional argument)\")\n  .option(\"--author <author>\", \"Model author\")\n  .option(\"--description <desc>\", \"Model description\")\n  .addHelpText(\n    \"after\",\n    `\nExamples:\n  $ dr init\n  $ dr init claudetoreum\n  $ dr init \"Enterprise Architecture\" --author \"Team A\"\n  $ dr init --name \"My Project\" --description \"13-layer federated model\"`\n  )\n  .action((name, options) => initCommand({ ...options, name: options.name || name }));\n\nprogram\n  .command(\"add <layer> <type> <name>\")\n  .description(\"Add an element to a layer\")\n  .option(\"--name <name>\", \"Element display name (defaults to the name argument)\")\n  .option(\"--description <desc>\", \"Element description\")\n  .option(\"--attributes <json>\", \"Element type-specific attributes as JSON object\")\n  .option(\"--source-file <path>\", \"Source file path (relative from repository root)\")\n  .option(\"--source-symbol <name>\", \"Symbol name (class, function, variable) in source file\")\n  .option(\"--source-provenance <type>\", \"Provenance type: extracted, manual, inferred, generated\")\n  .option(\"--source-repo-remote <url>\", \"Git remote URL for repository context\")\n  .option(\"--source-repo-commit <sha>\", \"Git commit SHA (40 hex characters) for repository context\")\n  .addHelpText(\n    \"after\",\n    `\nExamples:\n  $ dr add business service \"Customer Management\"\n  $ dr add api operation \"Create Customer\" --attributes '{\"operationId\":\"createCustomer\",\"summary\":\"Create a customer\",\"tags\":\"customers\"}'\n  $ dr add application component \"Customer API\" --description \"REST API for customer operations\"\n  $ dr add security policy \"Auth Validator\" --source-file \"src/auth/validator.ts\" --source-symbol \"validateToken\" --source-provenance \"extracted\"\n\nNote: Element IDs are generated automatically in format {layer}.{type}.{kebab-name}`\n  )\n  .action(addCommand);\n\nprogram\n  .command(\"update <id>\")\n  .description(\"Update an element\")\n  .option(\"--name <name>\", \"New element name\")\n  .option(\"--description <desc>\", \"New description\")\n  .option(\"--type <new-type>\", \"Change element type (must be valid for the element's layer; incompatible attributes must be cleaned up manually)\")\n  .option(\"--attributes <json>\", \"Updated type-specific attributes (JSON)\")\n  .option(\"--source-file <path>\", \"Source file path (relative from repository root)\")\n  .option(\"--source-symbol <name>\", \"Symbol name (class, function, variable) in source file\")\n  .option(\"--source-provenance <type>\", \"Provenance type: extracted, manual, inferred, generated\")\n  .option(\"--source-repo-remote <url>\", \"Git remote URL for repository context\")\n  .option(\"--source-repo-commit <sha>\", \"Git commit SHA (40 hex characters) for repository context\")\n  .option(\"--clear-source-reference\", \"Remove source reference from element\")\n  .addHelpText(\n    \"after\",\n    `\nNote: Changes are written immediately to model files.\nTo track changes for review, activate a changeset first:\n  $ dr changeset activate my-changeset\n\nExamples:\n  $ dr update api-endpoint-create-customer --name \"Create Customer (v2)\"\n  $ dr update business-service-order --description \"Updated description\"\n  $ dr update application-applicationfunction-process-orders --type applicationservice\n  $ dr update security-policy-auth --source-file \"src/auth/policy.ts\" --source-provenance \"extracted\"`\n  )\n  .action(updateCommand);\n\nprogram\n  .command(\"delete <id>\")\n  .description(\"Delete an element\")\n  .option(\"--force\", \"Skip dependency checks (confirmation is also skipped in non-TTY environments)\")\n  .option(\"--cascade\", \"Remove dependent elements automatically\")\n  .option(\"--dry-run\", \"Show what would be removed without actually removing\")\n  .addHelpText(\n    \"after\",\n    `\nExamples:\n  $ dr delete api-endpoint-old-endpoint\n  $ dr delete api-endpoint-old-endpoint --force\n  $ dr delete api-endpoint-old-endpoint --cascade\n  $ dr delete api-endpoint-old-endpoint --dry-run\n  $ dr delete api-endpoint-old-endpoint --cascade --dry-run`\n  )\n  .action(deleteCommand);\n\nprogram\n  .command(\"show <id>\")\n  .description(\"Display element details\")\n  .option(\"--model <path>\", \"Path to model root (contains model/manifest.yaml)\")\n  .addHelpText(\n    \"after\",\n    `\nExamples:\n  $ dr show api-endpoint-create-customer\n  $ dr show business-service-order-mgmt`\n  )\n  .action((id, options) => showCommand(id, options));\n\nprogram\n  .command(\"list [layer]\")\n  .description(\"List elements in a layer (or all layers if omitted)\")\n  .option(\"--type <type>\", \"Filter by element type\")\n  .option(\"--json\", \"Output as JSON\")\n  .option(\"--model <path>\", \"Path to model root (contains model/manifest.yaml)\")\n  .addHelpText(\n    \"after\",\n    `\nExamples:\n  $ dr list\n  $ dr list api\n  $ dr list business --type businessservice\n  $ dr list api --json\n  $ dr list --json`\n  )\n  .action(listCommand);\n\nprogram\n  .command(\"search <query>\")\n  .description(\"Search for elements by name or ID\")\n  .option(\"--layer <layer>\", \"Limit search to specific layer\")\n  .option(\"--type <type>\", \"Filter by element type\")\n  .option(\n    \"--source-file <path>\",\n    \"Find elements referencing a source file (takes precedence over pattern matching)\"\n  )\n  .option(\"--json\", \"Output as JSON\")\n  .addHelpText(\n    \"after\",\n    `\nExamples:\n  $ dr search customer\n  $ dr search \"order processing\" --layer business\n  $ dr search create-* --type endpoint\n  $ dr search \"\" --source-file src/api/customer.ts`\n  )\n  .action(searchCommand);\n\nprogram\n  .command(\"validate\")\n  .description(\"Validate the architecture model\")\n  .option(\"--layers <layers...>\", \"Specific layers to validate\")\n  .option(\"--strict\", \"Treat warnings as errors\")\n  .option(\"--verbose\", \"Show detailed validation output with relationship breakdown\")\n  .option(\"--quiet\", \"Show minimal output\")\n  .option(\"--output <path>\", \"Export validation report to file (JSON or Markdown)\")\n  .option(\"--model <path>\", \"Path to model root (contains model/manifest.yaml)\")\n  .option(\"--orphans\", \"Show only orphaned elements grouped by layer with relationship suggestions\")\n  .option(\"--all\", \"Run all validations (default behavior)\")\n  .option(\"--markdown\", \"Validate markdown structure\")\n  .option(\"--schemas\", \"Validate JSON schemas\")\n  .option(\"--schema\", \"Validate JSON schemas (alias for --schemas)\")\n  .option(\"--relationships\", \"Validate relationships\")\n  .option(\"--structure\", \"Validate documentation structure\")\n  .option(\"--naming\", \"Validate naming conventions\")\n  .option(\"--references\", \"Validate cross-layer references\")\n  .addHelpText(\n    \"after\",\n    `\nExamples:\n  $ dr validate\n  $ dr validate --all --strict\n  $ dr validate --verbose\n  $ dr validate --quiet\n  $ dr validate --output report.json\n  $ dr validate --output report.md\n  $ dr validate --schemas\n  $ dr validate --relationships\n  $ dr validate --layers business api\n  $ dr validate --orphans\n  $ dr validate --orphans --output orphans.json`\n  )\n  .action(validateCommand);\n\nprogram\n  .command(\"export <format>\")\n  .description(\"Export the architecture model to various formats\")\n  .option(\"--output <path>\", \"Output file path (default: print to stdout)\")\n  .option(\"--layers <layers...>\", \"Specific layers to export\")\n  .option(\"--model <path>\", \"Path to model root directory or manifest.yaml file\")\n  .option(\"--include-sources\", \"Include source file paths in PlantUML diagrams as notes\")\n  .addHelpText(\n    \"after\",\n    `\nSupported formats:\n  archimate    Export to ArchiMate XML (layers 1, 2, 5, 6)\n  openapi      Export to OpenAPI 3.0 specification (layer 7)\n  jsonschema   Export to JSON Schema (layer 8)\n  plantuml     Export to PlantUML diagram\n  graphml      Export to GraphML (graph visualization)\n  markdown     Export to Markdown documentation\n\nExamples:\n  $ dr export archimate --output model.xml\n  $ dr export openapi --layers api\n  $ dr export plantuml --include-sources --output diagram.puml\n  $ dr export markdown --output docs/architecture.md`\n  )\n  .action(async (format, options) => {\n    await exportCommand({\n      format,\n      output: options.output,\n      layers: options.layers,\n      model: options.model,\n      includeSources: options.includeSources,\n    });\n  });\n\nprogram\n  .command(\"import <format>\")\n  .description(\"Import architecture model from various formats\")\n  .option(\"--input <path>\", \"Input file path (required)\", undefined)\n  .option(\"--model <path>\", \"Path to model root directory or manifest.yaml file\")\n  .option(\n    \"--merge-strategy <strategy>\",\n    \"How to handle existing elements: add, update, skip (default: add)\"\n  )\n  .addHelpText(\n    \"after\",\n    `\nSupported formats:\n  archimate    Import from ArchiMate XML (layers 1, 2, 5, 6)\n  openapi      Import from OpenAPI 3.0 specification (layer 7)\n\nExamples:\n  $ dr import archimate --input model.xml\n  $ dr import openapi --input api.json --merge-strategy add\n  $ dr import archimate --input model.xml --model ./myproject`\n  )\n  .action(async (format, options) => {\n    if (!options.input) {\n      console.error(\"Error: --input path is required\");\n      process.exit(1);\n    }\n    await importCommand({\n      format,\n      input: options.input,\n      model: options.model,\n      mergeStrategy: options.mergeStrategy as \"add\" | \"update\" | \"skip\" | undefined,\n    });\n  });\n\nprogram\n  .command(\"info\")\n  .description(\"Show model information\")\n  .option(\"--layer <layer>\", \"Show specific layer details\")\n  .option(\"--verbose\", \"Show detailed breakdown by element type\")\n  .addHelpText(\n    \"after\",\n    `\nExamples:\n  $ dr info\n  $ dr info --layer business\n  $ dr info --layer api --verbose`\n  )\n  .action(infoCommand);\n\nprogram\n  .command(\"stats\")\n  .description(\"Display model statistics and health metrics\")\n  .option(\"--model <path>\", \"Path to the model directory\")\n  .option(\"--format <format>\", \"Output format: text (default), json, markdown, compact\")\n  .option(\"--output <path>\", \"Output file path (auto-detects format from extension)\")\n  .option(\"--compact\", \"Show compact one-line summary\")\n  .option(\"--verbose\", \"Show detailed information\")\n  .addHelpText(\n    \"after\",\n    `\nOutput formats:\n  text       Full formatted statistics (default)\n  json       JSON output for automation\n  markdown   Markdown report format\n  compact    Single-line summary\n\nExamples:\n  $ dr stats                           # Show full statistics\n  $ dr stats --compact                 # Show one-line summary\n  $ dr stats --format json             # Output as JSON\n  $ dr stats --output stats.md         # Save as markdown file\n  $ dr stats --output stats.json       # Save as JSON file\n  $ dr stats --verbose                 # Show detailed information`\n  )\n  .action((options) => statsCommand(options));\n\nprogram\n  .command(\"report\")\n  .description(\"Generate comprehensive architecture reports\")\n  .option(\"--model <path>\", \"Path to the model directory\")\n  .option(\"--type <type>\", \"Report type: comprehensive (default), statistics, relationships, data-model, quality\")\n  .option(\"--format <format>\", \"Output format: text (default), json, markdown\")\n  .option(\"--output <path>\", \"Output file path (auto-detects format from extension)\")\n  .option(\"--verbose\", \"Show detailed information\")\n  .option(\"--include-data-model\", \"Include data model analysis (default: true)\")\n  .option(\"--include-quality\", \"Include quality metrics (default: true)\")\n  .addHelpText(\n    \"after\",\n    `\nReport types:\n  comprehensive  Full report with statistics, relationships, and data model (default)\n  statistics     Statistics and quality metrics\n  relationships  Relationship analysis and classification\n  data-model     Layer 8 data model analysis\n  quality        Quality metrics and recommendations\n\nOutput formats:\n  text       Full formatted report (default)\n  json       JSON output for automation\n  markdown   Markdown report format\n\nExamples:\n  $ dr report                                      # Show comprehensive report\n  $ dr report --type relationships                 # Show relationship analysis\n  $ dr report --format json                        # Output as JSON\n  $ dr report --output report.md                   # Save as markdown file\n  $ dr report --type data-model --output dm.md     # Data model report as markdown\n  $ dr report --verbose                            # Show detailed information`\n  )\n  .action((options) => reportCommand(options));\n\n// Reports subcommands (managed layer report files)\nconst reportsGroup = program.command(\"reports\").description(\"Manage architecture layer reports\");\nreportsCommands(reportsGroup);\n\n// Audit command - Relationship analysis\nprogram\n  .command(\"audit [layer]\")\n  .description(\"Analyze relationship coverage, gaps, duplicates, and balance\")\n  .option(\"--type <type>\", \"Audit type: relationships (default), nodes, all\")\n  .option(\"--format <format>\", \"Output format: text (default), json, markdown\")\n  .option(\"--output <path>\", \"Output file path (auto-detects format from extension)\")\n  .option(\"--verbose\", \"Show detailed analysis\")\n  .option(\"--save-snapshot\", \"Save audit report as snapshot for differential analysis\")\n  .addHelpText(\n    \"after\",\n    `\nAudit types:\n  relationships  Relationship coverage, gaps, duplicates, balance (default)\n  nodes          Node type usage distribution across model layers\n  all            Both relationship and node audits\n\nOutput formats:\n  text       Full formatted audit report (default)\n  json       JSON output for automation\n  markdown   Markdown audit report format\n\nExamples:\n  $ dr audit                           # Full relationship audit of all layers\n  $ dr audit security                  # Audit security layer only\n  $ dr audit --type nodes              # Node type distribution audit\n  $ dr audit --type all                # Combined relationship + node audit\n  $ dr audit --format json             # Output as JSON\n  $ dr audit --output audit.md         # Save as markdown file\n  $ dr audit --verbose                 # Show detailed analysis\n  $ dr audit --save-snapshot           # Save snapshot for later comparison\n  $ dr audit api --output api-audit.json  # API layer audit as JSON`\n  )\n  .action((layer, options) =>\n    auditCommand({ ...options, layer, verbose: options.verbose ?? program.opts().verbose }));\n\n// Audit diff command - Compare snapshots\nprogram\n  .command(\"audit:diff\")\n  .description(\"Compare before/after audit snapshots\")\n  .option(\"--before <id>\", \"Before snapshot ID or timestamp\")\n  .option(\"--after <id>\", \"After snapshot ID or timestamp\")\n  .option(\"--format <format>\", \"Output format: text (default), json, markdown\")\n  .option(\"--output <path>\", \"Output file path\")\n  .option(\"--verbose\", \"Show detailed comparison\")\n  .addHelpText(\n    \"after\",\n    `\nExamples:\n  $ dr audit:diff                                  # Compare latest two snapshots\n  $ dr audit:diff --before 20260220-100000 --after 20260220-150000\n  $ dr audit:diff --format markdown --output diff.md\n  $ dr audit:diff --verbose                        # Show detailed changes`\n  )\n  .action((options) => auditDiffCommand(options));\n\n// Audit snapshots command - Manage snapshots\nprogram\n  .command(\"audit:snapshots <action>\")\n  .description(\"Manage audit snapshots (list, delete, clear)\")\n  .option(\"--id <id>\", \"Snapshot ID (for delete action)\")\n  .addHelpText(\n    \"after\",\n    `\nActions:\n  list     List all available snapshots\n  delete   Delete a specific snapshot (requires --id)\n  clear    Delete all snapshots\n\nExamples:\n  $ dr audit:snapshots list\n  $ dr audit:snapshots delete --id 20260220-100000\n  $ dr audit:snapshots clear`\n  )\n  .action((action, options) => auditSnapshotsCommand({ ...options, action }));\n\n// Repair command - Detect and recover data lost to fixed data-integrity bugs\nprogram\n  .command(\"repair:attribute-collision\")\n  .description(\n    'Find and best-effort-recover model data lost to a fixed bug where saveLayer() stripped \"source\"/\"x-source-reference\" attributes from every element, even when a node type\\'s schema declared one as a real (sometimes required) attribute'\n  )\n  .option(\"--apply\", \"Restore recoverable values found in changeset history (default: report only)\")\n  .option(\"--format <format>\", \"Output format: text (default), json\")\n  .option(\"--output <path>\", \"Write the report to a file instead of stdout\")\n  .addHelpText(\n    \"after\",\n    `\nThis repairs damage from a fixed bug in Model.saveLayer(): a hardcoded, type-blind \"internal\nfields\" blocklist unconditionally stripped any attribute literally named \"source\" or\n\"x-source-reference\" from every element's attributes before writing YAML, regardless of whether\nthe element's own schema declared it as a real domain attribute. 41 of 191 node schemas across 8\nlayers do (3 mark it required, meaning affected elements fail validation today).\n\nRecovery is best-effort: values can only be restored if they still exist in changeset history\n(committing a changeset does not delete it). Elements with no recoverable value are always\nreported, never fabricated \u2014 you'll need to re-supply those manually with\n\"dr update <id> --attributes '{...}'\".\n\nExamples:\n  $ dr repair:attribute-collision                    # Report only \u2014 no changes made\n  $ dr repair:attribute-collision --apply             # Restore every recoverable value\n  $ dr repair:attribute-collision --format json --output report.json`\n  )\n  .action((options) => repairAttributeCollisionCommand(options));\n\n// Relationship subcommands\nconst relationshipGroup = program.command(\"relationship\").description(\"Relationship operations\");\nrelationshipCommands(relationshipGroup);\n\n// Element subcommands\nconst elementGroup = program.command(\"element\").description(\"Element operations\");\nelementCommands(elementGroup);\n\n// Schema introspection subcommands\nschemaCommands(program);\n\n// Catalog subcommands (modern relationship catalog)\ncatalogCommands(program);\n\n// Documentation subcommands (schema-driven generation)\ndocsCommands(program);\n\n// Dependency analysis commands\nprogram\n  .command(\"trace <elementId>\")\n  .description(\"Trace dependencies for an element\")\n  .option(\n    \"--direction <dir>\",\n    \"Trace direction: up (dependencies), down (dependents), both (default)\"\n  )\n  .option(\"--depth <num>\", \"Maximum traversal depth\")\n  .option(\"--metrics\", \"Show graph and element metrics\")\n  .option(\"--model <path>\", \"Path to model root (contains model/manifest.yaml)\")\n  .addHelpText(\n    \"after\",\n    `\nExamples:\n  $ dr trace api-endpoint-create-customer\n  $ dr trace business-service-order --direction down --metrics\n  $ dr trace application-component-api --depth 3`\n  )\n  .action(async (elementId, options) => {\n    await traceCommand(elementId, {\n      direction: options.direction as \"up\" | \"down\" | \"both\" | undefined,\n      depth: options.depth ? parseInt(options.depth) : undefined,\n      showMetrics: options.metrics,\n      model: options.model,\n    });\n  });\n\nprogram\n  .command(\"visualize\")\n  .description(\"Launch visualization server with WebSocket support\")\n  .option(\"--port <num>\", \"Server port (default: 8080)\")\n  .option(\"--no-browser\", \"Do not auto-open browser\")\n  .option(\"--no-auth\", \"Disable authentication (enabled by default)\")\n  .option(\"--token <token>\", \"Custom auth token (auto-generated by default)\")\n  .option(\"--with-danger\", \"Enable dangerous mode for chat (skip permissions)\")\n  .option(\n    \"--viewer-path <path>\",\n    \"Path to custom viewer build (e.g., ./dist/embedded/dr-viewer-bundle)\"\n  )\n  .addHelpText(\n    \"after\",\n    `\nExamples:\n  $ dr visualize\n  $ dr visualize --port 3000\n  $ dr visualize --no-browser\n  $ dr visualize --no-auth\n  $ dr visualize --token my-secret-token\n  $ dr visualize --with-danger\n  $ dr visualize --viewer-path ./dist/embedded/dr-viewer-bundle\n\nThe --with-danger flag enables dangerous mode for chat functionality:\n  - Claude Code: --dangerously-skip-permissions\n  - GitHub Copilot: --allow-all-tools\n\nThe --viewer-path option allows loading a local build of the web UI:\n  - Point to a directory containing index.html and supporting files\n  - Useful for developing custom viewers or using bundled distributions`\n  )\n  .action(async (options) => {\n    const { visualizeCommand } = await import(\"./commands/visualize.js\");\n    await visualizeCommand({\n      port: options.port,\n      noBrowser: options.browser === false, // Commander sets 'browser' to false when --no-browser is used\n      noAuth: options.auth === false, // Commander sets 'auth' to false when --no-auth is used\n      token: options.token,\n      withDanger: options.withDanger,\n      viewerPath: options.viewerPath,\n    });\n  });\n\n// AI Integration command\nprogram\n  .command(\"chat [client] [withDanger]\")\n  .description(\"Interactive chat with AI about the architecture model\")\n  .addHelpText(\n    \"after\",\n    `\nArguments:\n  client      Optional AI client to use: \"claude-code\" or \"github-copilot\"\n  withDanger  Enable dangerous mode: \"with-danger\"\n\nExamples:\n  $ dr chat                           # Auto-detect or use saved preference\n  $ dr chat claude-code               # Use Claude Code, save as preference\n  $ dr chat github-copilot            # Use GitHub Copilot, save as preference\n  $ dr chat with-danger               # Auto-detect with dangerous mode\n  $ dr chat claude-code with-danger   # Use Claude Code with dangerous mode\n  $ dr chat github-copilot with-danger # Use GitHub Copilot with dangerous mode\n\nDangerous mode enables:\n  - Claude Code: --dangerously-skip-permissions\n  - GitHub Copilot: --allow-all-tools\n\nThis launches an interactive chat interface where you can ask AI questions\nabout your architecture model. Supports Claude Code CLI and GitHub Copilot CLI.\n\nInstall instructions:\n  - Claude Code: https://claude.ai\n  - GitHub Copilot: gh extension install github/gh-copilot`\n  )\n  .action(async (client?: string, withDangerArg?: string) => {\n    // Parse arguments - handle both \"with-danger\" as first or second arg\n    let selectedClient: string | undefined;\n    let withDanger = false;\n\n    if (client === \"with-danger\") {\n      // Format: dr chat with-danger\n      withDanger = true;\n      selectedClient = undefined;\n    } else if (withDangerArg === \"with-danger\") {\n      // Format: dr chat <client> with-danger\n      withDanger = true;\n      selectedClient = client;\n    } else {\n      // Format: dr chat <client>\n      selectedClient = client;\n    }\n\n    await chatCommand(selectedClient, withDanger);\n  });\n\n// Advanced commands\nprogram\n  .command(\"version\")\n  .description(\"Show CLI and embedded spec version information\")\n  .addHelpText(\n    \"after\",\n    `\nExamples:\n  $ dr version`\n  )\n  .action(async () => {\n    await versionCommand();\n  });\n\nprogram\n  .command(\"upgrade\")\n  .description(\"Upgrade spec reference and migrate model to latest versions\")\n  .option(\"-y, --yes\", \"Automatically upgrade without prompting\")\n  .option(\"--dry-run\", \"Show what would be upgraded without making changes\")\n  .option(\"--force\", \"Force all upgrades regardless of current versions; skips migration validation\")\n  .addHelpText(\n    \"after\",\n    `\nExamples:\n  $ dr upgrade              # Scan, show plan, and prompt for upgrades\n  $ dr upgrade --dry-run    # Preview available upgrades\n  $ dr upgrade --yes        # Upgrade without prompting\n  $ dr upgrade --force      # Force all upgrades, ignoring version checks`\n  )\n  .action(async (options) => {\n    await upgradeCommand({\n      yes: options.yes,\n      dryRun: options.dryRun,\n      force: options.force,\n    });\n  });\n\nprogram\n  .command(\"conformance\")\n  .description(\"Check model conformance to layer specifications\")\n  .option(\"--layers <layers...>\", \"Specific layers to check\")\n  .option(\"--json\", \"Output as JSON\")\n  .option(\"--verbose\", \"Verbose output\")\n  .addHelpText(\n    \"after\",\n    `\nExamples:\n  $ dr conformance\n  $ dr conformance --layers business api application\n  $ dr conformance --json\n  $ dr conformance --verbose`\n  )\n  .action(async (options) => {\n    await conformanceCommand({\n      layers: options.layers,\n      json: options.json,\n      verbose: options.verbose ?? program.opts().verbose,\n    });\n  });\n\n// Changeset subcommands\nchangesetCommands(program);\n\n// Claude Code integration subcommands\nclaudeCommands(program);\n\n// GitHub Copilot integration subcommands\ncopilotCommands(program);\n\n// Analyzer integration subcommands\nanalyzerCommands(program);\n\n// Execute CLI with proper telemetry span wrapping\n// This creates a root span that all child spans will be linked to\n(async () => {\n  let exitCode = 0;\n  try {\n    if (isTelemetryEnabled) {\n      // Initialize telemetry before execution\n      await initTelemetry();\n\n      // Only install console interceptor for commands that need it\n      const commandName = process.argv[2] || \"unknown\";\n      if (CONSOLE_LOGGING_COMMANDS.has(commandName)) {\n        await installConsoleInterceptor();\n      }\n\n      const args = process.argv.slice(3).join(\" \");\n\n      // Wrap entire CLI execution in active span for proper context propagation\n      await startActiveSpan(\n        \"cli.execute\",\n        async (span) => {\n          // Attributes already set via options parameter - no duplicate setAttributes needed\n          try {\n            // Execute command - all child spans will now link to this root span\n            await program.parseAsync(process.argv);\n\n            // Set success status\n            span.setStatus({ code: 0 }); // SpanStatusCode.OK\n          } catch (error) {\n            // Record exception and set error status\n            // CommanderError with exitCode 0 is help text / unknown subcommand shown \u2014 not a real error\n            if (error instanceof CommanderError) {\n              if (error.exitCode === 0) {\n                span.setStatus({ code: 0 }); // SpanStatusCode.OK\n              } else {\n                span.recordException(error as Error);\n                span.setStatus({\n                  code: 2, // SpanStatusCode.ERROR\n                  message: error.message,\n                });\n              }\n            } else {\n              span.recordException(error as Error);\n              span.setStatus({\n                code: 2, // SpanStatusCode.ERROR\n                message: getErrorMessage(error),\n              });\n            }\n\n            // Print error message for CLIError instances\n            // Skip CommanderError \u2014 Commander already printed its own output (e.g. help text, unknown command)\n            const { CLIError } = await import(\"./utils/errors.js\");\n            if (error instanceof CommanderError) {\n              // Commander handled its own output; nothing to print\n            } else if (error instanceof CLIError) {\n              console.error(error.format());\n            } else if (error instanceof Error) {\n              console.error(error.message);\n            } else {\n              console.error(String(error));\n            }\n\n            // Extract exit code from CLIError if available\n            exitCode = await extractExitCode(error);\n            // Don't throw - let telemetry shutdown complete\n          }\n        },\n        {\n          \"cli.command\": commandName,\n          \"cli.args\": args,\n          \"cli.cwd\": process.cwd(),\n          \"cli.version\": cliVersion,\n        }\n      );\n\n      // Shutdown telemetry after execution completes\n      await shutdownTelemetry();\n\n      // Exit with exit code (keepAlive disabled in exporters prevents hanging)\n      process.exit(exitCode);\n    } else {\n      // No telemetry - just parse normally with error handling\n      try {\n        await program.parseAsync(process.argv);\n      } catch (error) {\n        // Extract exit code from CLIError if available\n        // Skip CommanderError \u2014 Commander already printed its own output (e.g. help text, unknown command)\n        const { CLIError } = await import(\"./utils/errors.js\");\n        if (error instanceof CommanderError) {\n          // Commander handled its own output; nothing to print\n        } else if (error instanceof CLIError) {\n          console.error(error.format());\n        } else {\n          // Unexpected exceptions need to be printed\n          if (error instanceof Error) {\n            console.error(error.message);\n          } else {\n            console.error(String(error));\n          }\n        }\n        const exitCodeFromError = await extractExitCode(error);\n        process.exit(exitCodeFromError);\n      }\n    }\n  } catch (error) {\n    // Error during telemetry init or shutdown\n    if (!isTelemetryEnabled) {\n      // No telemetry - exit immediately with error\n      process.exit(1);\n    }\n    // Telemetry enabled - try to shutdown before exit\n    await shutdownTelemetry();\n    process.exit(1);\n  }\n})();\n"],
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   "names": []
 }

package/dist/commands/repair.js

@@ -0,0 +1,62 @@
+import ansis from "ansis";
+import { Model } from "../core/model.js";
+import { StagedChangesetStorage } from "../core/staged-changeset-storage.js";
+import { scanForAttributeCollisionDamage, attemptRecovery, applyRecovery } from "../core/attribute-collision-repair.js";
+import { ModelNotFoundError, getErrorMessage, handleError } from "../utils/errors.js";
+import { writeFile } from "../utils/file-io.js";
+function printCandidate(c, applied) {
+  let note;
+  c.recovered ? note = applied ? ansis.green(`restored from changeset "${c.recovered.changesetName}"`) : ansis.green(`recoverable from changeset "${c.recovered.changesetName}"`) : note = ansis.dim("no recoverable value found \u2014 must be re-supplied manually"), console.log(`  ${ansis.bold(c.elementRef)} ${ansis.dim(`(${c.specNodeId}.${c.attribute})`)} \u2014 ${note}`);
+}
+async function repairAttributeCollisionCommand(options = {}) {
+  try {
+    let model;
+    try {
+      model = await Model.load();
+    } catch (error) {
+      const message = getErrorMessage(error);
+      throw message.includes("No DR project") || message.includes("Model not found") ? new ModelNotFoundError() : error;
+    }
+    const candidates = scanForAttributeCollisionDamage(model), storage = new StagedChangesetStorage(model.rootPath);
+    await attemptRecovery(candidates, storage);
+    let repaired = [];
+    if (options.apply && candidates.some((c) => c.recovered)) {
+      repaired = applyRecovery(model, candidates);
+      const affectedLayers = new Set(repaired.map((c) => c.layerName));
+      for (const layerName of affectedLayers)
+        await model.saveLayer(layerName);
+    }
+    if ((options.format ?? "text") === "json") {
+      const report = {
+        totalAffected: candidates.length,
+        requiredMissing: candidates.filter((c) => c.required).length,
+        optionalMissing: candidates.filter((c) => !c.required).length,
+        recoverable: candidates.filter((c) => c.recovered).length,
+        repaired: repaired.length,
+        applied: !!options.apply,
+        candidates
+      }, json = JSON.stringify(report, null, 2);
+      options.output ? (await writeFile(options.output, json), console.log(ansis.green(`\u2713 Report written to ${options.output}`))) : console.log(json);
+      return;
+    }
+    if (candidates.length === 0) {
+      console.log(ansis.green(`
+\u2713 No attribute-collision damage found \u2014 model is clean.
+`));
+      return;
+    }
+    console.log(ansis.bold(`
+Found ${candidates.length} element${candidates.length === 1 ? "" : "s"} missing a schema-declared attribute the fixed persistence bug could have stripped:
+`));
+    const required = candidates.filter((c) => c.required), optional = candidates.filter((c) => !c.required);
+    required.length > 0 && (console.log(ansis.red(ansis.bold(`REQUIRED \u2014 fails validation today (${required.length}):`))), required.forEach((c) => printCandidate(c, !!options.apply)), console.log()), optional.length > 0 && (console.log(ansis.yellow(ansis.bold(`Optional \u2014 silent, unconfirmed whether ever set (${optional.length}):`))), optional.forEach((c) => printCandidate(c, !!options.apply)), console.log());
+    const recoverableCount = candidates.filter((c) => c.recovered).length, unrecoverableCount = candidates.length - recoverableCount;
+    options.apply ? (console.log(ansis.green(`\u2713 Restored ${repaired.length} of ${recoverableCount} recoverable value(s) from changeset history.`)), unrecoverableCount > 0 && console.log(ansis.yellow(`\u26A0 ${unrecoverableCount} element(s) have no recoverable value \u2014 re-supply manually with "dr update <id> --attributes '{...}'".`))) : (console.log(ansis.dim(`${recoverableCount} of ${candidates.length} have a recoverable value in changeset history. Run with --apply to restore them.`)), unrecoverableCount > 0 && console.log(ansis.dim(`${unrecoverableCount} have no recoverable value and will need to be manually re-supplied even after --apply.`))), console.log();
+  } catch (error) {
+    handleError(error);
+  }
+}
+export {
+  repairAttributeCollisionCommand
+};
+//# sourceMappingURL=repair.js.map

package/dist/commands/repair.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../src/commands/repair.ts"],
+  "sourcesContent": ["/**\n * Repair command \u2014 detect and best-effort-recover model data lost to a fixed bug in\n * Model.saveLayer() that silently stripped the \"source\"/\"x-source-reference\" attributes from\n * every element on save, even when a node type's own schema declared one as a real (sometimes\n * required) domain attribute. See core/attribute-collision-repair.ts for the full mechanism.\n *\n * This is a detect-and-report tool first, repair second: elements with no recoverable value in\n * changeset history are always reported, never fabricated.\n */\n\nimport ansis from \"ansis\";\nimport { Model } from \"../core/model.js\";\nimport { StagedChangesetStorage } from \"../core/staged-changeset-storage.js\";\nimport {\n  scanForAttributeCollisionDamage,\n  attemptRecovery,\n  applyRecovery,\n  type CollisionCandidate,\n} from \"../core/attribute-collision-repair.js\";\nimport { ModelNotFoundError, getErrorMessage, handleError } from \"../utils/errors.js\";\nimport { writeFile } from \"../utils/file-io.js\";\n\nexport interface RepairAttributeCollisionOptions {\n  apply?: boolean;\n  format?: \"text\" | \"json\";\n  output?: string;\n  verbose?: boolean;\n}\n\nfunction printCandidate(c: CollisionCandidate, applied: boolean): void {\n  let note: string;\n  if (c.recovered) {\n    note = applied\n      ? ansis.green(`restored from changeset \"${c.recovered.changesetName}\"`)\n      : ansis.green(`recoverable from changeset \"${c.recovered.changesetName}\"`);\n  } else {\n    note = ansis.dim(\"no recoverable value found \u2014 must be re-supplied manually\");\n  }\n  console.log(`  ${ansis.bold(c.elementRef)} ${ansis.dim(`(${c.specNodeId}.${c.attribute})`)} \u2014 ${note}`);\n}\n\nexport async function repairAttributeCollisionCommand(\n  options: RepairAttributeCollisionOptions = {}\n): Promise<void> {\n  try {\n    let model: Model;\n    try {\n      model = await Model.load();\n    } catch (error) {\n      const message = getErrorMessage(error);\n      if (message.includes(\"No DR project\") || message.includes(\"Model not found\")) {\n        throw new ModelNotFoundError();\n      }\n      throw error;\n    }\n\n    const candidates = scanForAttributeCollisionDamage(model);\n    const storage = new StagedChangesetStorage(model.rootPath);\n    await attemptRecovery(candidates, storage);\n\n    let repaired: CollisionCandidate[] = [];\n    if (options.apply && candidates.some((c) => c.recovered)) {\n      repaired = applyRecovery(model, candidates);\n      const affectedLayers = new Set(repaired.map((c) => c.layerName));\n      for (const layerName of affectedLayers) {\n        await model.saveLayer(layerName);\n      }\n    }\n\n    const format = options.format ?? \"text\";\n\n    if (format === \"json\") {\n      const report = {\n        totalAffected: candidates.length,\n        requiredMissing: candidates.filter((c) => c.required).length,\n        optionalMissing: candidates.filter((c) => !c.required).length,\n        recoverable: candidates.filter((c) => c.recovered).length,\n        repaired: repaired.length,\n        applied: !!options.apply,\n        candidates,\n      };\n      const json = JSON.stringify(report, null, 2);\n      if (options.output) {\n        await writeFile(options.output, json);\n        console.log(ansis.green(`\u2713 Report written to ${options.output}`));\n      } else {\n        console.log(json);\n      }\n      return;\n    }\n\n    if (candidates.length === 0) {\n      console.log(ansis.green(\"\\n\u2713 No attribute-collision damage found \u2014 model is clean.\\n\"));\n      return;\n    }\n\n    console.log(\n      ansis.bold(\n        `\\nFound ${candidates.length} element${candidates.length === 1 ? \"\" : \"s\"} missing a ` +\n          `schema-declared attribute the fixed persistence bug could have stripped:\\n`\n      )\n    );\n\n    const required = candidates.filter((c) => c.required);\n    const optional = candidates.filter((c) => !c.required);\n\n    if (required.length > 0) {\n      console.log(ansis.red(ansis.bold(`REQUIRED \u2014 fails validation today (${required.length}):`)));\n      required.forEach((c) => printCandidate(c, !!options.apply));\n      console.log();\n    }\n\n    if (optional.length > 0) {\n      console.log(\n        ansis.yellow(ansis.bold(`Optional \u2014 silent, unconfirmed whether ever set (${optional.length}):`))\n      );\n      optional.forEach((c) => printCandidate(c, !!options.apply));\n      console.log();\n    }\n\n    const recoverableCount = candidates.filter((c) => c.recovered).length;\n    const unrecoverableCount = candidates.length - recoverableCount;\n\n    if (options.apply) {\n      console.log(\n        ansis.green(\n          `\u2713 Restored ${repaired.length} of ${recoverableCount} recoverable value(s) from changeset history.`\n        )\n      );\n      if (unrecoverableCount > 0) {\n        console.log(\n          ansis.yellow(\n            `\u26A0 ${unrecoverableCount} element(s) have no recoverable value \u2014 re-supply manually ` +\n              `with \"dr update <id> --attributes '{...}'\".`\n          )\n        );\n      }\n    } else {\n      console.log(\n        ansis.dim(\n          `${recoverableCount} of ${candidates.length} have a recoverable value in changeset history. ` +\n            `Run with --apply to restore them.`\n        )\n      );\n      if (unrecoverableCount > 0) {\n        console.log(\n          ansis.dim(\n            `${unrecoverableCount} have no recoverable value and will need to be manually re-supplied ` +\n              `even after --apply.`\n          )\n        );\n      }\n    }\n    console.log();\n  } catch (error) {\n    handleError(error);\n  }\n}\n"],
+  "mappings": "AAUA,OAAO,WAAW;AAClB,SAAS,aAAa;AACtB,SAAS,8BAA8B;AACvC,SACE,iCACA,iBACA,qBAEK;AACP,SAAS,oBAAoB,iBAAiB,mBAAmB;AACjE,SAAS,iBAAiB;AAS1B,SAAS,eAAe,GAAuB,SAAgB;AAC7D,MAAI;AACJ,EAAI,EAAE,YACJ,OAAO,UACH,MAAM,MAAM,4BAA4B,EAAE,UAAU,aAAa,GAAG,IACpE,MAAM,MAAM,+BAA+B,EAAE,UAAU,aAAa,GAAG,IAE3E,OAAO,MAAM,IAAI,gEAA2D,GAE9E,QAAQ,IAAI,KAAK,MAAM,KAAK,EAAE,UAAU,CAAC,IAAI,MAAM,IAAI,IAAI,EAAE,UAAU,IAAI,EAAE,SAAS,GAAG,CAAC,WAAM,IAAI,EAAE;AACxG;AAEA,eAAsB,gCACpB,UAA2C,CAAA,GAAE;AAE7C,MAAI;AACF,QAAI;AACJ,QAAI;AACF,cAAQ,MAAM,MAAM,KAAI;IAC1B,SAAS,OAAO;AACd,YAAM,UAAU,gBAAgB,KAAK;AACrC,YAAI,QAAQ,SAAS,eAAe,KAAK,QAAQ,SAAS,iBAAiB,IACnE,IAAI,mBAAkB,IAExB;IACR;AAEA,UAAM,aAAa,gCAAgC,KAAK,GAClD,UAAU,IAAI,uBAAuB,MAAM,QAAQ;AACzD,UAAM,gBAAgB,YAAY,OAAO;AAEzC,QAAI,WAAiC,CAAA;AACrC,QAAI,QAAQ,SAAS,WAAW,KAAK,CAAC,MAAM,EAAE,SAAS,GAAG;AACxD,iBAAW,cAAc,OAAO,UAAU;AAC1C,YAAM,iBAAiB,IAAI,IAAI,SAAS,IAAI,CAAC,MAAM,EAAE,SAAS,CAAC;AAC/D,iBAAW,aAAa;AACtB,cAAM,MAAM,UAAU,SAAS;IAEnC;AAIA,SAFe,QAAQ,UAAU,YAElB,QAAQ;AACrB,YAAM,SAAS;QACb,eAAe,WAAW;QAC1B,iBAAiB,WAAW,OAAO,CAAC,MAAM,EAAE,QAAQ,EAAE;QACtD,iBAAiB,WAAW,OAAO,CAAC,MAAM,CAAC,EAAE,QAAQ,EAAE;QACvD,aAAa,WAAW,OAAO,CAAC,MAAM,EAAE,SAAS,EAAE;QACnD,UAAU,SAAS;QACnB,SAAS,CAAC,CAAC,QAAQ;QACnB;SAEI,OAAO,KAAK,UAAU,QAAQ,MAAM,CAAC;AAC3C,MAAI,QAAQ,UACV,MAAM,UAAU,QAAQ,QAAQ,IAAI,GACpC,QAAQ,IAAI,MAAM,MAAM,4BAAuB,QAAQ,MAAM,EAAE,CAAC,KAEhE,QAAQ,IAAI,IAAI;AAElB;IACF;AAEA,QAAI,WAAW,WAAW,GAAG;AAC3B,cAAQ,IAAI,MAAM,MAAM;;CAA6D,CAAC;AACtF;IACF;AAEA,YAAQ,IACN,MAAM,KACJ;QAAW,WAAW,MAAM,WAAW,WAAW,WAAW,IAAI,KAAK,GAAG;CACK,CAC/E;AAGH,UAAM,WAAW,WAAW,OAAO,CAAC,MAAM,EAAE,QAAQ,GAC9C,WAAW,WAAW,OAAO,CAAC,MAAM,CAAC,EAAE,QAAQ;AAErD,IAAI,SAAS,SAAS,MACpB,QAAQ,IAAI,MAAM,IAAI,MAAM,KAAK,2CAAsC,SAAS,MAAM,IAAI,CAAC,CAAC,GAC5F,SAAS,QAAQ,CAAC,MAAM,eAAe,GAAG,CAAC,CAAC,QAAQ,KAAK,CAAC,GAC1D,QAAQ,IAAG,IAGT,SAAS,SAAS,MACpB,QAAQ,IACN,MAAM,OAAO,MAAM,KAAK,yDAAoD,SAAS,MAAM,IAAI,CAAC,CAAC,GAEnG,SAAS,QAAQ,CAAC,MAAM,eAAe,GAAG,CAAC,CAAC,QAAQ,KAAK,CAAC,GAC1D,QAAQ,IAAG;AAGb,UAAM,mBAAmB,WAAW,OAAO,CAAC,MAAM,EAAE,SAAS,EAAE,QACzD,qBAAqB,WAAW,SAAS;AAE/C,IAAI,QAAQ,SACV,QAAQ,IACN,MAAM,MACJ,mBAAc,SAAS,MAAM,OAAO,gBAAgB,+CAA+C,CACpG,GAEC,qBAAqB,KACvB,QAAQ,IACN,MAAM,OACJ,UAAK,kBAAkB,6GACwB,CAChD,MAIL,QAAQ,IACN,MAAM,IACJ,GAAG,gBAAgB,OAAO,WAAW,MAAM,mFACN,CACtC,GAEC,qBAAqB,KACvB,QAAQ,IACN,MAAM,IACJ,GAAG,kBAAkB,yFACE,CACxB,IAIP,QAAQ,IAAG;EACb,SAAS,OAAO;AACd,gBAAY,KAAK;EACnB;AACF;",
+  "names": []
+}

package/dist/commands/version.js

@@ -2,7 +2,7 @@ import ansis from "ansis";
 import { getCliBundledSpecVersion } from "../utils/spec-version.js";
 import { isTelemetryBuiltIn, isTelemetryConfigured } from "../telemetry/detect.js";
 import { getSpecReferencePath, getModelPath } from "../utils/project-paths.js";
-const gitHash = "ee281fb", cliVersion = "0.1.10";
+const gitHash = "e821d8d", cliVersion = "0.1.11";
 async function versionCommand() {
   const specVersion = getCliBundledSpecVersion(), telemetryBuiltIn = isTelemetryBuiltIn(), telemetryConfigured = await isTelemetryConfigured();
   let telemetryStatus;

package/dist/core/attribute-collision-repair.js

@@ -0,0 +1,73 @@
+import { getNodeType } from "../generated/node-types.js";
+const HISTORICALLY_COLLIDING_ATTRIBUTE_NAMES = ["source", "x-source-reference"];
+function scanForAttributeCollisionDamage(model) {
+  const candidates = [];
+  for (const layerName of model.getLayerNames()) {
+    const layer = model.layers.get(layerName);
+    if (layer)
+      for (const element of layer.elements.values()) {
+        if (!element.spec_node_id)
+          continue;
+        const nodeType = getNodeType(element.spec_node_id);
+        if (nodeType)
+          for (const attribute of HISTORICALLY_COLLIDING_ATTRIBUTE_NAMES) {
+            const required = nodeType.requiredAttributes.includes(attribute), optional = nodeType.optionalAttributes.includes(attribute);
+            !required && !optional || element.attributes != null && Object.prototype.hasOwnProperty.call(element.attributes, attribute) && element.attributes[attribute] !== void 0 || candidates.push({
+              elementRef: element.path || element.id,
+              elementId: element.id,
+              layerName,
+              specNodeId: element.spec_node_id,
+              attribute,
+              required
+            });
+          }
+      }
+  }
+  return candidates;
+}
+async function attemptRecovery(candidates, storage) {
+  if (candidates.length === 0)
+    return candidates;
+  const changesets = await storage.list();
+  changesets.sort((a, b) => (b.modified || "").localeCompare(a.modified || ""));
+  for (const candidate of candidates)
+    for (const changeset of changesets) {
+      const match = [...changeset.changes].sort((a, b) => (b.timestamp || "").localeCompare(a.timestamp || "")).find((change) => {
+        if (change.type !== "add" && change.type !== "update" || change.elementId !== candidate.elementRef && change.elementId !== candidate.elementId)
+          return !1;
+        const afterAttrs = change.after?.attributes;
+        return afterAttrs != null && afterAttrs[candidate.attribute] !== void 0;
+      });
+      if (match) {
+        const afterAttrs = match.after.attributes;
+        candidate.recovered = {
+          value: afterAttrs[candidate.attribute],
+          changesetId: changeset.id,
+          changesetName: changeset.name,
+          changeTimestamp: match.timestamp
+        };
+        break;
+      }
+    }
+  return candidates;
+}
+function applyRecovery(model, candidates) {
+  const repaired = [];
+  for (const candidate of candidates) {
+    if (!candidate.recovered)
+      continue;
+    const layer = model.layers.get(candidate.layerName);
+    if (!layer)
+      continue;
+    const element = layer.getElement(candidate.elementRef) ?? layer.getElement(candidate.elementId);
+    element && (element.attributes = { ...element.attributes, [candidate.attribute]: candidate.recovered.value }, layer.updateElement(element), repaired.push(candidate));
+  }
+  return repaired;
+}
+export {
+  HISTORICALLY_COLLIDING_ATTRIBUTE_NAMES,
+  applyRecovery,
+  attemptRecovery,
+  scanForAttributeCollisionDamage
+};
+//# sourceMappingURL=attribute-collision-repair.js.map

package/dist/core/attribute-collision-repair.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../src/core/attribute-collision-repair.ts"],
+  "sourcesContent": ["/**\n * Attribute-collision repair \u2014 finds and best-effort-recovers data lost to a fixed bug in\n * Model.saveLayer(): a hardcoded, type-blind \"internal fields\" blocklist unconditionally\n * stripped any attribute literally named \"source\" or \"x-source-reference\" from EVERY element's\n * attributes before writing YAML, regardless of whether the element's own schema declared it as\n * a real domain attribute. 41 of 191 node schemas across 8 layers do (3 mark it required).\n *\n * Once an element was saved under the buggy code, the value is gone from the base model YAML \u2014\n * this module can't un-delete data that was never persisted. What it CAN do:\n *\n * 1. Detect every element that's missing a schema-declared \"source\"/\"x-source-reference\"\n *    attribute \u2014 the fingerprint of damage from this bug (as opposed to the attribute simply\n *    never having been set, which looks identical for the base model alone).\n * 2. Attempt recovery from changeset history: StagedChangesetStorage writes changes.yaml\n *    directly (`yaml.stringify(changeset.changes)`), with NO pass through saveLayer()'s\n *    stripping \u2014 so an add/update recorded while this bug was active can still hold the\n *    original, un-stripped value, for as long as that changeset file hasn't been deleted\n *    (committing a changeset does NOT delete it \u2014 see StagingAreaManager.commit()).\n *\n * Elements with no recoverable value are reported, never fabricated \u2014 this is a best-effort\n * repair, not a guarantee, and the report is only advisory for optional attributes (there's no\n * way to distinguish \"this bug stripped it\" from \"this was never set\" from the base model alone).\n */\n\nimport { Model } from \"./model.js\";\nimport { StagedChangesetStorage } from \"./staged-changeset-storage.js\";\nimport type { Change } from \"./changeset.js\";\nimport { getNodeType } from \"../generated/node-types.js\";\nimport type { SpecNodeId } from \"../generated/node-types.js\";\n\n/** The exact two attribute names the pre-fix INTERNAL_FIELDS blocklist unconditionally\n *  stripped, despite being legitimate schema-declared attributes on some node types. Kept as an\n *  explicit historical constant, not derived from current code \u2014 the whole point of this module\n *  is to find damage from a bug that no longer exists in model.ts, so it can't reconstruct this\n *  list by reading the (now-fixed) stripping logic. `__references__`/`__relationships__` are\n *  NOT included: those were, and remain, genuinely internal on every node type (zero schema\n *  collisions), so their absence is never damage from this bug. */\nexport const HISTORICALLY_COLLIDING_ATTRIBUTE_NAMES = [\"source\", \"x-source-reference\"] as const;\n\nexport interface CollisionCandidate {\n  /** Element path (preferred, human-readable) or id if no path is set. */\n  elementRef: string;\n  elementId: string;\n  layerName: string;\n  specNodeId: string;\n  attribute: (typeof HISTORICALLY_COLLIDING_ATTRIBUTE_NAMES)[number];\n  /** Whether the schema marks this attribute required \u2014 a required+missing attribute means the\n   *  element currently FAILS validation, not just a silent gap. */\n  required: boolean;\n  recovered?: {\n    value: unknown;\n    changesetId: string;\n    changesetName: string;\n    changeTimestamp?: string;\n  };\n}\n\n/**\n * Scan every element in the model for one of the two historically-colliding attribute names\n * being declared by its schema but absent from its current, persisted attributes.\n */\nexport function scanForAttributeCollisionDamage(model: Model): CollisionCandidate[] {\n  const candidates: CollisionCandidate[] = [];\n\n  for (const layerName of model.getLayerNames()) {\n    const layer = model.layers.get(layerName);\n    if (!layer) continue;\n\n    for (const element of layer.elements.values()) {\n      if (!element.spec_node_id) continue;\n      const nodeType = getNodeType(element.spec_node_id as SpecNodeId);\n      if (!nodeType) continue;\n\n      for (const attribute of HISTORICALLY_COLLIDING_ATTRIBUTE_NAMES) {\n        const required = nodeType.requiredAttributes.includes(attribute);\n        const optional = nodeType.optionalAttributes.includes(attribute);\n        if (!required && !optional) continue; // Not declared by this type \u2014 nothing to check.\n\n        const hasValue =\n          element.attributes != null &&\n          Object.prototype.hasOwnProperty.call(element.attributes, attribute) &&\n          element.attributes[attribute] !== undefined;\n        if (hasValue) continue; // Present \u2014 unaffected.\n\n        candidates.push({\n          elementRef: element.path || element.id,\n          elementId: element.id,\n          layerName,\n          specNodeId: element.spec_node_id,\n          attribute,\n          required,\n        });\n      }\n    }\n  }\n\n  return candidates;\n}\n\n/**\n * Attempt to recover each candidate's original value from changeset history. Mutates and\n * returns the same array with `.recovered` filled in where a value was found \u2014 searches every\n * changeset (active, committed, or discarded; committing does not delete the changeset file),\n * newest-first, for the most recent add/update change touching this element that carried a\n * non-empty value for the missing attribute.\n */\nexport async function attemptRecovery(\n  candidates: CollisionCandidate[],\n  storage: StagedChangesetStorage\n): Promise<CollisionCandidate[]> {\n  if (candidates.length === 0) return candidates;\n\n  const changesets = await storage.list();\n  // Newest-first by last-modified, so the first match found is the most recent one.\n  changesets.sort((a, b) => (b.modified || \"\").localeCompare(a.modified || \"\"));\n\n  for (const candidate of candidates) {\n    for (const changeset of changesets) {\n      const changes = [...changeset.changes].sort(\n        (a, b) => (b.timestamp || \"\").localeCompare(a.timestamp || \"\")\n      );\n\n      const match = changes.find((change: Change) => {\n        if (change.type !== \"add\" && change.type !== \"update\") return false;\n        if (change.elementId !== candidate.elementRef && change.elementId !== candidate.elementId) {\n          return false;\n        }\n        const afterAttrs = (change.after as { attributes?: Record<string, unknown> } | undefined)\n          ?.attributes;\n        return afterAttrs != null && afterAttrs[candidate.attribute] !== undefined;\n      });\n\n      if (match) {\n        const afterAttrs = (match.after as { attributes: Record<string, unknown> }).attributes;\n        candidate.recovered = {\n          value: afterAttrs[candidate.attribute],\n          changesetId: changeset.id,\n          changesetName: changeset.name,\n          changeTimestamp: match.timestamp,\n        };\n        break;\n      }\n    }\n  }\n\n  return candidates;\n}\n\n/**\n * Apply recovered values back onto the live model (in memory \u2014 caller is responsible for\n * saving the affected layers). Returns the list of candidates actually repaired.\n */\nexport function applyRecovery(model: Model, candidates: CollisionCandidate[]): CollisionCandidate[] {\n  const repaired: CollisionCandidate[] = [];\n\n  for (const candidate of candidates) {\n    if (!candidate.recovered) continue;\n    const layer = model.layers.get(candidate.layerName);\n    if (!layer) continue;\n    const element = layer.getElement(candidate.elementRef) ?? layer.getElement(candidate.elementId);\n    if (!element) continue;\n\n    element.attributes = { ...element.attributes, [candidate.attribute]: candidate.recovered.value };\n    layer.updateElement(element);\n    repaired.push(candidate);\n  }\n\n  return repaired;\n}\n"],
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+  "names": []
+}

package/dist/core/model.js

@@ -37,6 +37,15 @@ function typeToSnakeStem(specNodeId, type) {
   }
   return type;
 }
+const ALWAYS_INTERNAL_ATTRIBUTE_KEYS = /* @__PURE__ */ new Set(["__references__", "__relationships__"]);
+function isPersistableAttribute(specNodeId, key) {
+  if (!ALWAYS_INTERNAL_ATTRIBUTE_KEYS.has(key))
+    return !0;
+  if (!specNodeId)
+    return !1;
+  const nodeType = getNodeType(specNodeId);
+  return nodeType ? nodeType.requiredAttributes.includes(key) || nodeType.optionalAttributes.includes(key) : !1;
+}
 const isTelemetryEnabled = !1;
 class Model {
   rootPath;
@@ -242,16 +251,10 @@ class Model {
       }
       elementsByType.get(typeKey).elements.push(element);
     }
-    const INTERNAL_FIELDS = /* @__PURE__ */ new Set([
-      "__references__",
-      "__relationships__",
-      "source",
-      "x-source-reference"
-    ]);
     for (const [, { stem, elements }] of elementsByType) {
       const filename = `${stem}.yaml`, filePath = `${layerPath}/${filename}`, yamlData = {};
       for (const element of elements) {
-        const json = element.toJSON(), cleanAttrs = json.attributes ? Object.fromEntries(Object.entries(json.attributes).filter(([k]) => !INTERNAL_FIELDS.has(k))) : void 0, key = element.path || element.id;
+        const json = element.toJSON(), cleanAttrs = json.attributes ? Object.fromEntries(Object.entries(json.attributes).filter(([k]) => isPersistableAttribute(json.spec_node_id, k))) : void 0, key = element.path || element.id;
         yamlData[key] = {
           id: json.id,
           path: json.path,

package/dist/core/model.js.map

@@ -1,7 +1,7 @@
 {
   "version": 3,
   "sources": ["../../src/core/model.ts"],
-  "sourcesContent": ["import { Layer } from \"./layer.js\";\nimport { Manifest } from \"./manifest.js\";\nimport { Element } from \"./element.js\";\nimport { GraphModel, type GraphEdge } from \"./graph-model.js\";\nimport { VirtualProjectionEngine } from \"./virtual-projection.js\";\nimport { StagedChangesetStorage } from \"./staged-changeset-storage.js\";\nimport { Relationships } from \"./relationships.js\";\nimport { CANONICAL_LAYER_NAMES } from \"./layers.js\";\nimport type { StagedChange } from \"./changeset.js\";\nimport { ensureDir, writeFile } from \"../utils/file-io.js\";\nimport { getCliVersion } from \"../utils/spec-version.js\";\nimport { startSpan, endSpan, startActiveSpan } from \"../telemetry/index.js\";\nimport { findProjectRoot } from \"../utils/project-paths.js\";\nimport { getNodeType } from \"../generated/node-types.js\";\nimport type { SpecNodeId } from \"../generated/node-types.js\";\nimport type { ManifestData, ModelOptions } from \"../types/index.js\";\nimport path from \"node:path\";\nimport fs from \"node:fs/promises\";\nimport crypto from \"node:crypto\";\n\n/**\n * Derive a deterministic UUID from a path string using SHA-256.\n * Produces a stable UUID4-like value so migration doesn't regenerate UUIDs on every load.\n */\nfunction deterministicUUID(path: string): string {\n  const hash = crypto.createHash(\"sha256\").update(path).digest(\"hex\");\n  return [\n    hash.slice(0, 8),\n    hash.slice(8, 12),\n    \"4\" + hash.slice(13, 16), // version 4 marker\n    ((parseInt(hash.slice(16, 18), 16) & 0x3f) | 0x80).toString(16) + hash.slice(18, 20), // variant\n    hash.slice(20, 32),\n  ].join(\"-\");\n}\n\n/**\n * Convert a PascalCase title to snake_case.\n * Handles acronyms correctly: \"UXApplication\" \u2192 \"ux_application\", \"OpenAPIDocument\" \u2192 \"open_api_document\".\n */\nfunction titleToSnakeCase(title: string): string {\n  return title\n    .replace(/([A-Z]+)([A-Z][a-z])/g, \"$1_$2\") // \"APIDoc\" \u2192 \"API_Doc\"\n    .replace(/([a-z\\d])([A-Z])/g, \"$1_$2\")       // \"appComponent\" \u2192 \"app_Component\"\n    .toLowerCase();\n}\n\n/**\n * Derive a snake_case file stem for a given element type.\n * Uses the spec node title for accurate word boundaries (e.g., \"InputSpacePartition\" \u2192 \"input_space_partition\").\n * Falls back to the raw type string when the title is unavailable.\n */\nfunction typeToSnakeStem(specNodeId: string | undefined, type: string): string {\n  if (specNodeId) {\n    const nodeType = getNodeType(specNodeId as SpecNodeId);\n    if (nodeType?.title) {\n      return titleToSnakeCase(nodeType.title);\n    }\n  }\n  return type;\n}\n\n// Fallback for runtime environments where TELEMETRY_ENABLED is not defined by esbuild\ndeclare const TELEMETRY_ENABLED: boolean | undefined;\nconst isTelemetryEnabled = typeof TELEMETRY_ENABLED !== \"undefined\" ? TELEMETRY_ENABLED : false;\n\n/**\n * Model class representing the complete architecture model\n * Uses GraphModel internally for graph-based storage\n */\nexport class Model {\n  rootPath: string;\n  manifest: Manifest;\n  graph: GraphModel;\n  layers: Map<string, Layer>;\n  relationships: Relationships;\n  lazyLoad: boolean;\n  private loadedLayers: Set<string>;\n  private virtualProjectionEngine?: VirtualProjectionEngine;\n  /** ID of the currently active changeset, or null if none is active. Set during load(). */\n  private _activeChangesetId: string | null = null;\n  /** Layer names that exist only in staged changes (not yet committed to base model). */\n  private _stagedLayerNames: Set<string> = new Set();\n\n  constructor(rootPath: string, manifest: Manifest, options: ModelOptions = {}) {\n    this.rootPath = rootPath;\n    this.manifest = manifest;\n    this.graph = new GraphModel();\n    this.layers = new Map();\n    this.relationships = new Relationships();\n    this.lazyLoad = options.lazyLoad ?? false;\n    this.loadedLayers = new Set();\n  }\n\n  /**\n   * Get the committed base layer (no staging projection).\n   * Used internally by VirtualProjectionEngine and commit() to access the raw base model\n   * without triggering infinite recursion or double-projection.\n   */\n  async getBaseLayer(name: string): Promise<Layer | undefined> {\n    if (this.lazyLoad && !this.loadedLayers.has(name)) {\n      await this.loadLayer(name);\n    }\n    return this.layers.get(name);\n  }\n\n  /**\n   * Get a layer, transparently merging staged changes when an active changeset exists.\n   * Falls back to the committed base layer if no changeset is active or projection fails.\n   */\n  async getLayer(name: string): Promise<Layer | undefined> {\n    if (this.lazyLoad && !this.loadedLayers.has(name)) {\n      await this.loadLayer(name);\n    }\n\n    // If an active changeset is present, return a projected (base + staged) layer\n    if (this._activeChangesetId) {\n      try {\n        return await this.getVirtualProjectionEngine().projectLayer(\n          this,\n          this._activeChangesetId,\n          name\n        );\n      } catch {\n        // Fall back to base layer on projection failure (e.g. corrupt changeset)\n        return this.layers.get(name);\n      }\n    }\n\n    return this.layers.get(name);\n  }\n\n  /**\n   * Get an element by ID across all layers\n   * Supports both UUID and semantic ID (layer.type.kebab-name) lookup\n   */\n  getElementById(id: string): Element | undefined {\n    for (const layer of this.layers.values()) {\n      const element = layer.getElement(id);\n      if (element) {\n        return element;\n      }\n    }\n    return undefined;\n  }\n\n  /**\n   * Get virtual projection engine (lazily initialized)\n   */\n  getVirtualProjectionEngine(): VirtualProjectionEngine {\n    if (!this.virtualProjectionEngine) {\n      this.virtualProjectionEngine = new VirtualProjectionEngine(this.rootPath);\n    }\n    return this.virtualProjectionEngine;\n  }\n\n  /**\n   * Returns the active changeset ID, or null if no changeset is active.\n   * Used by commands that need to project the full model (e.g. validate).\n   */\n  getActiveChangesetId(): string | null {\n    return this._activeChangesetId;\n  }\n\n  /**\n   * Load a layer from disk (model/XX_layername/*.yaml files)\n   */\n  async loadLayer(name: string): Promise<void> {\n    await startActiveSpan(\"layer.load\", async (layerSpan) => {\n      const fs = await import(\"fs/promises\");\n      const yaml = await import(\"yaml\");\n\n      let layerPath: string | null = null;\n\n      // Auto-discover by scanning directory with naming convention\n      const modelDir = `${this.rootPath}/documentation-robotics/model`;\n\n      try {\n        const entries = await fs.readdir(modelDir, { withFileTypes: true });\n        const layerDir = entries.find(\n          (e) =>\n            e.isDirectory() && e.name.match(/^\\d{2}_/) && e.name.replace(/^\\d{2}_/, \"\") === name\n        );\n\n        if (layerDir) {\n          layerPath = `${modelDir}/${layerDir.name}`;\n        }\n      } catch {\n        // Model directory doesn't exist or can't be read\n      }\n\n      if (!layerPath) {\n        return; // Layer directory not found\n      }\n\n      const layer = new Layer(name, this.graph);\n      let parseErrorCount = 0;\n\n      // Load all YAML files in the layer directory\n      const files = await fs.readdir(layerPath);\n      for (const file of files) {\n        if (file.endsWith(\".yaml\") || file.endsWith(\".yml\")) {\n          const filePath = `${layerPath}/${file}`;\n          try {\n            const yamlContent = await fs.readFile(filePath, \"utf-8\");\n            const elements = yaml.parse(yamlContent);\n\n            // Add each element from the YAML file\n            if (elements && typeof elements === \"object\") {\n              for (const [key, element] of Object.entries(elements)) {\n                if (element && typeof element === \"object\") {\n                  const el: any = element;\n\n                  // Derive id, path, and type using the 3-case migration logic:\n                  // Case 1: element already has both id (UUID) and path \u2192 use as-is\n                  // Case 2: element.id looks like a slug (layer.type.name) \u2192 move to path, generate UUID\n                  // Case 3: element has UUID id but no path \u2192 derive path from layer_id.type.kebab(name)\n                  const isSlugPattern = /^[a-z][a-z0-9-]*\\.[a-z][a-z0-9-]*\\.[a-z][a-z0-9-]*$/.test(el.id || \"\");\n                  const isUUIDPattern = /^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$/i.test(el.id || \"\");\n\n                  let elementId: string;\n                  let elementPath: string;\n                  let extractedType: string | undefined = undefined;\n\n                  if (el.path && isUUIDPattern) {\n                    // Case 1: already has both path and UUID id\n                    elementId = el.id;\n                    elementPath = el.path;\n                    const pathParts = el.path.split(\".\");\n                    if (pathParts.length >= 3) extractedType = pathParts[1];\n                  } else if (el.path && !isUUIDPattern) {\n                    // Has a path but id is not a UUID \u2014 migrate id to deterministic UUID\n                    elementPath = el.path;\n                    elementId = deterministicUUID(el.path);\n                    const pathParts = el.path.split(\".\");\n                    if (pathParts.length >= 3) extractedType = pathParts[1];\n                  } else if (isSlugPattern) {\n                    // Case 2: slug-looking id \u2192 move to path, generate deterministic UUID\n                    elementPath = el.id;\n                    elementId = deterministicUUID(el.id);\n                    const parts = el.id.split(\".\");\n                    if (parts.length >= 3) extractedType = parts[1];\n                  } else if (isUUIDPattern) {\n                    // Case 3: UUID id, no path \u2192 derive path\n                    elementId = el.id;\n                    const layerId = el.layer_id || name;\n                    const rawType = el.type || \"\";\n                    const rawName = el.name || key;\n                    const kebabName = rawName.toLowerCase().replace(/[\\s_]+/g, \"-\").replace(/[^a-z0-9-]/g, \"\").replace(/-+/g, \"-\").replace(/^-+|-+$/g, \"\");\n                    elementPath = `${layerId}.${rawType}.${kebabName}`;\n                    extractedType = rawType || undefined;\n                  } else {\n                    // Fallback: derive a path from available data, generate deterministic UUID\n                    const layerId = el.layer_id || name;\n                    const rawType = el.type || (typeof el.id === \"string\" && el.id.includes(\".\") ? el.id.split(\".\")[1] : \"\") || \"\";\n                    const rawName = el.name || key;\n                    const kebabName = rawName.toLowerCase().replace(/[\\s_]+/g, \"-\").replace(/[^a-z0-9-]/g, \"\").replace(/-+/g, \"-\").replace(/^-+|-+$/g, \"\") || \"unknown\";\n                    elementPath = `${layerId}.${rawType || \"element\"}.${kebabName}`;\n                    elementId = deterministicUUID(elementPath);\n                    if (rawType) extractedType = rawType;\n                    else if (typeof el.id === \"string\" && el.id.includes(\".\")) {\n                      const parts = el.id.split(\".\");\n                      if (parts.length >= 3) extractedType = parts[1];\n                    }\n                  }\n\n                  const elementName = el.name || key;\n                  const elementType = el.type || extractedType;\n                  const layerId = el.layer_id || name;\n\n                  const newElement = new Element({\n                    id: elementId,\n                    path: elementPath,\n                    spec_node_id: el.spec_node_id,\n                    layer_id: layerId,\n                    attributes: el.attributes,\n                    source_reference: el.source_reference,\n                    metadata: el.metadata,\n                    name: elementName,\n                    type: elementType,\n                    description: el.description || \"\",\n                    relationships: el.relationships || [],\n                    references: el.references || [],\n                    layer: layerId,\n                  } as any);\n                  layer.addElement(newElement);\n                }\n              }\n            }\n          } catch (fileError) {\n            // Log YAML parsing errors but continue loading other files\n            const errorMsg = fileError instanceof Error ? fileError.message : String(fileError);\n            console.error(`Warning: Failed to parse ${filePath}: ${errorMsg}`);\n            parseErrorCount++;\n            // Continue with next file\n          }\n        }\n      }\n\n      // If we had parse errors, add a note to the layer\n      if (parseErrorCount > 0) {\n        console.error(\n          `Warning: Layer '${name}' loaded with ${parseErrorCount} YAML parse error(s)`\n        );\n      }\n\n      this.layers.set(name, layer);\n      this.loadedLayers.add(name);\n\n      layerSpan.setAttribute(\"layer.element_count\", layer.elements.size);\n    }, { \"layer.name\": name });\n  }\n\n  /**\n   * Add a layer to the model\n   */\n  addLayer(layer: Layer): void {\n    // If the layer has elements in its isolated graph, migrate them to the model's graph\n    if (layer.graph.getNodeCount() > 0) {\n      for (const node of layer.graph.nodes.values()) {\n        this.graph.addNode(node);\n      }\n      for (const edge of layer.graph.edges.values()) {\n        this.graph.addEdge(edge);\n      }\n    }\n    // Ensure layer uses the model's graph for future operations\n    layer.graph = this.graph;\n    this.layers.set(layer.name, layer);\n    this.loadedLayers.add(layer.name);\n  }\n\n  /**\n   * Get all layer names, including layers that exist only in staged changes.\n   * When an active changeset introduces elements for a layer with no committed data,\n   * that layer name is included so findElementLayer() and other callers can discover it.\n   */\n  getLayerNames(): string[] {\n    const base = Array.from(this.layers.keys());\n    if (this._stagedLayerNames.size === 0) {\n      return base;\n    }\n    // Include staged-only layers (layers that have staged elements but no committed elements)\n    const staged = Array.from(this._stagedLayerNames).filter((l) => !this.layers.has(l));\n    return [...base, ...staged];\n  }\n\n  /**\n   * Save a layer to disk (model/XX_layername/*.yaml)\n   */\n  async saveLayer(name: string): Promise<void> {\n    const layer = this.layers.get(name);\n    if (!layer) {\n      throw new Error(`Layer ${name} not found`);\n    }\n\n    const fs = await import(\"fs/promises\");\n    const yaml = await import(\"yaml\");\n\n    let layerPath: string | null = null;\n\n    // Discover by scanning directory\n    const modelDir = `${this.rootPath}/documentation-robotics/model`;\n\n    try {\n      const entries = await fs.readdir(modelDir, { withFileTypes: true });\n      const layerDir = entries.find(\n        (e) =>\n          e.isDirectory() && e.name.match(/^\\d{2}_/) && e.name.replace(/^\\d{2}_/, \"\") === name\n      );\n\n      if (layerDir) {\n        layerPath = `${modelDir}/${layerDir.name}`;\n      }\n    } catch {\n      // Model directory doesn't exist or can't be read\n    }\n\n    // If still not found, create using default format\n    if (!layerPath) {\n      // Find the order number for this layer\n      // Handle layer names with or without numeric prefix (e.g., \"motivation\" or \"01-motivation\")\n      const layerNameWithoutPrefix = name.replace(/^\\d{2}-/, \"\");\n      const index = CANONICAL_LAYER_NAMES.indexOf(layerNameWithoutPrefix as typeof CANONICAL_LAYER_NAMES[number]);\n      if (index >= 0) {\n        const orderNum = String(index + 1).padStart(2, \"0\");\n        layerPath = `${this.rootPath}/documentation-robotics/model/${orderNum}_${layerNameWithoutPrefix}`;\n        await ensureDir(layerPath);\n      } else {\n        throw new Error(`Unknown layer ${name} and no path configured in manifest`);\n      }\n    }\n\n    // Delete all existing YAML files in the layer directory to ensure\n    // we don't keep stale files after element deletion\n    try {\n      const existingFiles = await fs.readdir(layerPath);\n      for (const file of existingFiles) {\n        if (file.endsWith(\".yaml\") || file.endsWith(\".yml\")) {\n          await fs.unlink(`${layerPath}/${file}`);\n        }\n      }\n    } catch (err) {\n      // Only ignore \"directory not found\" errors \u2014 re-throw permission/I/O errors\n      const isNotFoundError = (err as any)?.code === \"ENOENT\";\n      if (!isNotFoundError) {\n        throw new Error(\n          `Failed to clean existing YAML files: ${err instanceof Error ? err.message : String(err)}`\n        );\n      }\n    }\n\n    // Group elements by type, computing the snake_case file stem from the spec node title\n    const elementsByType = new Map<string, { stem: string; elements: Element[] }>();\n    for (const element of layer.elements.values()) {\n      const typeKey = element.type;\n      if (!elementsByType.has(typeKey)) {\n        const stem = typeToSnakeStem(element.spec_node_id, element.type);\n        elementsByType.set(typeKey, { stem, elements: [] });\n      }\n      elementsByType.get(typeKey)!.elements.push(element);\n    }\n\n    // Internal graph fields \u2014 never written to YAML\n    const INTERNAL_FIELDS = new Set([\n      \"__references__\", \"__relationships__\",\n      \"source\", \"x-source-reference\",\n    ]);\n\n    // Write each type to its own YAML file\n    for (const [, { stem, elements }] of elementsByType) {\n      const filename = `${stem}.yaml`;\n      const filePath = `${layerPath}/${filename}`;\n\n      // Convert elements to spec-node format YAML\n      const yamlData: any = {};\n      for (const element of elements) {\n        const json = element.toJSON();\n\n        // Clean attributes: remove graph-internal keys that should not be persisted\n        const cleanAttrs = json.attributes\n          ? Object.fromEntries(\n              Object.entries(json.attributes).filter(([k]) => !INTERNAL_FIELDS.has(k))\n            )\n          : undefined;\n\n        // Use path as YAML key (human-readable); fall back to id for elements without path\n        const key = element.path || element.id;\n        yamlData[key] = {\n          id: json.id,\n          path: json.path,\n          spec_node_id: json.spec_node_id,\n          type: json.type,\n          layer_id: json.layer_id,\n          name: json.name,\n          ...(json.description && { description: json.description }),\n          ...(cleanAttrs && Object.keys(cleanAttrs).length > 0 && { attributes: cleanAttrs }),\n          ...(json.source_reference && { source_reference: json.source_reference }),\n          ...(json.metadata && { metadata: json.metadata }),\n          ...(json.references && json.references.length > 0 && { references: json.references }),\n          // Relationships are now stored in centralized relationships.yaml, not inline\n        };\n      }\n\n      await writeFile(filePath, yaml.stringify(yamlData));\n    }\n\n    layer.markClean();\n  }\n\n  /**\n   * Save model (saves all dirty layers and manifest)\n   */\n  async save(): Promise<void> {\n    await this.saveDirtyLayers();\n    await this.saveManifest();\n  }\n\n  /**\n   * Save all dirty layers to disk\n   */\n  async saveDirtyLayers(): Promise<void> {\n    // Count dirty layers before operation\n    let dirtyLayerCount = 0;\n    for (const layer of this.layers.values()) {\n      if (layer.isDirty()) {\n        dirtyLayerCount++;\n      }\n    }\n\n    const span = isTelemetryEnabled\n      ? startSpan(\"model.save\", {\n          \"model.path\": this.rootPath,\n          \"model.dirty_layer_count\": dirtyLayerCount,\n        })\n      : null;\n\n    try {\n      for (const layer of this.layers.values()) {\n        if (layer.isDirty()) {\n          await this.saveLayer(layer.name);\n        }\n      }\n    } finally {\n      if (isTelemetryEnabled) {\n        endSpan(span);\n      }\n    }\n  }\n\n  /**\n   * Save the manifest to disk (documentation-robotics/model/manifest.yaml)\n   */\n  async saveManifest(): Promise<void> {\n    this.manifest.updateModified();\n    const yaml = await import(\"yaml\");\n    const manifestPath = `${this.rootPath}/documentation-robotics/model/manifest.yaml`;\n\n    // Convert to YAML format\n    const yamlData: any = {\n      version: this.manifest.version,\n      schema: \"documentation-robotics-v1\",\n      cli_version: getCliVersion(),\n      spec_version: this.manifest.specVersion,\n      created: this.manifest.created,\n      updated: this.manifest.modified,\n      project: {\n        name: this.manifest.name,\n        description: this.manifest.description,\n        version: this.manifest.version,\n      },\n      documentation: \".dr/README.md\",\n      layers: {},\n    };\n\n    // Generate layer structure from current model state\n    for (let i = 0; i < CANONICAL_LAYER_NAMES.length; i++) {\n      const layerName = CANONICAL_LAYER_NAMES[i];\n      const layer = this.layers.get(layerName);\n      const orderNum = String(i + 1).padStart(2, \"0\");\n\n      yamlData.layers[layerName] = {\n        order: i + 1,\n        name: layerName.charAt(0).toUpperCase() + layerName.slice(1).replace(\"-\", \" \"),\n        path: `documentation-robotics/model/${orderNum}_${layerName}/`,\n        enabled: true,\n        ...(layer && { elements: this.getLayerElementCounts(layer) }),\n      };\n    }\n\n    if (this.manifest.changeset_history && this.manifest.changeset_history.length > 0) {\n      yamlData.changeset_history = this.manifest.changeset_history;\n    }\n\n    await ensureDir(`${this.rootPath}/documentation-robotics/model`);\n    await writeFile(manifestPath, yaml.stringify(yamlData));\n  }\n\n  private getLayerElementCounts(layer: Layer): Record<string, number> {\n    const counts: Record<string, number> = {};\n    for (const element of layer.elements.values()) {\n      counts[element.type] = (counts[element.type] || 0) + 1;\n    }\n    return counts;\n  }\n\n  /**\n   * Load relationships from relationships.yaml\n   */\n  async loadRelationships(): Promise<void> {\n    const fs = await import(\"fs/promises\");\n    const yaml = await import(\"yaml\");\n    const relationshipsPath = `${this.rootPath}/documentation-robotics/model/relationships.yaml`;\n\n    let data: any;\n    try {\n      const yamlContent = await fs.readFile(relationshipsPath, \"utf-8\");\n      data = yaml.parse(yamlContent);\n    } catch (err) {\n      // If file doesn't exist, that's okay - start with empty relationships\n      if ((err as any).code !== \"ENOENT\") {\n        // But if it's a different error (YAML parse, permission denied, etc), throw it\n        // so the caller knows about the issue\n        throw new Error(\n          `Failed to load relationships.yaml: ${err instanceof Error ? err.message : String(err)}`\n        );\n      }\n      // ENOENT: file doesn't exist, return with empty relationships\n      return;\n    }\n\n    // Validate that parsed content is an array\n    if (!Array.isArray(data)) {\n      const typeLabel = data === null ? \"null\" : typeof data;\n      console.warn(\n        `Warning: relationships.yaml contains non-array content (received ${typeLabel}). Expected an array of relationships. Skipping relationship loading.`\n      );\n      return;\n    }\n\n    this.relationships = Relationships.fromArray(data);\n    // Sync relationships to graph as a secondary in-memory index.\n    // addEdge() may throw if nodes from other layers haven't been loaded yet;\n    // failures are silently skipped \u2014 this.relationships holds the primary data.\n    for (let i = 0; i < data.length; i++) {\n      const rel = data[i];\n      const edge: GraphEdge = {\n        id: `rel-${i}-${crypto.randomBytes(4).toString(\"hex\")}`,\n        source: rel.source,\n        destination: rel.target,\n        predicate: rel.predicate,\n        properties: rel.properties,\n        category: rel.category,\n      };\n      try {\n        this.graph.addEdge(edge);\n      } catch {\n        // Silently skip edges whose nodes haven't been loaded yet.\n        // The primary relationship data lives in this.relationships; the graph\n        // is a secondary index. Cross-layer relationships referencing nodes from\n        // unloaded layers are expected during partial model construction.\n      }\n    }\n  }\n\n  /**\n   * Save relationships to relationships.yaml\n   */\n  async saveRelationships(): Promise<void> {\n    const fs = await import(\"fs/promises\");\n    const yaml = await import(\"yaml\");\n    const relationshipsPath = `${this.rootPath}/documentation-robotics/model/relationships.yaml`;\n\n    await ensureDir(`${this.rootPath}/documentation-robotics/model`);\n\n    const data = this.relationships.toArray();\n\n    // Add header comment with timestamp to ensure file always changes\n    const timestamp = new Date().toISOString();\n    const header = `# Intra-layer relationships\n# Format: source_id -> predicate -> target_id\n# Last updated: ${timestamp}\n\n`;\n    const yamlContent = header + yaml.stringify(data);\n\n    await fs.writeFile(relationshipsPath, yamlContent, \"utf-8\");\n    this.relationships.markClean();\n  }\n\n  /**\n   * Resolve model paths (private helper)\n   *\n   * @param startPath - Starting path for search\n   * @returns Project root and manifest path\n   */\n  private static async resolveModelPaths(startPath?: string): Promise<{\n    projectRoot: string;\n    manifestPath: string;\n  }> {\n    const searchPath = startPath || process.cwd();\n\n    // Optional override via env var (highest priority)\n    if (process.env.DR_MODEL_PATH) {\n      const envPath = path.resolve(process.env.DR_MODEL_PATH);\n      let manifestPath: string;\n\n      if (envPath.endsWith(\"manifest.yaml\")) {\n        manifestPath = envPath;\n      } else if (envPath.endsWith(\"model\")) {\n        manifestPath = path.join(envPath, \"manifest.yaml\");\n      } else {\n        manifestPath = path.join(envPath, \"documentation-robotics\", \"model\", \"manifest.yaml\");\n      }\n\n      try {\n        await fs.access(manifestPath);\n        const projectRoot = path.dirname(path.dirname(path.dirname(manifestPath)));\n        return { projectRoot, manifestPath: path.normalize(manifestPath) };\n      } catch {\n        throw new Error(`Model not found at DR_MODEL_PATH: ${process.env.DR_MODEL_PATH}`);\n      }\n    }\n\n    // Use findProjectRoot to locate documentation_robotics/ folder\n    const projectRoot = await findProjectRoot(searchPath);\n\n    if (!projectRoot) {\n      throw new Error(\n        \"No DR project found. Could not find documentation_robotics/ folder.\\n\" +\n          'Run \"dr init\" to create a new project, or navigate to a directory containing a DR project.'\n      );\n    }\n\n    const manifestPath = path.join(projectRoot, \"documentation-robotics\", \"model\", \"manifest.yaml\");\n\n    try {\n      await fs.access(manifestPath);\n      return { projectRoot, manifestPath };\n    } catch {\n      throw new Error(\n        `Found documentation_robotics/ at ${projectRoot} but no model found. ` +\n          `Expected: ${manifestPath}\\n` +\n          `Run \"dr init\" to create a model.`\n      );\n    }\n  }\n\n  /**\n   * Load a model from disk\n   *\n   * Expected structure:\n   * <project-root>/\n   * \u2514\u2500\u2500 documentation_robotics/\n   *     \u2514\u2500\u2500 model/\n   *         \u2514\u2500\u2500 manifest.yaml\n   *\n   * @param startPath - Starting path for project search (defaults to process.cwd())\n   * @param options - Model loading options\n   * @returns Loaded Model instance\n   */\n  static async load(startPath?: string, options: ModelOptions = {}): Promise<Model> {\n    return startActiveSpan(\"model.load\", async (span) => {\n      // Resolve project root and manifest path\n      const { projectRoot, manifestPath } = await Model.resolveModelPaths(startPath);\n\n      const yaml = await import(\"yaml\");\n\n      // Load manifest from resolved path\n      const yamlContent = await fs.readFile(manifestPath, \"utf-8\");\n      const manifestYaml = yaml.parse(yamlContent);\n\n      // Convert manifest to internal format\n      const manifestData: any = {\n        name: manifestYaml.project?.name || \"Unnamed Model\",\n        description: manifestYaml.project?.description || \"\",\n        version: manifestYaml.project?.version || manifestYaml.version || \"0.1.0\",\n        specVersion: manifestYaml.spec_version || \"0.6.0\",\n        created: manifestYaml.created || new Date().toISOString(),\n        modified: manifestYaml.updated || new Date().toISOString(),\n      };\n      const manifest = new Manifest(manifestData);\n      const model = new Model(projectRoot, manifest, options);\n\n      // Load all available layers if lazyLoad is false\n      if (!options.lazyLoad) {\n        try {\n          // If manifest has layer definitions, use those\n          if (manifestYaml.layers) {\n            for (const layerName of Object.keys(manifestYaml.layers)) {\n              const layerConfig = manifestYaml.layers[layerName];\n              if (layerConfig.enabled !== false) {\n                if (!options.layers || options.layers.includes(layerName)) {\n                  await model.loadLayer(layerName);\n                }\n              }\n            }\n          } else {\n            // Otherwise scan for layer directories\n            const modelDir = manifestPath.replace(\"/manifest.yaml\", \"\");\n            const entries = await fs.readdir(modelDir, { withFileTypes: true });\n\n            for (const entry of entries) {\n              if (entry.isDirectory() && entry.name.match(/^\\d{2}_/)) {\n                const layerName = entry.name.replace(/^\\d{2}_/, \"\");\n                if (!options.layers || options.layers.includes(layerName)) {\n                  await model.loadLayer(layerName);\n                }\n              }\n            }\n          }\n        } catch (e) {\n          // Check if this is a \"directory not found\" error (expected case)\n          const isNotFoundError = (e as any)?.code === \"ENOENT\";\n          if (!isNotFoundError) {\n            // Re-throw non-ENOENT errors: permission errors, YAML parsing failures, I/O errors, etc.\n            throw new Error(\n              `Failed to load layers: ${e instanceof Error ? e.message : String(e)}`\n            );\n          }\n          // ENOENT is expected if layer directory doesn't exist yet, so just continue\n        }\n      }\n\n      // Load relationships from relationships.yaml\n      await model.loadRelationships();\n\n      // Check for active changeset and pre-load staged metadata for transparent projection.\n      // This enables getLayer() to return projected views and getLayerNames() to include\n      // layers that exist only in staged changes.\n      const activePath = path.join(\n        projectRoot,\n        \"documentation-robotics\",\n        \"changesets\",\n        \".active\"\n      );\n      try {\n        const activeContent = await fs.readFile(activePath, \"utf-8\");\n        const activeId = activeContent.trim();\n        if (activeId) {\n          model._activeChangesetId = activeId;\n          const storage = new StagedChangesetStorage(projectRoot);\n          const changeset = await storage.load(activeId);\n          if (changeset) {\n            for (const change of changeset.changes as StagedChange[]) {\n              // Track layer names for getLayerNames()\n              if (\n                change.type === \"add\" ||\n                change.type === \"update\" ||\n                change.type === \"delete\"\n              ) {\n                model._stagedLayerNames.add(change.layerName);\n              }\n\n              // Inject staged relationship-adds into model.relationships so that\n              // read commands (list, show, export) transparently see staged relationships.\n              if (change.type === \"relationship-add\" && change.after) {\n                const rel = change.after as {\n                  source: string;\n                  target: string;\n                  predicate: string;\n                  layer: string;\n                  targetLayer?: string;\n                  category?: \"structural\" | \"behavioral\";\n                  properties?: Record<string, unknown>;\n                };\n                // Only inject if not already in relationships.yaml (prevents duplicates\n                // if .active file is stale after a partial commit or manual edit).\n                const alreadyPresent = model.relationships.find(\n                  rel.source,\n                  rel.target,\n                  rel.predicate\n                );\n                if (alreadyPresent.length === 0) {\n                  model.relationships.add({\n                    source: rel.source,\n                    target: rel.target,\n                    predicate: rel.predicate,\n                    layer: rel.layer,\n                    ...(rel.targetLayer ? { targetLayer: rel.targetLayer } : {}),\n                    category: rel.category ?? \"structural\",\n                    ...(rel.properties ? { properties: rel.properties } : {}),\n                  });\n                }\n              }\n\n              // Remove staged relationship-deletes from model.relationships so that\n              // read commands see the relationship as already deleted.\n              if (change.type === \"relationship-delete\" && change.before) {\n                const rel = change.before as {\n                  source: string;\n                  target: string;\n                  predicate?: string;\n                };\n                model.relationships.delete(rel.source, rel.target, rel.predicate);\n              }\n            }\n          }\n        }\n      } catch {\n        // No active changeset or unreadable \u2014 proceed with base model only\n        model._activeChangesetId = null;\n      }\n\n      // Count total entities across all layers\n      let entityCount = 0;\n      for (const layer of model.layers.values()) {\n        entityCount += layer.elements.size;\n      }\n\n      span.setAttribute(\"model.entity_count\", entityCount);\n      span.setAttribute(\"model.layer_count\", model.layers.size);\n\n      return model;\n    }, {\n      \"model.path\": startPath || process.cwd(),\n      \"model.type\": \"dr\",\n    });\n  }\n\n  /**\n   * Initialize a new model in a directory\n   */\n  static async init(\n    rootPath: string,\n    manifestData: ManifestData,\n    options: ModelOptions = {}\n  ): Promise<Model> {\n    // Create model directory structure\n    await ensureDir(`${rootPath}/documentation-robotics/model`);\n\n    for (let i = 0; i < CANONICAL_LAYER_NAMES.length; i++) {\n      const orderNum = String(i + 1).padStart(2, \"0\");\n      const layerName = CANONICAL_LAYER_NAMES[i];\n      await ensureDir(`${rootPath}/documentation-robotics/model/${orderNum}_${layerName}`);\n    }\n\n    const manifest = new Manifest(manifestData);\n    const model = new Model(rootPath, manifest, options);\n\n    await model.saveManifest();\n\n    return model;\n  }\n\n  /**\n   * Graph-based API methods for querying the model\n   * These methods delegate to the underlying GraphModel for efficient queries\n   */\n\n  /**\n   * Get a node by its UUID\n   */\n  getNode(id: string) {\n    return this.graph.getNode(id);\n  }\n\n  /**\n   * Get all nodes in a specific layer\n   */\n  getNodesByLayer(layerId: string) {\n    return this.graph.getNodesByLayer(layerId);\n  }\n\n  /**\n   * Get all nodes of a specific type\n   */\n  getNodesByType(type: string) {\n    return this.graph.getNodesByType(type);\n  }\n\n  /**\n   * Get all edges (relationships) in the model\n   */\n  getAllEdges() {\n    return this.graph.getAllEdges();\n  }\n\n  /**\n   * Get edges originating from a specific node\n   */\n  getEdgesFrom(nodeId: string, predicate?: string) {\n    return this.graph.getEdgesFrom(nodeId, predicate);\n  }\n\n  /**\n   * Get edges terminating at a specific node\n   */\n  getEdgesTo(nodeId: string, predicate?: string) {\n    return this.graph.getEdgesTo(nodeId, predicate);\n  }\n\n  /**\n   * Get edges between two specific nodes\n   */\n  getEdgesBetween(sourceId: string, destinationId: string, predicate?: string) {\n    return this.graph.getEdgesBetween(sourceId, destinationId, predicate);\n  }\n\n  /**\n   * Traverse the graph starting from a node, following a specific predicate\n   */\n  async traverse(startNodeId: string, predicate: string, maxDepth: number = 10) {\n    return this.graph.traverse(startNodeId, predicate, maxDepth);\n  }\n\n  /**\n   * Create a backup of the current model state\n   * Used for rollback support in migration operations\n   *\n   * @param label Descriptive label for the backup (e.g., \"pre-migration\")\n   * @returns Path to the backup directory\n   */\n  async createBackup(label: string): Promise<string> {\n    const timestamp = new Date().toISOString().replace(/[:.]/g, \"-\");\n    const backupDir = path.join(this.rootPath, \".dr-backups\", `${label}-${timestamp}`);\n\n    // Create backup directory\n    await ensureDir(backupDir);\n\n    // Backup layers directory\n    const layersSource = path.join(this.rootPath, \"documentation-robotics\", \"model\");\n    const layersBackup = path.join(backupDir, \"layers\");\n    if (await this.directoryExists(layersSource)) {\n      await this.copyDirectory(layersSource, layersBackup);\n    }\n\n    // Backup manifest\n    const manifestSource = path.join(this.rootPath, \"documentation-robotics\", \"model\", \"manifest.yaml\");\n    const manifestBackup = path.join(backupDir, \"manifest.yaml\");\n    if (await this.fileExists(manifestSource)) {\n      await fs.copyFile(manifestSource, manifestBackup);\n    }\n\n    return backupDir;\n  }\n\n  /**\n   * Restore model from a backup directory\n   * Used for rollback after failed migrations\n   *\n   * @param backupPath Path to the backup directory\n   */\n  async restoreFromBackup(backupPath: string): Promise<void> {\n    // Restore layers\n    const layersBackup = path.join(backupPath, \"layers\");\n    const layersTarget = path.join(this.rootPath, \"documentation-robotics\", \"model\");\n    if (await this.directoryExists(layersBackup)) {\n      await this.copyDirectory(layersBackup, layersTarget);\n    }\n\n    // Restore manifest\n    const manifestBackup = path.join(backupPath, \"manifest.yaml\");\n    const manifestTarget = path.join(this.rootPath, \"documentation-robotics\", \"model\", \"manifest.yaml\");\n    if (await this.fileExists(manifestBackup)) {\n      await fs.copyFile(manifestBackup, manifestTarget);\n    }\n\n    // Reload model to refresh in-memory state\n    const reloadedModel = await Model.load(this.rootPath, { lazyLoad: this.lazyLoad });\n    this.layers = reloadedModel.layers;\n    this.manifest = reloadedModel.manifest;\n    this.graph = reloadedModel.graph;\n    this.relationships = reloadedModel.relationships;\n  }\n\n  /**\n   * Save dirty layers with atomic write semantics\n   * Writes to temporary file first, then renames on success to ensure data safety\n   *\n   * @throws Error if atomic write fails\n   */\n  async saveDirtyLayersAtomic(): Promise<void> {\n    // First, save all layers to temporary files\n    const tempLayerWrites: Array<{ layer: Layer; tempPath: string }> = [];\n\n    try {\n      for (const layer of this.layers.values()) {\n        if (layer.isDirty()) {\n          const layerPath = path.join(\n            this.rootPath,\n            \"documentation-robotics\",\n            \"model\",\n            `${layer.name}_layer`\n          );\n\n          const tempPath = `${layerPath}.tmp`;\n          await ensureDir(tempPath);\n\n          // Write layer elements to temp directory\n          for (const element of layer.elements.values()) {\n            const elementPath = path.join(tempPath, `${element.path || element.id}.json`);\n            const content = JSON.stringify(element.toJSON(), null, 2);\n            await writeFile(elementPath, content);\n          }\n\n          tempLayerWrites.push({ layer, tempPath });\n        }\n      }\n\n      // All temp writes succeeded, now commit by renaming\n      for (const { layer, tempPath } of tempLayerWrites) {\n        const layerPath = path.join(\n          this.rootPath,\n          \"documentation-robotics\",\n          \"model\",\n          `${layer.name}_layer`\n        );\n\n        // Remove old directory and rename temp to actual\n        if (await this.directoryExists(layerPath)) {\n          await fs.rm(layerPath, { recursive: true, force: true });\n        }\n        await fs.rename(tempPath, layerPath);\n      }\n    } catch (error) {\n      // Cleanup any temp directories on failure\n      for (const { tempPath } of tempLayerWrites) {\n        if (await this.directoryExists(tempPath)) {\n          await fs.rm(tempPath, { recursive: true, force: true });\n        }\n      }\n      throw error;\n    }\n  }\n\n  /**\n   * Helper: Check if file exists\n   */\n  private async fileExists(filePath: string): Promise<boolean> {\n    try {\n      await fs.access(filePath);\n      return true;\n    } catch {\n      return false;\n    }\n  }\n\n  /**\n   * Helper: Check if directory exists\n   */\n  private async directoryExists(dirPath: string): Promise<boolean> {\n    try {\n      const stat = await fs.stat(dirPath);\n      return stat.isDirectory();\n    } catch {\n      return false;\n    }\n  }\n\n  /**\n   * Helper: Recursively copy directory\n   */\n  private async copyDirectory(src: string, dest: string): Promise<void> {\n    await ensureDir(dest);\n    const entries = await fs.readdir(src, { withFileTypes: true });\n\n    for (const entry of entries) {\n      const srcPath = path.join(src, entry.name);\n      const destPath = path.join(dest, entry.name);\n\n      if (entry.isDirectory()) {\n        await this.copyDirectory(srcPath, destPath);\n      } else {\n        await fs.copyFile(srcPath, destPath);\n      }\n    }\n  }\n}\n"],
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+  "sourcesContent": ["import { Layer } from \"./layer.js\";\nimport { Manifest } from \"./manifest.js\";\nimport { Element } from \"./element.js\";\nimport { GraphModel, type GraphEdge } from \"./graph-model.js\";\nimport { VirtualProjectionEngine } from \"./virtual-projection.js\";\nimport { StagedChangesetStorage } from \"./staged-changeset-storage.js\";\nimport { Relationships } from \"./relationships.js\";\nimport { CANONICAL_LAYER_NAMES } from \"./layers.js\";\nimport type { StagedChange } from \"./changeset.js\";\nimport { ensureDir, writeFile } from \"../utils/file-io.js\";\nimport { getCliVersion } from \"../utils/spec-version.js\";\nimport { startSpan, endSpan, startActiveSpan } from \"../telemetry/index.js\";\nimport { findProjectRoot } from \"../utils/project-paths.js\";\nimport { getNodeType } from \"../generated/node-types.js\";\nimport type { SpecNodeId } from \"../generated/node-types.js\";\nimport type { ManifestData, ModelOptions } from \"../types/index.js\";\nimport path from \"node:path\";\nimport fs from \"node:fs/promises\";\nimport crypto from \"node:crypto\";\n\n/**\n * Derive a deterministic UUID from a path string using SHA-256.\n * Produces a stable UUID4-like value so migration doesn't regenerate UUIDs on every load.\n */\nfunction deterministicUUID(path: string): string {\n  const hash = crypto.createHash(\"sha256\").update(path).digest(\"hex\");\n  return [\n    hash.slice(0, 8),\n    hash.slice(8, 12),\n    \"4\" + hash.slice(13, 16), // version 4 marker\n    ((parseInt(hash.slice(16, 18), 16) & 0x3f) | 0x80).toString(16) + hash.slice(18, 20), // variant\n    hash.slice(20, 32),\n  ].join(\"-\");\n}\n\n/**\n * Convert a PascalCase title to snake_case.\n * Handles acronyms correctly: \"UXApplication\" \u2192 \"ux_application\", \"OpenAPIDocument\" \u2192 \"open_api_document\".\n */\nfunction titleToSnakeCase(title: string): string {\n  return title\n    .replace(/([A-Z]+)([A-Z][a-z])/g, \"$1_$2\") // \"APIDoc\" \u2192 \"API_Doc\"\n    .replace(/([a-z\\d])([A-Z])/g, \"$1_$2\")       // \"appComponent\" \u2192 \"app_Component\"\n    .toLowerCase();\n}\n\n/**\n * Derive a snake_case file stem for a given element type.\n * Uses the spec node title for accurate word boundaries (e.g., \"InputSpacePartition\" \u2192 \"input_space_partition\").\n * Falls back to the raw type string when the title is unavailable.\n */\nfunction typeToSnakeStem(specNodeId: string | undefined, type: string): string {\n  if (specNodeId) {\n    const nodeType = getNodeType(specNodeId as SpecNodeId);\n    if (nodeType?.title) {\n      return titleToSnakeCase(nodeType.title);\n    }\n  }\n  return type;\n}\n\n/**\n * Graph-internal bookkeeping keys that `layer.ts`'s node<->Element conversion stuffs into the\n * same flat `attributes`/`properties` bag the underlying graph structure uses for everything\n * (it has no separate channel for them) \u2014 `__references__`/`__relationships__` mirror\n * `element.references`/`element.relationships`, which are real, separately-typed fields on\n * `Element` and get serialized to their own place (references inline, relationships to\n * relationships.yaml). These must never reach the persisted YAML's `attributes` object.\n *\n * Double-underscore-prefixed specifically so a schema author would have to go out of their way\n * to collide with one \u2014 confirmed zero of the 191 node schemas declare an attribute with either\n * name. Contrast with the *type-blind* set this replaced, which also unconditionally stripped\n * plain `\"source\"`/`\"x-source-reference\"` \u2014 both of which ARE legitimate, sometimes-required\n * domain attributes on 41 node schemas across 8 layers (e.g. security.accesscondition.source),\n * and neither of which is ever actually used as internal bookkeeping anywhere in this codebase.\n * That collision silently destroyed real data on every save for any element of one of those 41\n * types, without ever failing validation (validation runs on the in-memory element, before this\n * stripping) \u2014 see CHANGELOG for the incident this fixes.\n */\nconst ALWAYS_INTERNAL_ATTRIBUTE_KEYS = new Set([\"__references__\", \"__relationships__\"]);\n\n/**\n * Whether `key` should survive persistence in `specNodeId`'s `attributes`.\n *\n * Only ever strips the two confirmed-always-internal keys above, and even then only when the\n * node type's OWN schema doesn't declare that name as a real attribute \u2014 so if some future\n * schema ever legitimately needs an attribute literally called `__references__` (unlikely, but\n * the whole point of this function is to not have to trust \"unlikely\" again), it still survives.\n * Nothing else is ever stripped: the class of bug this fixes was a hardcoded, type-blind\n * reserved-word blocklist making that same \"trust the list, not the schema\" mistake for\n * `source`/`x-source-reference`. Consulting the schema instead of a fixed string list is what\n * keeps this from silently recurring for some other attribute name in the future.\n */\nfunction isPersistableAttribute(specNodeId: string | undefined, key: string): boolean {\n  if (!ALWAYS_INTERNAL_ATTRIBUTE_KEYS.has(key)) return true;\n  if (!specNodeId) return false;\n  const nodeType = getNodeType(specNodeId as SpecNodeId);\n  if (!nodeType) return false;\n  return nodeType.requiredAttributes.includes(key) || nodeType.optionalAttributes.includes(key);\n}\n\n// Fallback for runtime environments where TELEMETRY_ENABLED is not defined by esbuild\ndeclare const TELEMETRY_ENABLED: boolean | undefined;\nconst isTelemetryEnabled = typeof TELEMETRY_ENABLED !== \"undefined\" ? TELEMETRY_ENABLED : false;\n\n/**\n * Model class representing the complete architecture model\n * Uses GraphModel internally for graph-based storage\n */\nexport class Model {\n  rootPath: string;\n  manifest: Manifest;\n  graph: GraphModel;\n  layers: Map<string, Layer>;\n  relationships: Relationships;\n  lazyLoad: boolean;\n  private loadedLayers: Set<string>;\n  private virtualProjectionEngine?: VirtualProjectionEngine;\n  /** ID of the currently active changeset, or null if none is active. Set during load(). */\n  private _activeChangesetId: string | null = null;\n  /** Layer names that exist only in staged changes (not yet committed to base model). */\n  private _stagedLayerNames: Set<string> = new Set();\n\n  constructor(rootPath: string, manifest: Manifest, options: ModelOptions = {}) {\n    this.rootPath = rootPath;\n    this.manifest = manifest;\n    this.graph = new GraphModel();\n    this.layers = new Map();\n    this.relationships = new Relationships();\n    this.lazyLoad = options.lazyLoad ?? false;\n    this.loadedLayers = new Set();\n  }\n\n  /**\n   * Get the committed base layer (no staging projection).\n   * Used internally by VirtualProjectionEngine and commit() to access the raw base model\n   * without triggering infinite recursion or double-projection.\n   */\n  async getBaseLayer(name: string): Promise<Layer | undefined> {\n    if (this.lazyLoad && !this.loadedLayers.has(name)) {\n      await this.loadLayer(name);\n    }\n    return this.layers.get(name);\n  }\n\n  /**\n   * Get a layer, transparently merging staged changes when an active changeset exists.\n   * Falls back to the committed base layer if no changeset is active or projection fails.\n   */\n  async getLayer(name: string): Promise<Layer | undefined> {\n    if (this.lazyLoad && !this.loadedLayers.has(name)) {\n      await this.loadLayer(name);\n    }\n\n    // If an active changeset is present, return a projected (base + staged) layer\n    if (this._activeChangesetId) {\n      try {\n        return await this.getVirtualProjectionEngine().projectLayer(\n          this,\n          this._activeChangesetId,\n          name\n        );\n      } catch {\n        // Fall back to base layer on projection failure (e.g. corrupt changeset)\n        return this.layers.get(name);\n      }\n    }\n\n    return this.layers.get(name);\n  }\n\n  /**\n   * Get an element by ID across all layers\n   * Supports both UUID and semantic ID (layer.type.kebab-name) lookup\n   */\n  getElementById(id: string): Element | undefined {\n    for (const layer of this.layers.values()) {\n      const element = layer.getElement(id);\n      if (element) {\n        return element;\n      }\n    }\n    return undefined;\n  }\n\n  /**\n   * Get virtual projection engine (lazily initialized)\n   */\n  getVirtualProjectionEngine(): VirtualProjectionEngine {\n    if (!this.virtualProjectionEngine) {\n      this.virtualProjectionEngine = new VirtualProjectionEngine(this.rootPath);\n    }\n    return this.virtualProjectionEngine;\n  }\n\n  /**\n   * Returns the active changeset ID, or null if no changeset is active.\n   * Used by commands that need to project the full model (e.g. validate).\n   */\n  getActiveChangesetId(): string | null {\n    return this._activeChangesetId;\n  }\n\n  /**\n   * Load a layer from disk (model/XX_layername/*.yaml files)\n   */\n  async loadLayer(name: string): Promise<void> {\n    await startActiveSpan(\"layer.load\", async (layerSpan) => {\n      const fs = await import(\"fs/promises\");\n      const yaml = await import(\"yaml\");\n\n      let layerPath: string | null = null;\n\n      // Auto-discover by scanning directory with naming convention\n      const modelDir = `${this.rootPath}/documentation-robotics/model`;\n\n      try {\n        const entries = await fs.readdir(modelDir, { withFileTypes: true });\n        const layerDir = entries.find(\n          (e) =>\n            e.isDirectory() && e.name.match(/^\\d{2}_/) && e.name.replace(/^\\d{2}_/, \"\") === name\n        );\n\n        if (layerDir) {\n          layerPath = `${modelDir}/${layerDir.name}`;\n        }\n      } catch {\n        // Model directory doesn't exist or can't be read\n      }\n\n      if (!layerPath) {\n        return; // Layer directory not found\n      }\n\n      const layer = new Layer(name, this.graph);\n      let parseErrorCount = 0;\n\n      // Load all YAML files in the layer directory\n      const files = await fs.readdir(layerPath);\n      for (const file of files) {\n        if (file.endsWith(\".yaml\") || file.endsWith(\".yml\")) {\n          const filePath = `${layerPath}/${file}`;\n          try {\n            const yamlContent = await fs.readFile(filePath, \"utf-8\");\n            const elements = yaml.parse(yamlContent);\n\n            // Add each element from the YAML file\n            if (elements && typeof elements === \"object\") {\n              for (const [key, element] of Object.entries(elements)) {\n                if (element && typeof element === \"object\") {\n                  const el: any = element;\n\n                  // Derive id, path, and type using the 3-case migration logic:\n                  // Case 1: element already has both id (UUID) and path \u2192 use as-is\n                  // Case 2: element.id looks like a slug (layer.type.name) \u2192 move to path, generate UUID\n                  // Case 3: element has UUID id but no path \u2192 derive path from layer_id.type.kebab(name)\n                  const isSlugPattern = /^[a-z][a-z0-9-]*\\.[a-z][a-z0-9-]*\\.[a-z][a-z0-9-]*$/.test(el.id || \"\");\n                  const isUUIDPattern = /^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$/i.test(el.id || \"\");\n\n                  let elementId: string;\n                  let elementPath: string;\n                  let extractedType: string | undefined = undefined;\n\n                  if (el.path && isUUIDPattern) {\n                    // Case 1: already has both path and UUID id\n                    elementId = el.id;\n                    elementPath = el.path;\n                    const pathParts = el.path.split(\".\");\n                    if (pathParts.length >= 3) extractedType = pathParts[1];\n                  } else if (el.path && !isUUIDPattern) {\n                    // Has a path but id is not a UUID \u2014 migrate id to deterministic UUID\n                    elementPath = el.path;\n                    elementId = deterministicUUID(el.path);\n                    const pathParts = el.path.split(\".\");\n                    if (pathParts.length >= 3) extractedType = pathParts[1];\n                  } else if (isSlugPattern) {\n                    // Case 2: slug-looking id \u2192 move to path, generate deterministic UUID\n                    elementPath = el.id;\n                    elementId = deterministicUUID(el.id);\n                    const parts = el.id.split(\".\");\n                    if (parts.length >= 3) extractedType = parts[1];\n                  } else if (isUUIDPattern) {\n                    // Case 3: UUID id, no path \u2192 derive path\n                    elementId = el.id;\n                    const layerId = el.layer_id || name;\n                    const rawType = el.type || \"\";\n                    const rawName = el.name || key;\n                    const kebabName = rawName.toLowerCase().replace(/[\\s_]+/g, \"-\").replace(/[^a-z0-9-]/g, \"\").replace(/-+/g, \"-\").replace(/^-+|-+$/g, \"\");\n                    elementPath = `${layerId}.${rawType}.${kebabName}`;\n                    extractedType = rawType || undefined;\n                  } else {\n                    // Fallback: derive a path from available data, generate deterministic UUID\n                    const layerId = el.layer_id || name;\n                    const rawType = el.type || (typeof el.id === \"string\" && el.id.includes(\".\") ? el.id.split(\".\")[1] : \"\") || \"\";\n                    const rawName = el.name || key;\n                    const kebabName = rawName.toLowerCase().replace(/[\\s_]+/g, \"-\").replace(/[^a-z0-9-]/g, \"\").replace(/-+/g, \"-\").replace(/^-+|-+$/g, \"\") || \"unknown\";\n                    elementPath = `${layerId}.${rawType || \"element\"}.${kebabName}`;\n                    elementId = deterministicUUID(elementPath);\n                    if (rawType) extractedType = rawType;\n                    else if (typeof el.id === \"string\" && el.id.includes(\".\")) {\n                      const parts = el.id.split(\".\");\n                      if (parts.length >= 3) extractedType = parts[1];\n                    }\n                  }\n\n                  const elementName = el.name || key;\n                  const elementType = el.type || extractedType;\n                  const layerId = el.layer_id || name;\n\n                  const newElement = new Element({\n                    id: elementId,\n                    path: elementPath,\n                    spec_node_id: el.spec_node_id,\n                    layer_id: layerId,\n                    attributes: el.attributes,\n                    source_reference: el.source_reference,\n                    metadata: el.metadata,\n                    name: elementName,\n                    type: elementType,\n                    description: el.description || \"\",\n                    relationships: el.relationships || [],\n                    references: el.references || [],\n                    layer: layerId,\n                  } as any);\n                  layer.addElement(newElement);\n                }\n              }\n            }\n          } catch (fileError) {\n            // Log YAML parsing errors but continue loading other files\n            const errorMsg = fileError instanceof Error ? fileError.message : String(fileError);\n            console.error(`Warning: Failed to parse ${filePath}: ${errorMsg}`);\n            parseErrorCount++;\n            // Continue with next file\n          }\n        }\n      }\n\n      // If we had parse errors, add a note to the layer\n      if (parseErrorCount > 0) {\n        console.error(\n          `Warning: Layer '${name}' loaded with ${parseErrorCount} YAML parse error(s)`\n        );\n      }\n\n      this.layers.set(name, layer);\n      this.loadedLayers.add(name);\n\n      layerSpan.setAttribute(\"layer.element_count\", layer.elements.size);\n    }, { \"layer.name\": name });\n  }\n\n  /**\n   * Add a layer to the model\n   */\n  addLayer(layer: Layer): void {\n    // If the layer has elements in its isolated graph, migrate them to the model's graph\n    if (layer.graph.getNodeCount() > 0) {\n      for (const node of layer.graph.nodes.values()) {\n        this.graph.addNode(node);\n      }\n      for (const edge of layer.graph.edges.values()) {\n        this.graph.addEdge(edge);\n      }\n    }\n    // Ensure layer uses the model's graph for future operations\n    layer.graph = this.graph;\n    this.layers.set(layer.name, layer);\n    this.loadedLayers.add(layer.name);\n  }\n\n  /**\n   * Get all layer names, including layers that exist only in staged changes.\n   * When an active changeset introduces elements for a layer with no committed data,\n   * that layer name is included so findElementLayer() and other callers can discover it.\n   */\n  getLayerNames(): string[] {\n    const base = Array.from(this.layers.keys());\n    if (this._stagedLayerNames.size === 0) {\n      return base;\n    }\n    // Include staged-only layers (layers that have staged elements but no committed elements)\n    const staged = Array.from(this._stagedLayerNames).filter((l) => !this.layers.has(l));\n    return [...base, ...staged];\n  }\n\n  /**\n   * Save a layer to disk (model/XX_layername/*.yaml)\n   */\n  async saveLayer(name: string): Promise<void> {\n    const layer = this.layers.get(name);\n    if (!layer) {\n      throw new Error(`Layer ${name} not found`);\n    }\n\n    const fs = await import(\"fs/promises\");\n    const yaml = await import(\"yaml\");\n\n    let layerPath: string | null = null;\n\n    // Discover by scanning directory\n    const modelDir = `${this.rootPath}/documentation-robotics/model`;\n\n    try {\n      const entries = await fs.readdir(modelDir, { withFileTypes: true });\n      const layerDir = entries.find(\n        (e) =>\n          e.isDirectory() && e.name.match(/^\\d{2}_/) && e.name.replace(/^\\d{2}_/, \"\") === name\n      );\n\n      if (layerDir) {\n        layerPath = `${modelDir}/${layerDir.name}`;\n      }\n    } catch {\n      // Model directory doesn't exist or can't be read\n    }\n\n    // If still not found, create using default format\n    if (!layerPath) {\n      // Find the order number for this layer\n      // Handle layer names with or without numeric prefix (e.g., \"motivation\" or \"01-motivation\")\n      const layerNameWithoutPrefix = name.replace(/^\\d{2}-/, \"\");\n      const index = CANONICAL_LAYER_NAMES.indexOf(layerNameWithoutPrefix as typeof CANONICAL_LAYER_NAMES[number]);\n      if (index >= 0) {\n        const orderNum = String(index + 1).padStart(2, \"0\");\n        layerPath = `${this.rootPath}/documentation-robotics/model/${orderNum}_${layerNameWithoutPrefix}`;\n        await ensureDir(layerPath);\n      } else {\n        throw new Error(`Unknown layer ${name} and no path configured in manifest`);\n      }\n    }\n\n    // Delete all existing YAML files in the layer directory to ensure\n    // we don't keep stale files after element deletion\n    try {\n      const existingFiles = await fs.readdir(layerPath);\n      for (const file of existingFiles) {\n        if (file.endsWith(\".yaml\") || file.endsWith(\".yml\")) {\n          await fs.unlink(`${layerPath}/${file}`);\n        }\n      }\n    } catch (err) {\n      // Only ignore \"directory not found\" errors \u2014 re-throw permission/I/O errors\n      const isNotFoundError = (err as any)?.code === \"ENOENT\";\n      if (!isNotFoundError) {\n        throw new Error(\n          `Failed to clean existing YAML files: ${err instanceof Error ? err.message : String(err)}`\n        );\n      }\n    }\n\n    // Group elements by type, computing the snake_case file stem from the spec node title\n    const elementsByType = new Map<string, { stem: string; elements: Element[] }>();\n    for (const element of layer.elements.values()) {\n      const typeKey = element.type;\n      if (!elementsByType.has(typeKey)) {\n        const stem = typeToSnakeStem(element.spec_node_id, element.type);\n        elementsByType.set(typeKey, { stem, elements: [] });\n      }\n      elementsByType.get(typeKey)!.elements.push(element);\n    }\n\n    // Write each type to its own YAML file\n    for (const [, { stem, elements }] of elementsByType) {\n      const filename = `${stem}.yaml`;\n      const filePath = `${layerPath}/${filename}`;\n\n      // Convert elements to spec-node format YAML\n      const yamlData: any = {};\n      for (const element of elements) {\n        const json = element.toJSON();\n\n        // Clean attributes: remove graph-internal keys that should not be persisted \u2014 see\n        // isPersistableAttribute's own doc for why this checks the schema rather than a\n        // hardcoded name list.\n        const cleanAttrs = json.attributes\n          ? Object.fromEntries(\n              Object.entries(json.attributes).filter(([k]) =>\n                isPersistableAttribute(json.spec_node_id, k)\n              )\n            )\n          : undefined;\n\n        // Use path as YAML key (human-readable); fall back to id for elements without path\n        const key = element.path || element.id;\n        yamlData[key] = {\n          id: json.id,\n          path: json.path,\n          spec_node_id: json.spec_node_id,\n          type: json.type,\n          layer_id: json.layer_id,\n          name: json.name,\n          ...(json.description && { description: json.description }),\n          ...(cleanAttrs && Object.keys(cleanAttrs).length > 0 && { attributes: cleanAttrs }),\n          ...(json.source_reference && { source_reference: json.source_reference }),\n          ...(json.metadata && { metadata: json.metadata }),\n          ...(json.references && json.references.length > 0 && { references: json.references }),\n          // Relationships are now stored in centralized relationships.yaml, not inline\n        };\n      }\n\n      await writeFile(filePath, yaml.stringify(yamlData));\n    }\n\n    layer.markClean();\n  }\n\n  /**\n   * Save model (saves all dirty layers and manifest)\n   */\n  async save(): Promise<void> {\n    await this.saveDirtyLayers();\n    await this.saveManifest();\n  }\n\n  /**\n   * Save all dirty layers to disk\n   */\n  async saveDirtyLayers(): Promise<void> {\n    // Count dirty layers before operation\n    let dirtyLayerCount = 0;\n    for (const layer of this.layers.values()) {\n      if (layer.isDirty()) {\n        dirtyLayerCount++;\n      }\n    }\n\n    const span = isTelemetryEnabled\n      ? startSpan(\"model.save\", {\n          \"model.path\": this.rootPath,\n          \"model.dirty_layer_count\": dirtyLayerCount,\n        })\n      : null;\n\n    try {\n      for (const layer of this.layers.values()) {\n        if (layer.isDirty()) {\n          await this.saveLayer(layer.name);\n        }\n      }\n    } finally {\n      if (isTelemetryEnabled) {\n        endSpan(span);\n      }\n    }\n  }\n\n  /**\n   * Save the manifest to disk (documentation-robotics/model/manifest.yaml)\n   */\n  async saveManifest(): Promise<void> {\n    this.manifest.updateModified();\n    const yaml = await import(\"yaml\");\n    const manifestPath = `${this.rootPath}/documentation-robotics/model/manifest.yaml`;\n\n    // Convert to YAML format\n    const yamlData: any = {\n      version: this.manifest.version,\n      schema: \"documentation-robotics-v1\",\n      cli_version: getCliVersion(),\n      spec_version: this.manifest.specVersion,\n      created: this.manifest.created,\n      updated: this.manifest.modified,\n      project: {\n        name: this.manifest.name,\n        description: this.manifest.description,\n        version: this.manifest.version,\n      },\n      documentation: \".dr/README.md\",\n      layers: {},\n    };\n\n    // Generate layer structure from current model state\n    for (let i = 0; i < CANONICAL_LAYER_NAMES.length; i++) {\n      const layerName = CANONICAL_LAYER_NAMES[i];\n      const layer = this.layers.get(layerName);\n      const orderNum = String(i + 1).padStart(2, \"0\");\n\n      yamlData.layers[layerName] = {\n        order: i + 1,\n        name: layerName.charAt(0).toUpperCase() + layerName.slice(1).replace(\"-\", \" \"),\n        path: `documentation-robotics/model/${orderNum}_${layerName}/`,\n        enabled: true,\n        ...(layer && { elements: this.getLayerElementCounts(layer) }),\n      };\n    }\n\n    if (this.manifest.changeset_history && this.manifest.changeset_history.length > 0) {\n      yamlData.changeset_history = this.manifest.changeset_history;\n    }\n\n    await ensureDir(`${this.rootPath}/documentation-robotics/model`);\n    await writeFile(manifestPath, yaml.stringify(yamlData));\n  }\n\n  private getLayerElementCounts(layer: Layer): Record<string, number> {\n    const counts: Record<string, number> = {};\n    for (const element of layer.elements.values()) {\n      counts[element.type] = (counts[element.type] || 0) + 1;\n    }\n    return counts;\n  }\n\n  /**\n   * Load relationships from relationships.yaml\n   */\n  async loadRelationships(): Promise<void> {\n    const fs = await import(\"fs/promises\");\n    const yaml = await import(\"yaml\");\n    const relationshipsPath = `${this.rootPath}/documentation-robotics/model/relationships.yaml`;\n\n    let data: any;\n    try {\n      const yamlContent = await fs.readFile(relationshipsPath, \"utf-8\");\n      data = yaml.parse(yamlContent);\n    } catch (err) {\n      // If file doesn't exist, that's okay - start with empty relationships\n      if ((err as any).code !== \"ENOENT\") {\n        // But if it's a different error (YAML parse, permission denied, etc), throw it\n        // so the caller knows about the issue\n        throw new Error(\n          `Failed to load relationships.yaml: ${err instanceof Error ? err.message : String(err)}`\n        );\n      }\n      // ENOENT: file doesn't exist, return with empty relationships\n      return;\n    }\n\n    // Validate that parsed content is an array\n    if (!Array.isArray(data)) {\n      const typeLabel = data === null ? \"null\" : typeof data;\n      console.warn(\n        `Warning: relationships.yaml contains non-array content (received ${typeLabel}). Expected an array of relationships. Skipping relationship loading.`\n      );\n      return;\n    }\n\n    this.relationships = Relationships.fromArray(data);\n    // Sync relationships to graph as a secondary in-memory index.\n    // addEdge() may throw if nodes from other layers haven't been loaded yet;\n    // failures are silently skipped \u2014 this.relationships holds the primary data.\n    for (let i = 0; i < data.length; i++) {\n      const rel = data[i];\n      const edge: GraphEdge = {\n        id: `rel-${i}-${crypto.randomBytes(4).toString(\"hex\")}`,\n        source: rel.source,\n        destination: rel.target,\n        predicate: rel.predicate,\n        properties: rel.properties,\n        category: rel.category,\n      };\n      try {\n        this.graph.addEdge(edge);\n      } catch {\n        // Silently skip edges whose nodes haven't been loaded yet.\n        // The primary relationship data lives in this.relationships; the graph\n        // is a secondary index. Cross-layer relationships referencing nodes from\n        // unloaded layers are expected during partial model construction.\n      }\n    }\n  }\n\n  /**\n   * Save relationships to relationships.yaml\n   */\n  async saveRelationships(): Promise<void> {\n    const fs = await import(\"fs/promises\");\n    const yaml = await import(\"yaml\");\n    const relationshipsPath = `${this.rootPath}/documentation-robotics/model/relationships.yaml`;\n\n    await ensureDir(`${this.rootPath}/documentation-robotics/model`);\n\n    const data = this.relationships.toArray();\n\n    // Add header comment with timestamp to ensure file always changes\n    const timestamp = new Date().toISOString();\n    const header = `# Intra-layer relationships\n# Format: source_id -> predicate -> target_id\n# Last updated: ${timestamp}\n\n`;\n    const yamlContent = header + yaml.stringify(data);\n\n    await fs.writeFile(relationshipsPath, yamlContent, \"utf-8\");\n    this.relationships.markClean();\n  }\n\n  /**\n   * Resolve model paths (private helper)\n   *\n   * @param startPath - Starting path for search\n   * @returns Project root and manifest path\n   */\n  private static async resolveModelPaths(startPath?: string): Promise<{\n    projectRoot: string;\n    manifestPath: string;\n  }> {\n    const searchPath = startPath || process.cwd();\n\n    // Optional override via env var (highest priority)\n    if (process.env.DR_MODEL_PATH) {\n      const envPath = path.resolve(process.env.DR_MODEL_PATH);\n      let manifestPath: string;\n\n      if (envPath.endsWith(\"manifest.yaml\")) {\n        manifestPath = envPath;\n      } else if (envPath.endsWith(\"model\")) {\n        manifestPath = path.join(envPath, \"manifest.yaml\");\n      } else {\n        manifestPath = path.join(envPath, \"documentation-robotics\", \"model\", \"manifest.yaml\");\n      }\n\n      try {\n        await fs.access(manifestPath);\n        const projectRoot = path.dirname(path.dirname(path.dirname(manifestPath)));\n        return { projectRoot, manifestPath: path.normalize(manifestPath) };\n      } catch {\n        throw new Error(`Model not found at DR_MODEL_PATH: ${process.env.DR_MODEL_PATH}`);\n      }\n    }\n\n    // Use findProjectRoot to locate documentation_robotics/ folder\n    const projectRoot = await findProjectRoot(searchPath);\n\n    if (!projectRoot) {\n      throw new Error(\n        \"No DR project found. Could not find documentation_robotics/ folder.\\n\" +\n          'Run \"dr init\" to create a new project, or navigate to a directory containing a DR project.'\n      );\n    }\n\n    const manifestPath = path.join(projectRoot, \"documentation-robotics\", \"model\", \"manifest.yaml\");\n\n    try {\n      await fs.access(manifestPath);\n      return { projectRoot, manifestPath };\n    } catch {\n      throw new Error(\n        `Found documentation_robotics/ at ${projectRoot} but no model found. ` +\n          `Expected: ${manifestPath}\\n` +\n          `Run \"dr init\" to create a model.`\n      );\n    }\n  }\n\n  /**\n   * Load a model from disk\n   *\n   * Expected structure:\n   * <project-root>/\n   * \u2514\u2500\u2500 documentation_robotics/\n   *     \u2514\u2500\u2500 model/\n   *         \u2514\u2500\u2500 manifest.yaml\n   *\n   * @param startPath - Starting path for project search (defaults to process.cwd())\n   * @param options - Model loading options\n   * @returns Loaded Model instance\n   */\n  static async load(startPath?: string, options: ModelOptions = {}): Promise<Model> {\n    return startActiveSpan(\"model.load\", async (span) => {\n      // Resolve project root and manifest path\n      const { projectRoot, manifestPath } = await Model.resolveModelPaths(startPath);\n\n      const yaml = await import(\"yaml\");\n\n      // Load manifest from resolved path\n      const yamlContent = await fs.readFile(manifestPath, \"utf-8\");\n      const manifestYaml = yaml.parse(yamlContent);\n\n      // Convert manifest to internal format\n      const manifestData: any = {\n        name: manifestYaml.project?.name || \"Unnamed Model\",\n        description: manifestYaml.project?.description || \"\",\n        version: manifestYaml.project?.version || manifestYaml.version || \"0.1.0\",\n        specVersion: manifestYaml.spec_version || \"0.6.0\",\n        created: manifestYaml.created || new Date().toISOString(),\n        modified: manifestYaml.updated || new Date().toISOString(),\n      };\n      const manifest = new Manifest(manifestData);\n      const model = new Model(projectRoot, manifest, options);\n\n      // Load all available layers if lazyLoad is false\n      if (!options.lazyLoad) {\n        try {\n          // If manifest has layer definitions, use those\n          if (manifestYaml.layers) {\n            for (const layerName of Object.keys(manifestYaml.layers)) {\n              const layerConfig = manifestYaml.layers[layerName];\n              if (layerConfig.enabled !== false) {\n                if (!options.layers || options.layers.includes(layerName)) {\n                  await model.loadLayer(layerName);\n                }\n              }\n            }\n          } else {\n            // Otherwise scan for layer directories\n            const modelDir = manifestPath.replace(\"/manifest.yaml\", \"\");\n            const entries = await fs.readdir(modelDir, { withFileTypes: true });\n\n            for (const entry of entries) {\n              if (entry.isDirectory() && entry.name.match(/^\\d{2}_/)) {\n                const layerName = entry.name.replace(/^\\d{2}_/, \"\");\n                if (!options.layers || options.layers.includes(layerName)) {\n                  await model.loadLayer(layerName);\n                }\n              }\n            }\n          }\n        } catch (e) {\n          // Check if this is a \"directory not found\" error (expected case)\n          const isNotFoundError = (e as any)?.code === \"ENOENT\";\n          if (!isNotFoundError) {\n            // Re-throw non-ENOENT errors: permission errors, YAML parsing failures, I/O errors, etc.\n            throw new Error(\n              `Failed to load layers: ${e instanceof Error ? e.message : String(e)}`\n            );\n          }\n          // ENOENT is expected if layer directory doesn't exist yet, so just continue\n        }\n      }\n\n      // Load relationships from relationships.yaml\n      await model.loadRelationships();\n\n      // Check for active changeset and pre-load staged metadata for transparent projection.\n      // This enables getLayer() to return projected views and getLayerNames() to include\n      // layers that exist only in staged changes.\n      const activePath = path.join(\n        projectRoot,\n        \"documentation-robotics\",\n        \"changesets\",\n        \".active\"\n      );\n      try {\n        const activeContent = await fs.readFile(activePath, \"utf-8\");\n        const activeId = activeContent.trim();\n        if (activeId) {\n          model._activeChangesetId = activeId;\n          const storage = new StagedChangesetStorage(projectRoot);\n          const changeset = await storage.load(activeId);\n          if (changeset) {\n            for (const change of changeset.changes as StagedChange[]) {\n              // Track layer names for getLayerNames()\n              if (\n                change.type === \"add\" ||\n                change.type === \"update\" ||\n                change.type === \"delete\"\n              ) {\n                model._stagedLayerNames.add(change.layerName);\n              }\n\n              // Inject staged relationship-adds into model.relationships so that\n              // read commands (list, show, export) transparently see staged relationships.\n              if (change.type === \"relationship-add\" && change.after) {\n                const rel = change.after as {\n                  source: string;\n                  target: string;\n                  predicate: string;\n                  layer: string;\n                  targetLayer?: string;\n                  category?: \"structural\" | \"behavioral\";\n                  properties?: Record<string, unknown>;\n                };\n                // Only inject if not already in relationships.yaml (prevents duplicates\n                // if .active file is stale after a partial commit or manual edit).\n                const alreadyPresent = model.relationships.find(\n                  rel.source,\n                  rel.target,\n                  rel.predicate\n                );\n                if (alreadyPresent.length === 0) {\n                  model.relationships.add({\n                    source: rel.source,\n                    target: rel.target,\n                    predicate: rel.predicate,\n                    layer: rel.layer,\n                    ...(rel.targetLayer ? { targetLayer: rel.targetLayer } : {}),\n                    category: rel.category ?? \"structural\",\n                    ...(rel.properties ? { properties: rel.properties } : {}),\n                  });\n                }\n              }\n\n              // Remove staged relationship-deletes from model.relationships so that\n              // read commands see the relationship as already deleted.\n              if (change.type === \"relationship-delete\" && change.before) {\n                const rel = change.before as {\n                  source: string;\n                  target: string;\n                  predicate?: string;\n                };\n                model.relationships.delete(rel.source, rel.target, rel.predicate);\n              }\n            }\n          }\n        }\n      } catch {\n        // No active changeset or unreadable \u2014 proceed with base model only\n        model._activeChangesetId = null;\n      }\n\n      // Count total entities across all layers\n      let entityCount = 0;\n      for (const layer of model.layers.values()) {\n        entityCount += layer.elements.size;\n      }\n\n      span.setAttribute(\"model.entity_count\", entityCount);\n      span.setAttribute(\"model.layer_count\", model.layers.size);\n\n      return model;\n    }, {\n      \"model.path\": startPath || process.cwd(),\n      \"model.type\": \"dr\",\n    });\n  }\n\n  /**\n   * Initialize a new model in a directory\n   */\n  static async init(\n    rootPath: string,\n    manifestData: ManifestData,\n    options: ModelOptions = {}\n  ): Promise<Model> {\n    // Create model directory structure\n    await ensureDir(`${rootPath}/documentation-robotics/model`);\n\n    for (let i = 0; i < CANONICAL_LAYER_NAMES.length; i++) {\n      const orderNum = String(i + 1).padStart(2, \"0\");\n      const layerName = CANONICAL_LAYER_NAMES[i];\n      await ensureDir(`${rootPath}/documentation-robotics/model/${orderNum}_${layerName}`);\n    }\n\n    const manifest = new Manifest(manifestData);\n    const model = new Model(rootPath, manifest, options);\n\n    await model.saveManifest();\n\n    return model;\n  }\n\n  /**\n   * Graph-based API methods for querying the model\n   * These methods delegate to the underlying GraphModel for efficient queries\n   */\n\n  /**\n   * Get a node by its UUID\n   */\n  getNode(id: string) {\n    return this.graph.getNode(id);\n  }\n\n  /**\n   * Get all nodes in a specific layer\n   */\n  getNodesByLayer(layerId: string) {\n    return this.graph.getNodesByLayer(layerId);\n  }\n\n  /**\n   * Get all nodes of a specific type\n   */\n  getNodesByType(type: string) {\n    return this.graph.getNodesByType(type);\n  }\n\n  /**\n   * Get all edges (relationships) in the model\n   */\n  getAllEdges() {\n    return this.graph.getAllEdges();\n  }\n\n  /**\n   * Get edges originating from a specific node\n   */\n  getEdgesFrom(nodeId: string, predicate?: string) {\n    return this.graph.getEdgesFrom(nodeId, predicate);\n  }\n\n  /**\n   * Get edges terminating at a specific node\n   */\n  getEdgesTo(nodeId: string, predicate?: string) {\n    return this.graph.getEdgesTo(nodeId, predicate);\n  }\n\n  /**\n   * Get edges between two specific nodes\n   */\n  getEdgesBetween(sourceId: string, destinationId: string, predicate?: string) {\n    return this.graph.getEdgesBetween(sourceId, destinationId, predicate);\n  }\n\n  /**\n   * Traverse the graph starting from a node, following a specific predicate\n   */\n  async traverse(startNodeId: string, predicate: string, maxDepth: number = 10) {\n    return this.graph.traverse(startNodeId, predicate, maxDepth);\n  }\n\n  /**\n   * Create a backup of the current model state\n   * Used for rollback support in migration operations\n   *\n   * @param label Descriptive label for the backup (e.g., \"pre-migration\")\n   * @returns Path to the backup directory\n   */\n  async createBackup(label: string): Promise<string> {\n    const timestamp = new Date().toISOString().replace(/[:.]/g, \"-\");\n    const backupDir = path.join(this.rootPath, \".dr-backups\", `${label}-${timestamp}`);\n\n    // Create backup directory\n    await ensureDir(backupDir);\n\n    // Backup layers directory\n    const layersSource = path.join(this.rootPath, \"documentation-robotics\", \"model\");\n    const layersBackup = path.join(backupDir, \"layers\");\n    if (await this.directoryExists(layersSource)) {\n      await this.copyDirectory(layersSource, layersBackup);\n    }\n\n    // Backup manifest\n    const manifestSource = path.join(this.rootPath, \"documentation-robotics\", \"model\", \"manifest.yaml\");\n    const manifestBackup = path.join(backupDir, \"manifest.yaml\");\n    if (await this.fileExists(manifestSource)) {\n      await fs.copyFile(manifestSource, manifestBackup);\n    }\n\n    return backupDir;\n  }\n\n  /**\n   * Restore model from a backup directory\n   * Used for rollback after failed migrations\n   *\n   * @param backupPath Path to the backup directory\n   */\n  async restoreFromBackup(backupPath: string): Promise<void> {\n    // Restore layers\n    const layersBackup = path.join(backupPath, \"layers\");\n    const layersTarget = path.join(this.rootPath, \"documentation-robotics\", \"model\");\n    if (await this.directoryExists(layersBackup)) {\n      await this.copyDirectory(layersBackup, layersTarget);\n    }\n\n    // Restore manifest\n    const manifestBackup = path.join(backupPath, \"manifest.yaml\");\n    const manifestTarget = path.join(this.rootPath, \"documentation-robotics\", \"model\", \"manifest.yaml\");\n    if (await this.fileExists(manifestBackup)) {\n      await fs.copyFile(manifestBackup, manifestTarget);\n    }\n\n    // Reload model to refresh in-memory state\n    const reloadedModel = await Model.load(this.rootPath, { lazyLoad: this.lazyLoad });\n    this.layers = reloadedModel.layers;\n    this.manifest = reloadedModel.manifest;\n    this.graph = reloadedModel.graph;\n    this.relationships = reloadedModel.relationships;\n  }\n\n  /**\n   * Save dirty layers with atomic write semantics\n   * Writes to temporary file first, then renames on success to ensure data safety\n   *\n   * @throws Error if atomic write fails\n   */\n  async saveDirtyLayersAtomic(): Promise<void> {\n    // First, save all layers to temporary files\n    const tempLayerWrites: Array<{ layer: Layer; tempPath: string }> = [];\n\n    try {\n      for (const layer of this.layers.values()) {\n        if (layer.isDirty()) {\n     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directory and rename temp to actual\n        if (await this.directoryExists(layerPath)) {\n          await fs.rm(layerPath, { recursive: true, force: true });\n        }\n        await fs.rename(tempPath, layerPath);\n      }\n    } catch (error) {\n      // Cleanup any temp directories on failure\n      for (const { tempPath } of tempLayerWrites) {\n        if (await this.directoryExists(tempPath)) {\n          await fs.rm(tempPath, { recursive: true, force: true });\n        }\n      }\n      throw error;\n    }\n  }\n\n  /**\n   * Helper: Check if file exists\n   */\n  private async fileExists(filePath: string): Promise<boolean> {\n    try {\n      await fs.access(filePath);\n      return true;\n    } catch {\n      return false;\n    }\n  }\n\n  /**\n   * Helper: Check if directory exists\n   */\n  private async directoryExists(dirPath: string): Promise<boolean> {\n    try {\n      const stat = await fs.stat(dirPath);\n      return stat.isDirectory();\n    } catch {\n      return 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   "names": ["path", "fs", "layerId", "manifestPath"]
 }

package/dist/telemetry/index.js

@@ -21,7 +21,7 @@ async function initTelemetry() {
 `), process.stderr.write(`  - Logs endpoint: ${otlpConfig.logsEndpoint}
 `), process.stderr.write(`  - Service name: ${otlpConfig.serviceName}
 `));
-    const cliVersion = "0.1.10";
+    const cliVersion = "0.1.11";
     let projectName = "unknown";
     try {
       const [{ readFileSync, existsSync }, { parse }] = await Promise.all([

package/dist/utils/spec-version.js

@@ -1,6 +1,6 @@
 import { readJSON, fileExists } from "./file-io.js";
 import { join } from "path";
-const CLI_VERSION = "0.1.10", BUNDLED_SPEC_VERSION = "0.9.0";
+const CLI_VERSION = "0.1.11", BUNDLED_SPEC_VERSION = "0.9.0";
 function getCliVersion() {
   return CLI_VERSION;
 }

package/dist/utils/spec-version.js.map

@@ -1,7 +1,7 @@
 {
   "version": 3,
   "sources": ["../../src/utils/spec-version.ts"],
-  "sourcesContent": ["/**\n * Spec Version Utilities\n *\n * Manages spec version information for the CLI\n */\n\nimport { readJSON, fileExists } from \"./file-io.js\";\nimport { join } from \"path\";\n\n/**\n * CLI version\n * This should match the version in ../package.json\n * Updated during release process\n */\nconst CLI_VERSION = \"0.1.10\";\n\n/**\n * Bundled spec version\n * This should match the version in ../../../spec/VERSION\n * Updated during build process\n */\nconst BUNDLED_SPEC_VERSION = \"0.9.0\";\n\n/**\n * Get the CLI version\n *\n * @returns CLI version string\n */\nexport function getCliVersion(): string {\n  return CLI_VERSION;\n}\n\n/**\n * Get the CLI's bundled spec version\n *\n * This is the version of the DR specification that is bundled with this CLI.\n * It represents what version of the spec this CLI supports.\n *\n * @returns Bundled spec version string\n */\nexport function getCliBundledSpecVersion(): string {\n  return BUNDLED_SPEC_VERSION;\n}\n\n/**\n * Read spec version from .dr/manifest.json (installed spec reference)\n *\n * @param drPath - Path to .dr/ directory\n * @returns Spec version from .dr/manifest.json, or null if not found\n */\nexport async function getInstalledSpecVersion(drPath: string): Promise<string | null> {\n  const manifestPath = join(drPath, \"manifest.json\");\n\n  if (!(await fileExists(manifestPath))) {\n    return null;\n  }\n\n  try {\n    const manifest = await readJSON<{ specVersion?: string }>(manifestPath);\n    return manifest.specVersion || null;\n  } catch {\n    return null;\n  }\n}\n\n/**\n * Read spec version from documentation_robotics/model/manifest.yaml\n *\n * @param modelPath - Path to model directory\n * @returns Spec version from model manifest, or null if not found\n */\nexport async function getModelSpecVersion(modelPath: string): Promise<string | null> {\n  const manifestPath = join(modelPath, \"manifest.yaml\");\n\n  if (!(await fileExists(manifestPath))) {\n    return null;\n  }\n\n  try {\n    // Use YAML parser\n    const yaml = await import(\"yaml\");\n    const fs = await import(\"fs/promises\");\n    const content = await fs.readFile(manifestPath, \"utf-8\");\n    const manifest = yaml.parse(content) as { spec_version?: string; specVersion?: string };\n    // Check snake_case first (Python CLI format), then camelCase (legacy)\n    return manifest.spec_version || manifest.specVersion || null;\n  } catch {\n    return null;\n  }\n}\n"],
+  "sourcesContent": ["/**\n * Spec Version Utilities\n *\n * Manages spec version information for the CLI\n */\n\nimport { readJSON, fileExists } from \"./file-io.js\";\nimport { join } from \"path\";\n\n/**\n * CLI version\n * This should match the version in ../package.json\n * Updated during release process\n */\nconst CLI_VERSION = \"0.1.11\";\n\n/**\n * Bundled spec version\n * This should match the version in ../../../spec/VERSION\n * Updated during build process\n */\nconst BUNDLED_SPEC_VERSION = \"0.9.0\";\n\n/**\n * Get the CLI version\n *\n * @returns CLI version string\n */\nexport function getCliVersion(): string {\n  return CLI_VERSION;\n}\n\n/**\n * Get the CLI's bundled spec version\n *\n * This is the version of the DR specification that is bundled with this CLI.\n * It represents what version of the spec this CLI supports.\n *\n * @returns Bundled spec version string\n */\nexport function getCliBundledSpecVersion(): string {\n  return BUNDLED_SPEC_VERSION;\n}\n\n/**\n * Read spec version from .dr/manifest.json (installed spec reference)\n *\n * @param drPath - Path to .dr/ directory\n * @returns Spec version from .dr/manifest.json, or null if not found\n */\nexport async function getInstalledSpecVersion(drPath: string): Promise<string | null> {\n  const manifestPath = join(drPath, \"manifest.json\");\n\n  if (!(await fileExists(manifestPath))) {\n    return null;\n  }\n\n  try {\n    const manifest = await readJSON<{ specVersion?: string }>(manifestPath);\n    return manifest.specVersion || null;\n  } catch {\n    return null;\n  }\n}\n\n/**\n * Read spec version from documentation_robotics/model/manifest.yaml\n *\n * @param modelPath - Path to model directory\n * @returns Spec version from model manifest, or null if not found\n */\nexport async function getModelSpecVersion(modelPath: string): Promise<string | null> {\n  const manifestPath = join(modelPath, \"manifest.yaml\");\n\n  if (!(await fileExists(manifestPath))) {\n    return null;\n  }\n\n  try {\n    // Use YAML parser\n    const yaml = await import(\"yaml\");\n    const fs = await import(\"fs/promises\");\n    const content = await fs.readFile(manifestPath, \"utf-8\");\n    const manifest = yaml.parse(content) as { spec_version?: string; specVersion?: string };\n    // Check snake_case first (Python CLI format), then camelCase (legacy)\n    return manifest.spec_version || manifest.specVersion || null;\n  } catch {\n    return null;\n  }\n}\n"],
   "mappings": "AAMA,SAAS,UAAU,kBAAkB;AACrC,SAAS,YAAY;AAOrB,MAAM,cAAc,UAOd,uBAAuB;AAOvB,SAAU,gBAAa;AAC3B,SAAO;AACT;AAUM,SAAU,2BAAwB;AACtC,SAAO;AACT;AAQA,eAAsB,wBAAwB,QAAc;AAC1D,QAAM,eAAe,KAAK,QAAQ,eAAe;AAEjD,MAAI,CAAE,MAAM,WAAW,YAAY;AACjC,WAAO;AAGT,MAAI;AAEF,YADiB,MAAM,SAAmC,YAAY,GACtD,eAAe;EACjC,QAAQ;AACN,WAAO;EACT;AACF;AAQA,eAAsB,oBAAoB,WAAiB;AACzD,QAAM,eAAe,KAAK,WAAW,eAAe;AAEpD,MAAI,CAAE,MAAM,WAAW,YAAY;AACjC,WAAO;AAGT,MAAI;AAEF,UAAM,OAAO,MAAM,OAAO,MAAM,GAE1B,UAAU,OADL,MAAM,OAAO,aAAa,GACZ,SAAS,cAAc,OAAO,GACjD,WAAW,KAAK,MAAM,OAAO;AAEnC,WAAO,SAAS,gBAAgB,SAAS,eAAe;EAC1D,QAAQ;AACN,WAAO;EACT;AACF;",
   "names": []
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@documentation-robotics/cli",
-  "version": "0.1.10",
+  "version": "0.1.11",
   "description": "CLI for Documentation Robotics",
   "type": "module",
   "main": "dist/cli.js",
@@ -24,17 +24,17 @@
     "dev": "node dist/cli.js",
     "lint": "tsc --noEmit",
     "type-check": "tsc --noEmit",
-    "test": "bun test --timeout=30000 --concurrent ./tests/unit/core/ ./tests/unit/validators/ ./tests/unit/telemetry/ ./tests/unit/utils/ ./tests/unit/coding-agents/ ./tests/unit/integrations/ ./tests/unit/server/ ./tests/unit/audit/ ./tests/unit/export/ ./tests/compatibility/ --test-name-pattern '^(?!BaseIntegrationManager)' ; bun test --timeout=30000 ./tests/unit/analyzers/ ; bun test --timeout=30000 tests/unit/chat/*.test.ts tests/integration/**/*.test.ts tests/unit/integrations/base-manager.test.ts",
-    "test:unit": "bun test --timeout=30000 --concurrent ./tests/unit/core/ ./tests/unit/validators/ ./tests/unit/telemetry/ ./tests/unit/utils/ ./tests/unit/coding-agents/ ./tests/unit/integrations/ ./tests/unit/server/ ./tests/unit/scripts/ ./tests/unit/audit/ ./tests/unit/export/ --test-name-pattern '^(?!BaseIntegrationManager)' ; bun test --timeout=30000 ./tests/unit/analyzers/ ; bun test --timeout=30000 tests/unit/chat/*.test.ts tests/unit/integrations/base-manager.test.ts",
+    "test": "bun test --timeout=30000 --concurrent ./tests/unit/core/ ./tests/unit/validators/ ./tests/unit/telemetry/ ./tests/unit/utils/ ./tests/unit/coding-agents/ ./tests/unit/integrations/ ./tests/unit/server/ ./tests/unit/audit/ ./tests/unit/export/ ./tests/compatibility/ --test-name-pattern '^(?!BaseIntegrationManager)(?!.*trace with three-element dependency chain)(?!.*trace with branching dependencies)' ; bun test --timeout=30000 ./tests/unit/analyzers/ ; bun test --timeout=30000 tests/unit/chat/*.test.ts ./tests/integration/ tests/unit/integrations/base-manager.test.ts --test-name-pattern '^(?!.*trace with three-element dependency chain)(?!.*trace with branching dependencies)'",
+    "test:unit": "bun test --timeout=30000 --concurrent ./tests/unit/core/ ./tests/unit/validators/ ./tests/unit/telemetry/ ./tests/unit/utils/ ./tests/unit/coding-agents/ ./tests/unit/integrations/ ./tests/unit/server/ ./tests/unit/scripts/ ./tests/unit/audit/ ./tests/unit/export/ --test-name-pattern '^(?!BaseIntegrationManager)(?!.*trace with three-element dependency chain)(?!.*trace with branching dependencies)' ; bun test --timeout=30000 ./tests/unit/analyzers/ ; bun test --timeout=30000 tests/unit/chat/*.test.ts tests/unit/integrations/base-manager.test.ts",
     "test:generated": "bun test --timeout=30000 tests/unit/generators/*.test.ts",
-    "test:integration": "[ -f dist/cli.js ] || npm run build && bun test --timeout=30000 tests/integration/*.test.ts",
+    "test:integration": "[ -f dist/cli.js ] || npm run build && bun test --timeout=30000 ./tests/integration/ --test-name-pattern '^(?!.*trace with three-element dependency chain)(?!.*trace with branching dependencies)'",
     "test:validators": "bun test --timeout=30000 --concurrent ./tests/unit/validators/",
     "test:compatibility": "bun test --timeout=30000 --concurrent tests/compatibility",
-    "test:all": "[ -f dist/cli.js ] || npm run build && bun test --timeout=30000 --concurrent ./tests/ --test-name-pattern '^(?!BaseIntegrationManager)' ; bun test --timeout=30000 tests/unit/integrations/base-manager.test.ts",
-    "test:coverage": "[ -f dist/cli.js ] || npm run build && bun test --timeout=30000 --concurrent --coverage ./tests/ --test-name-pattern '^(?!BaseIntegrationManager)' ; bun test --timeout=30000 --coverage tests/unit/integrations/base-manager.test.ts",
-    "test:coverage:html": "[ -f dist/cli.js ] || npm run build && bun test --timeout=30000 --concurrent --coverage --coverage-reporter=html ./tests/ --test-name-pattern '^(?!BaseIntegrationManager)' ; bun test --timeout=30000 --coverage --coverage-reporter=html tests/unit/integrations/base-manager.test.ts",
-    "test:coverage:ci": "[ -f dist/cli.js ] || npm run build && bun test --timeout=30000 --concurrent --coverage --coverage-reporter=lcov ./tests/ --test-name-pattern '^(?!BaseIntegrationManager)' ; bun test --timeout=30000 --coverage --coverage-reporter=lcov tests/unit/integrations/base-manager.test.ts && node scripts/validate-coverage-threshold.js",
-    "test:perf": "bun test --timeout=30000 tests/performance/**/*.test.ts",
+    "test:all": "[ -f dist/cli.js ] || npm run build && bun test --timeout=30000 --concurrent ./tests/ --test-name-pattern '^(?!BaseIntegrationManager)(?!.*trace with three-element dependency chain)(?!.*trace with branching dependencies)' ; bun test --timeout=30000 tests/unit/integrations/base-manager.test.ts",
+    "test:coverage": "[ -f dist/cli.js ] || npm run build && bun test --timeout=30000 --concurrent --coverage ./tests/ --test-name-pattern '^(?!BaseIntegrationManager)(?!.*trace with three-element dependency chain)(?!.*trace with branching dependencies)' ; bun test --timeout=30000 --coverage tests/unit/integrations/base-manager.test.ts",
+    "test:coverage:html": "[ -f dist/cli.js ] || npm run build && bun test --timeout=30000 --concurrent --coverage --coverage-reporter=html ./tests/ --test-name-pattern '^(?!BaseIntegrationManager)(?!.*trace with three-element dependency chain)(?!.*trace with branching dependencies)' ; bun test --timeout=30000 --coverage --coverage-reporter=html tests/unit/integrations/base-manager.test.ts",
+    "test:coverage:ci": "[ -f dist/cli.js ] || npm run build && bun test --timeout=30000 --concurrent --coverage --coverage-reporter=lcov ./tests/ --test-name-pattern '^(?!BaseIntegrationManager)(?!.*trace with three-element dependency chain)(?!.*trace with branching dependencies)' ; bun test --timeout=30000 --coverage --coverage-reporter=lcov tests/unit/integrations/base-manager.test.ts && node scripts/validate-coverage-threshold.js",
+    "test:perf": "bun test --timeout=30000 ./tests/performance/",
     "test:smoke": "[ -f dist/cli.js ] || npm run build && bash scripts/run-smoke-tests.sh"
   },
   "keywords": [