universal-dev-standards 6.9.0 → 6.10.0

package/src/commands/check.js

@@ -1,13 +1,13 @@
 import chalk from 'chalk';
 import { select } from '@inquirer/prompts';
-import ora from 'ora';
+import { createSpinner } from '../utils/spinner.js';
 import { existsSync, readFileSync } from 'fs';
 import { join, basename } from 'path';
 import { execSync } from 'child_process';
 import { readManifest, writeManifest, isInitialized, copyStandard, copyIntegration } from '../utils/copier.js';
 import {
   getAllStandards,
-  getRepositoryInfo, resolveStandardFilename, resolveStandardSourcePath } from '../utils/registry.js';
+  getRepositoryInfo, isShippedFilename, resolveStandardFilename, resolveStandardSourcePath } from '../utils/registry.js';
 import {
   computeFileHash,
   compareFileHash,
@@ -27,6 +27,7 @@ import {
 } from '../config/ai-agent-paths.js';
 import {
   parseReferences,
+  findBrokenPathMentions,
   compareStandardsWithReferences
 } from '../utils/reference-sync.js';
 import { extractMarkedContent, getToolFilePath, parseStandardsIndexCount, writeIntegrationFile } from '../utils/integration-generator.js';
@@ -60,6 +61,19 @@ function displayFileIntegritySummary(fileStatus, msg) {
     }
   }
 
+  // Reported apart from `missing`, and in grey rather than red, because the
+  // adopter who sees this did what the migration guide asked. The remedy named
+  // here is the one that works: `--restore` cannot resolve a source for any of
+  // them, and used to be the only thing offered.
+  if (fileStatus.retired?.length > 0) {
+    console.log();
+    console.log(chalk.gray(`  ${(msg.retiredHeader || '{count} tracked file(s) are no longer shipped by UDS:').replace('{count}', fileStatus.retired.length)}`));
+    for (const file of fileStatus.retired) {
+      console.log(chalk.gray(`  - ${file} (${msg.retired || 'no longer shipped by UDS'})`));
+    }
+    console.log(chalk.gray(`    ${msg.retiredHint || 'Run `uds update --prune` to drop their manifest entries.'}`));
+  }
+
   if (fileStatus.noHash.length > 0) {
     for (const file of fileStatus.noHash) {
       console.log(chalk.gray(`  ? ${file} (${msg.existsNoHash})`));
@@ -71,10 +85,39 @@ function displayFileIntegritySummary(fileStatus, msg) {
     .replace('{unchanged}', fileStatus.unchanged.length)
     .replace('{modified}', fileStatus.modified.length)
     .replace('{missing}', fileStatus.missing.length)}` +
+    (fileStatus.retired?.length > 0 ? `, ${fileStatus.retired.length} ${msg.retired || 'no longer shipped'}` : '') +
     (fileStatus.noHash.length > 0 ? `, ${fileStatus.noHash.length} no hash` : '')));
   console.log();
 }
 
+/**
+ * A file `fileHashes` tracks has gone. Is that a problem, or is it the migration
+ * guide's instruction carried out?
+ *
+ * MIGRATION-v6 §2 told adopters to delete the seven descoped `.ai.yaml` copies
+ * by hand. Doing so left the hash entries behind, and this check called each one
+ * `missing` and offered `uds check --restore` — a restore that then failed on
+ * every one with "could not determine source", because there has been no source
+ * upstream since 6.0.0. The tool asked the user to undo its own documentation,
+ * using a command it already knew could not work.
+ *
+ * The distinguishing question is whether UDS still ships a file by that name,
+ * which is the registry's to answer, not the manifest's. Anything outside
+ * `.standards/` is never retired: integration files are generated, not shipped
+ * under a standard's name, so a missing CLAUDE.md is exactly what it looks like.
+ *
+ * @param {string} relativePath - Path as recorded in fileHashes
+ * @param {Object} manifest - Project manifest (unused today; kept so callers
+ *   need not know whether the answer depends on project state)
+ * @returns {'missing'|'retired'}
+ */
+export function classifyMissingFile(relativePath, manifest) { // eslint-disable-line no-unused-vars
+  const normalized = String(relativePath).replace(/\\/g, '/');
+  if (!normalized.startsWith('.standards/')) return 'missing';
+  const fileName = normalized.split('/').pop();
+  return isShippedFilename(fileName) ? 'missing' : 'retired';
+}
+
 /**
  * Perform integrity check for standards and integration files
  * @returns {Object} File status object
@@ -84,6 +127,10 @@ function performFileIntegrityCheck(projectPath, manifest, msg) {
     unchanged: [],
     modified: [],
     missing: [],
+    // Tracked, gone, and gone on purpose: UDS stopped shipping it. Counted
+    // apart from `missing` so the summary line stops calling a completed
+    // migration a fault.
+    retired: [],
     noHash: []
   };
 
@@ -101,7 +148,7 @@ function performFileIntegrityCheck(projectPath, manifest, msg) {
           fileStatus.modified.push(relativePath);
           break;
         case 'missing':
-          fileStatus.missing.push(relativePath);
+          fileStatus[classifyMissingFile(relativePath, manifest)].push(relativePath);
           break;
       }
     }
@@ -1151,19 +1198,37 @@ function checkIntegrationFiles(manifest, projectPath, msg) {
   // After migrateStandardsPathsToIds(), manifest.standards contains IDs, so a plain
   // content.includes(id) check would fail for these mismatched entries.
   const allRegistryStds = getAllStandards();
-  const idToAiFilename = new Map(
-    allRegistryStds
-      .filter(s => s.source?.ai)
-      .map(s => [s.id, basename(s.source.ai)])
+  // 🔴 `source` is a string for some entries and an object for others. Reading
+  // `s.source.ai` on a string yields undefined, so `zh-tw-locale`
+  // (source: 'extensions/locales/zh-tw.md') fell out of this map and the file it
+  // installs — `.standards/zh-tw.md` — was never recognised: "67/68 項標準已參考,
+  // 缺少: zh-tw-locale" on a project whose index lists it (reported 2026-09-16).
+  const idToFilenames = new Map(
+    allRegistryStds.map(s => {
+      const sources = typeof s.source === 'string'
+        ? [s.source]
+        : [s.source?.ai, s.source?.human].filter(Boolean);
+      return [s.id, sources.map(src => basename(src))];
+    })
   );
 
   let hasIssues = false;
   let checkedCount = 0;
 
+  // codex and opencode both write AGENTS.md, so iterating tools printed the same
+  // file twice with identical verdicts (reported 2026-09-16). One file, one
+  // verdict — the tools that share it are named on the line instead.
+  const toolsByFile = new Map();
   for (const tool of manifest.aiTools) {
-    const toolFile = getToolFilePath(tool);
-    if (!toolFile) continue;
+    const file = getToolFilePath(tool);
+    if (!file) continue;
+    if (!toolsByFile.has(file)) toolsByFile.set(file, []);
+    toolsByFile.get(file).push(tool);
+  }
 
+  for (const [toolFile, sharingTools] of toolsByFile) {
+    const tool = sharingTools[0];
+    const sharedSuffix = sharingTools.length > 1 ? ` (${sharingTools.join(', ')})` : '';
     const fullPath = join(projectPath, toolFile);
 
     // Check if file exists
@@ -1201,9 +1266,9 @@ function checkIntegrationFiles(manifest, projectPath, msg) {
       // migration. For standards where the ID doesn't match the .ai.yaml basename
       // (e.g. ID "error-code-standards" → file "error-codes.ai.yaml"), we must
       // also check the actual filename so those aren't falsely reported as missing.
-      const aiFilename = idToAiFilename.get(stdFile);
+      const filenames = idToFilenames.get(stdFile) || [];
       const isReferenced = content.includes(stdFile) ||
-        (aiFilename !== undefined && aiFilename !== stdFile && content.includes(aiFilename)) ||
+        filenames.some(name => name !== stdFile && content.includes(name)) ||
         content.includes(`.standards/${stdFile}`) ||
         content.includes(`standards/${stdFile}`);
 
@@ -1224,7 +1289,7 @@ function checkIntegrationFiles(manifest, projectPath, msg) {
     const declaredCount = parseStandardsIndexCount(content);
     if (declaredCount !== null) {
       if (declaredCount === totalTrackable) {
-        console.log(chalk.green(`  ✓ ${toolFile}:`));
+        console.log(chalk.green(`  ✓ ${toolFile}${sharedSuffix}:`));
         console.log(chalk.gray(`    ${msg.standardsIndexPresent}`));
         console.log(chalk.gray(`    ${msg.standardsIndexCount
           ? msg.standardsIndexCount.replace('{count}', declaredCount)
@@ -1404,9 +1469,12 @@ function checkReferenceSync(manifest, projectPath, msg) {
     }
 
     const references = parseReferences(content);
-    if (references.length === 0) continue;
+    // Whole-file scan, separate from reference sync: the paths that matter here
+    // are the ones outside the UDS block, which no generation ever revisits.
+    const brokenMentions = findBrokenPathMentions(content, projectPath);
+    if (references.length === 0 && brokenMentions.length === 0) continue;
 
-    results.push({ integrationPath, references });
+    results.push({ integrationPath, references, brokenMentions });
   }
 
   // Skip entire section if no files have references
@@ -1416,14 +1484,42 @@ function checkReferenceSync(manifest, projectPath, msg) {
 
   let hasIssues = false;
 
-  for (const { integrationPath, references } of results) {
+  for (const { integrationPath, references, brokenMentions } of results) {
+    // Paths mentioned anywhere in the file that resolve to nothing. Reported
+    // first and separately from reference sync, because these are usually
+    // outside the UDS markers — left by an older `uds init`, never revisited by
+    // any regeneration, and followed by an AI tool that then finds nothing.
+    if (brokenMentions?.length > 0) {
+      hasIssues = true;
+      console.log(chalk.red(`  ✗ ${integrationPath}:`));
+      console.log(chalk.red(`    ${msg.brokenMentions || 'mentions paths that do not exist in this project:'}`));
+      for (const path of brokenMentions) {
+        console.log(chalk.red(`      - ${path}`));
+      }
+      console.log(chalk.gray(`    ${msg.brokenMentionsFix || 'These are usually outside the UDS block and must be corrected by hand; UDS does not rewrite text it did not write.'}`));
+    }
+
     // Compare with manifest standards
-    const { orphanedRefs, missingRefs, syncedRefs } = compareStandardsWithReferences(
+    const { orphanedRefs, missingRefs, syncedRefs, danglingRefs } = compareStandardsWithReferences(
       manifest.standards,
-      references
+      references,
+      { projectPath, options: manifest.options }
     );
 
     // Report results
+    // 🔴 A reference to a file that is not on disk is the one failure an AI tool
+    // cannot work around: it follows the link and finds nothing. Reported before
+    // the manifest-level findings because it needs no interpretation.
+    if (danglingRefs.length > 0) {
+      hasIssues = true;
+      console.log(chalk.red(`  ✗ ${integrationPath}:`));
+      console.log(chalk.red(`    ${msg.danglingRefs || 'references files that do not exist:'}`));
+      for (const ref of danglingRefs) {
+        console.log(chalk.red(`      - .standards/${ref}`));
+      }
+      console.log(chalk.gray(`    ${msg.danglingRefsFix || 'Run `uds update --integrations-only` to regenerate them.'}`));
+    }
+
     if (orphanedRefs.length > 0) {
       hasIssues = true;
       console.log(chalk.yellow(`  ⚠ ${integrationPath}:`));
@@ -1442,14 +1538,21 @@ function checkReferenceSync(manifest, projectPath, msg) {
       }
     }
 
-    if (orphanedRefs.length === 0 && missingRefs.length === 0) {
+    if (orphanedRefs.length === 0 && missingRefs.length === 0 && danglingRefs.length === 0) {
       console.log(chalk.green(`  ✓ ${msg.refsInSync.replace('{path}', integrationPath).replace('{count}', syncedRefs.length)}`));
     }
   }
 
   if (hasIssues) {
     console.log();
-    console.log(chalk.yellow(`  ${msg.runSyncRefs}`));
+    // `uds update --sync-refs` refuses to run without `integrationConfigs`, and a
+    // project initialised non-interactively never had that key — so this hint
+    // named a command that could not work (reproduced on a clean 6.9.0 project,
+    // 2026-09-16). Name the one that regenerates from the manifest instead.
+    const canSyncRefs = manifest.integrationConfigs && Object.keys(manifest.integrationConfigs).length > 0;
+    console.log(chalk.yellow(`  ${canSyncRefs
+      ? msg.runSyncRefs
+      : (msg.runIntegrationsOnly || 'Run `uds update --integrations-only` to regenerate integration files.')}`));
   }
 
   console.log();
@@ -1461,7 +1564,7 @@ function checkReferenceSync(manifest, projectPath, msg) {
  */
 async function checkCliVersion(bundledVersion) {
   const msg = t().commands.check;
-  const spinner = ora({ text: msg.checkingCliUpdates, spinner: 'dots' }).start();
+  const spinner = createSpinner({ text: msg.checkingCliUpdates, spinner: 'dots' }).start();
 
   try {
     const result = await checkForUpdates(bundledVersion, {
@@ -1582,17 +1685,17 @@ function checkSkillsIntegrity(manifest, projectPath, msg) {
  * @param {Object} msg - Localized messages
  * @returns {Object} Status { unchanged: [], modified: [], missing: [] }
  */
-function checkCommandsIntegrity(manifest, projectPath, msg) {
+export function checkCommandsIntegrity(manifest, projectPath, msg) {
   const commandHashes = manifest.commandHashes;
 
   // Skip if no command hashes tracked
   if (!commandHashes || Object.keys(commandHashes).length === 0) {
-    return { unchanged: [], modified: [], missing: [], tracked: false };
+    return { unchanged: [], modified: [], missing: [], untracked: [], tracked: false };
   }
 
   console.log(chalk.cyan(msg.commandsIntegrityCheck || 'Commands File Integrity'));
 
-  const status = { unchanged: [], modified: [], missing: [], tracked: true };
+  const status = { unchanged: [], modified: [], missing: [], untracked: [], tracked: true };
 
   for (const [hashKey, hashInfo] of Object.entries(commandHashes)) {
     // Parse key format: agent/filename.md
@@ -1632,8 +1735,42 @@ function checkCommandsIntegrity(manifest, projectPath, msg) {
     }
   }
 
+  // 🔴 The loop above measures only what the manifest happens to track. When a
+  // partial apply dropped 48 of 51 entries (6.9.0, fixed in plan-executor.js),
+  // this section printed "All command files intact (3 files)" while the adoption
+  // summary printed "Commands: 51 installed" from a directory listing — two
+  // numbers, two sources, never compared, so the gap read as a pass.
+  const trackedKeys = new Set(Object.keys(commandHashes));
+  const agentsToScan = new Set(Object.keys(commandHashes).map(k => k.split('/')[0]));
+  for (const entry of manifest.commands?.installations || []) {
+    const agentName = typeof entry === 'string' ? entry : entry?.agent;
+    if (agentName) agentsToScan.add(agentName);
+  }
+  for (const agentName of agentsToScan) {
+    // Reuse the installer's own listing so this file filter cannot drift from it.
+    const info = getInstalledCommandsForAgent(agentName, 'project', projectPath);
+    if (!info?.installed) continue;
+    const ext = agentName === 'gemini-cli' ? '.toml' : '.md';
+    for (const name of info.commands || []) {
+      const key = `${agentName}/${name}${ext}`;
+      if (!trackedKeys.has(key)) status.untracked.push(key);
+    }
+  }
+  if (status.untracked.length > 0) {
+    console.log(chalk.yellow(`  ⚠ ${(msg.commandsUntracked || '{count} installed command file(s) are covered by no hash — integrity is not checked for them')
+      .replace('{count}', status.untracked.length)}`));
+    for (const key of status.untracked.slice(0, 5)) {
+      console.log(chalk.yellow(`      - ${key}`));
+    }
+    if (status.untracked.length > 5) {
+      console.log(chalk.yellow(`      … +${status.untracked.length - 5}`));
+    }
+    console.log(chalk.gray(`  ${msg.commandsUntrackedFix || 'Run `uds update --commands` to record them again.'}`));
+  }
+
+
   // Summary
-  if (status.modified.length === 0 && status.missing.length === 0) {
+  if (status.modified.length === 0 && status.missing.length === 0 && status.untracked.length === 0) {
     console.log(chalk.green(`  ✓ ${msg.allCommandsIntact || 'All command files intact'} (${status.unchanged.length} files)`));
   } else {
     console.log(chalk.gray(`  ${(msg.commandsIntegritySummary || '{unchanged} unchanged, {modified} modified, {missing} missing')

package/src/commands/config.js

@@ -1,6 +1,6 @@
 import chalk from 'chalk';
 import { select, confirm as inquirerConfirm } from '@inquirer/prompts';
-import ora from 'ora';
+import { createSpinner } from '../utils/spinner.js';
 import { unlinkSync, existsSync, writeFileSync, mkdirSync } from 'fs';
 import { join, basename } from 'path';
 import { config } from '../utils/config-manager.js';
@@ -381,12 +381,12 @@ async function handleDisplayLanguageChange() {
     if (confirmReinstall) {
       const cmdLocale = displayLanguageToLocale(newLang);
       if (hasSkillInstalls) {
-        const spinner = ora(t('config.reinstallingSkills', 'Reinstalling Skills...')).start();
+        const spinner = createSpinner(t('config.reinstallingSkills', 'Reinstalling Skills...')).start();
         await installSkillsToMultipleAgents(manifest.skills.installations, null, projectPath, cmdLocale);
         spinner.succeed(t('config.skillsReinstalled', 'Skills reinstalled'));
       }
       if (hasCommandInstalls) {
-        const spinner = ora(t('config.reinstallingCommands', 'Reinstalling Commands...')).start();
+        const spinner = createSpinner(t('config.reinstallingCommands', 'Reinstalling Commands...')).start();
         await installCommandsToMultipleAgents(manifest.commands.installations, null, projectPath, cmdLocale);
         spinner.succeed(t('config.commandsReinstalled', 'Commands reinstalled'));
       }
@@ -401,7 +401,7 @@ async function handleDisplayLanguageChange() {
     });
 
     if (confirmRegen) {
-      const spinner = ora(t('config.applyingPreset', 'Applying...')).start();
+      const spinner = createSpinner(t('config.applyingPreset', 'Applying...')).start();
       regenerateIntegrations(projectPath, manifest);
       spinner.succeed(t('config.integrationsRegenerated', 'Integrations regenerated'));
     }
@@ -665,7 +665,7 @@ export async function runProjectConfiguration(options) {
       newAITools = newAITools.filter(tool => !result.tools.includes(tool));
 
       // Remove integration files for removed tools
-      const spinner = ora(msgObj.removingIntegrations).start();
+      const spinner = createSpinner(msgObj.removingIntegrations).start();
       for (const tool of result.tools) {
         const filePath = join(projectPath, getToolFilePath(tool));
         if (existsSync(filePath)) {
@@ -854,7 +854,7 @@ export async function runProjectConfiguration(options) {
   }
 
   // Apply changes
-  const spinner = ora(msgObj.updatingConfig).start();
+  const spinner = createSpinner(msgObj.updatingConfig).start();
 
   const results = {
     copied: [],
@@ -914,7 +914,7 @@ export async function runProjectConfiguration(options) {
 
   // Regenerate integration files if needed
   if (needsIntegrationRegeneration && newAITools.length > 0) {
-    const intSpinner = ora(msgObj.regeneratingIntegrations).start();
+    const intSpinner = createSpinner(msgObj.regeneratingIntegrations).start();
 
     // Build installed standards list
     // Raw, not basename()d. Resolution needs the registry (an ID is not a
@@ -989,7 +989,7 @@ export async function runProjectConfiguration(options) {
 
           if (confirmSkills) {
             const newInstallations = skillCapableTools.map(agent => ({ agent, level }));
-            const spinner = ora(t('config.installingSkillsForNewTools', 'Installing Skills for new tools...')).start();
+            const spinner = createSpinner(t('config.installingSkillsForNewTools', 'Installing Skills for new tools...')).start();
             const skillResult = await installSkillsToMultipleAgents(newInstallations, null, projectPath, cmdLocale);
             spinner.succeed(t('config.skillsInstalledForNewTools', 'Skills installed for new tools'));
 
@@ -1026,7 +1026,7 @@ export async function runProjectConfiguration(options) {
 
           if (confirmCmds) {
             const newCmdInstallations = commandCapableTools.map(agent => ({ agent, level }));
-            const spinner = ora(t('config.installingCommandsForNewTools', 'Installing Commands for new tools...')).start();
+            const spinner = createSpinner(t('config.installingCommandsForNewTools', 'Installing Commands for new tools...')).start();
             const cmdResult = await installCommandsToMultipleAgents(newCmdInstallations, null, projectPath, cmdLocale);
             spinner.succeed(t('config.commandsInstalledForNewTools', 'Commands installed for new tools'));
 
@@ -1124,7 +1124,7 @@ export async function runProjectConfiguration(options) {
 
     if (options.yes) {
       // --yes flag: auto-apply without prompting
-      const applySpinner = ora(msgObj.applyingChanges).start();
+      const applySpinner = createSpinner(msgObj.applyingChanges).start();
       const applyResults = regenerateIntegrations(projectPath, manifest);
       applySpinner.succeed(msgObj.changesApplied || msgObj.regeneratedIntegrations.replace('{count}', applyResults.updated.length));
 
@@ -1146,7 +1146,7 @@ export async function runProjectConfiguration(options) {
       });
 
       if (apply) {
-        const applySpinner = ora(msgObj.applyingChanges).start();
+        const applySpinner = createSpinner(msgObj.applyingChanges).start();
         const applyResults = regenerateIntegrations(projectPath, manifest);
         applySpinner.succeed(msgObj.changesApplied || msgObj.regeneratedIntegrations.replace('{count}', applyResults.updated.length));
 
@@ -1172,12 +1172,12 @@ export async function runProjectConfiguration(options) {
     if (hasSkillInstalls || hasCommandInstalls) {
       const cmdLocale = displayLanguageToLocale(newOptions.display_language);
       if (hasSkillInstalls) {
-        const skillSpinner = ora(t('config.reinstallingSkills', 'Reinstalling Skills...')).start();
+        const skillSpinner = createSpinner(t('config.reinstallingSkills', 'Reinstalling Skills...')).start();
         await installSkillsToMultipleAgents(manifest.skills.installations, null, projectPath, cmdLocale);
         skillSpinner.succeed(t('config.skillsReinstalled', 'Skills reinstalled'));
       }
       if (hasCommandInstalls) {
-        const cmdSpinner = ora(t('config.reinstallingCommands', 'Reinstalling Commands...')).start();
+        const cmdSpinner = createSpinner(t('config.reinstallingCommands', 'Reinstalling Commands...')).start();
         await installCommandsToMultipleAgents(manifest.commands.installations, null, projectPath, cmdLocale);
         cmdSpinner.succeed(t('config.commandsReinstalled', 'Commands reinstalled'));
       }
@@ -1222,7 +1222,7 @@ async function handleSkillsConfiguration(manifest, projectPath, msgObj, common,
 
     // Install to specified level (defaults to project)
     const installations = [{ agent: specificTool, level }];
-    const spinner = ora(`Installing Skills for ${getAgentDisplayName(specificTool)} (${level} level)...`).start();
+    const spinner = createSpinner(`Installing Skills for ${getAgentDisplayName(specificTool)} (${level} level)...`).start();
     const result = await installSkillsToMultipleAgents(installations, null, projectPath);
     spinner.stop();
 
@@ -1359,7 +1359,7 @@ async function handleSkillsConfiguration(manifest, projectPath, msgObj, common,
     }));
 
     // Install Skills
-    const spinner = ora(msgObj.installingSkills || 'Installing Skills...').start();
+    const spinner = createSpinner(msgObj.installingSkills || 'Installing Skills...').start();
     const result = await installSkillsToMultipleAgents(installations, null, projectPath);
     spinner.stop();
 
@@ -1394,7 +1394,7 @@ async function handleSkillsConfiguration(manifest, projectPath, msgObj, common,
   }
 
   // Install Skills
-  const spinner = ora(msgObj.installingSkills || 'Installing Skills...').start();
+  const spinner = createSpinner(msgObj.installingSkills || 'Installing Skills...').start();
   const result = await installSkillsToMultipleAgents(installations, null, projectPath);
   spinner.stop();
 
@@ -1453,7 +1453,7 @@ async function handleCommandsConfiguration(manifest, projectPath, msgObj, common
 
     // Install to selected level
     const installations = [{ agent: specificTool, level: commandsLevel }];
-    const spinner = ora(`Installing Commands for ${getAgentDisplayName(specificTool)} (${commandsLevel} level)...`).start();
+    const spinner = createSpinner(`Installing Commands for ${getAgentDisplayName(specificTool)} (${commandsLevel} level)...`).start();
     const cmdLocale = displayLanguageToLocale(manifest.options?.display_language);
     const result = await installCommandsToMultipleAgents(installations, null, projectPath, cmdLocale);
     spinner.stop();
@@ -1559,7 +1559,7 @@ async function handleCommandsConfiguration(manifest, projectPath, msgObj, common
     }
 
     // Install Commands
-    const spinner = ora(msgObj.installingCommands || 'Installing Commands...').start();
+    const spinner = createSpinner(msgObj.installingCommands || 'Installing Commands...').start();
     const cmdLocale = displayLanguageToLocale(manifest.options?.display_language);
     const result = await installCommandsToMultipleAgents(declinedCommandsWithSupport, null, projectPath, cmdLocale);
     spinner.stop();
@@ -1595,7 +1595,7 @@ async function handleCommandsConfiguration(manifest, projectPath, msgObj, common
   }
 
   // Install Commands
-  const spinner = ora(msgObj.installingCommands || 'Installing Commands...').start();
+  const spinner = createSpinner(msgObj.installingCommands || 'Installing Commands...').start();
   const cmdLocale = displayLanguageToLocale(manifest.options?.display_language);
   const result = await installCommandsToMultipleAgents(selectedAgents, null, projectPath, cmdLocale);
   spinner.stop();

package/src/commands/init.js

@@ -1,8 +1,8 @@
 import chalk from 'chalk';
-import ora from 'ora';
+import { createSpinner } from '../utils/spinner.js';
 import { execSync } from 'child_process';
 import { existsSync, mkdirSync, readFileSync, writeFileSync } from 'fs';
-import { basename, join } from 'path';
+import { join } from 'path';
 import {
   manifestExists as isInitialized,
   normalizeContentMode,
@@ -55,7 +55,7 @@ export async function initCommand(options) {
   }
 
   // STEP 2: Detect project characteristics
-  const spinner = ora(msg.detectingProject).start();
+  const spinner = createSpinner(msg.detectingProject).start();
   const detected = detectAll(projectPath);
   spinner.succeed(msg.analysisComplete);
 
@@ -123,7 +123,16 @@ export async function initCommand(options) {
         apply: async () => {
           // 1. Install Standards
           const standardsResults = await installStandards(config, projectPath);
-          config.installedStandards = standardsResults.standards.map(s => basename(s));
+          // Paths, not basenames. Everything downstream classifies an option
+          // by an `/options/` segment, so reducing to basenames here is not a
+          // simplification — it deletes the only signal that distinguishes the
+          // two, and `contentLayout: flat` installs option files with no
+          // directory to recover it from. The index block consequently said
+          // "options 0" on every project for two releases, while the manifest
+          // right beside it listed seven. `buildToolIntegrationConfig` (the
+          // update path's equivalent) has carried a comment warning against
+          // exactly this reduction the whole time; only this call site did it.
+          config.installedStandards = standardsResults.standards;
 
           // 1.5. Generate release-config.yaml if non-default mode selected
           if (config.releaseMode && config.releaseMode !== 'ci-cd') {

package/src/commands/spec.js

@@ -9,7 +9,7 @@
  */
 
 import chalk from 'chalk';
-import ora from 'ora';
+import { createSpinner } from '../utils/spinner.js';
 import { select, confirm as inquirerConfirm } from '@inquirer/prompts';
 import { existsSync, readFileSync } from 'node:fs';
 import { join } from 'node:path';
@@ -48,7 +48,7 @@ export async function specCreateCommand(intent, options = {}) {
     output: options.output
   });
 
-  const spinner = ora({
+  const spinner = createSpinner({
     text: t('spec.generating', 'Generating micro-spec...'),
     color: 'cyan'
   }).start();