devlyn-cli 4.2.6 → 4.2.8

package/README.md

@@ -35,7 +35,7 @@ That's it. The installer asks:
 
 In a project, AGENTS.md readers load the skills from `.agents/skills/`; Claude Code loads only `.claude/skills/` and reads AGENTS.md when the project has no CLAUDE.md; a CLAUDE.md the installer creates imports an existing AGENTS.md (`@AGENTS.md`). Global installs skills only: `~/.agents/skills/` (omp, Pi, Grok) and `~/.codex/skills/` (Codex), plus `~/.claude/skills/` for Claude Code. Every target gets the `devlyn-ideate` skill and the `devlyn-engines` utility. In Codex / omp / Pi, invoke them as skills (`$devlyn-ideate`); in Claude Code and Grok they're slash commands (`/devlyn-ideate`). Rerunning refreshes skills and the managed instruction block while preserving project rules outside it. See [Migration from earlier versions](#migration-from-earlier-versions) for legacy migration and merge recovery.
 
-Without prompts, `npx devlyn-cli -y` installs AGENTS.md + `.agents/skills/` plus every target this project already has; add `--claude` for Claude Code. With `--global` it installs for every project on this machine, plus `~/.claude/skills/` with `--claude` or when it already has a devlyn install.
+Without prompts, `npx devlyn-cli -y` installs AGENTS.md + `.agents/skills/` plus every target this project already has; add `--claude` for Claude Code. With `--global` it installs for every project on this machine, plus `~/.claude/skills/` with `--claude` or when it already has a devlyn install. After a project install or update, the installer names the changed files to commit so teammates and `/devlyn-ideate` drains can use them.
 
 ---
 
@@ -215,7 +215,9 @@ Selected during install. Run `npx devlyn-cli` again to add more.
 
 ---
 
-Installer updates preserve user work: before writing any selected target, devlyn refuses to replace or remove git-tracked skills, edited skills, or directories with extra files (including hidden files). `-y` does not bypass this check. Commit your work or move conflicting folders to a backup and migrate them manually; tracked folders must be moved out of the install path before rerunning. Unchanged installer copies and pristine untracked 4.1.0 installs upgrade automatically. Older copies without verifiable content history require manual migration.
+Installer updates preserve user work: before writing any selected target, devlyn refuses to replace or remove edited skills, directories with extra files (including hidden files), links, or unknown copies. `-y` does not bypass this check. Unedited copies from every published version upgrade automatically, including committed copies, historical install-path stamps and generated Python bytecode caches. Release packaging derives the offline skill history from Git with `node scripts/update-skill-history.js`. Move conflicting folders to a backup and migrate them manually; also remove conflicting tracked paths from the Git index before rerunning.
+
+Only `__pycache__` directories containing exclusively regular `*.pyc` files count as generated Python caches. Other entries make the directory ordinary content; links and special files are refused. Standalone `*.pyc` files count as content: none of the 113 published versions through 4.2.5 shipped them. Historical path normalization applies only to the escaped absolute assignment defaults written into Markdown by the 2.8.0–4.0.0 installers.
 
 ## Requirements
 

package/bin/devlyn.js

@@ -1,16 +1,15 @@
 #!/usr/bin/env node
 
-const crypto = require('crypto');
 const fs = require('fs');
 const path = require('path');
 const os = require('os');
-const { execSync } = require('child_process');
+const { execSync, spawnSync } = require('child_process');
 
 const CONFIG_SOURCE = path.join(__dirname, '..', 'config');
 const OPTIONAL_SKILLS_SOURCE = path.join(__dirname, '..', 'optional-skills');
 const PKG = require('../package.json');
 const { updateInstructions, InstructionError, holdsDevlynDefaults, importsAgentsMd } = require('./instructions');
-const { contentHash, fingerprint, isOsMetadata, trackedPaths } = require('./skill-ownership');
+const { contentHash, fingerprint, gitEnvironment, isIgnoredEntry, trackedPaths } = require('./skill-ownership');
 const SKILL_HISTORY = require('./skill-history.json');
 
 // The devlyn skill bundle installed into every skill-capable agent's loader
@@ -83,16 +82,15 @@ const RETIRED_SKILL_MD_SHA256 = {
   ]),
 };
 
-// Whether `dir` is a real folder whose only file, besides OS metadata, is a SKILL.md
+// Whether `dir` is a real folder whose only file, besides generated metadata, is a SKILL.md
 // with an LF-normalized SHA-256 in `hashes`: an unedited copy devlyn-cli shipped, not something
 // the user added to or wrote.
 function isShippedCopy(dir, hashes) {
   const skill = path.join(dir, 'SKILL.md');
   return fs.lstatSync(dir, { throwIfNoEntry: false })?.isDirectory() === true
-    && fs.readdirSync(dir).filter((name) => !isOsMetadata(path.join(dir, name))).length === 1
+    && fs.readdirSync(dir).filter((name) => !isIgnoredEntry(path.join(dir, name))).length === 1
     && fs.lstatSync(skill, { throwIfNoEntry: false })?.isFile() === true
-    && hashes.has(crypto.createHash('sha256')
-      .update(fs.readFileSync(skill, 'utf8').replace(/\r\n/g, '\n')).digest('hex'));
+    && hashes.has(contentHash(skill));
 }
 
 // Skill roots of each target. In a project, `.agents/skills` serves Codex, omp, Pi and Grok,
@@ -348,13 +346,14 @@ function listContents() {
 }
 
 // Old and retired skills in one skill root; nothing outside it.
-function cleanupDeprecated(skillsDir) {
+function cleanupDeprecated(skillsDir, written) {
   let removed = 0;
   const deprecated = DEPRECATED_DIRS.flatMap((relPath) =>
     legacySkillPaths(skillsDir, path.basename(relPath)).map((fullPath) => [relPath, fullPath]));
   for (const [relPath, fullPath] of deprecated) {
     if (fs.existsSync(fullPath)) {
       fs.rmSync(fullPath, { recursive: true });
+      written.push(fullPath);
       log(`  ✕ ${relPath}/ (removed)`, 'dim');
       removed++;
     }
@@ -363,6 +362,7 @@ function cleanupDeprecated(skillsDir) {
     const fullPath = path.join(skillsDir, name);
     if (isShippedCopy(fullPath, hashes)) {
       fs.rmSync(fullPath, { recursive: true });
+      written.push(fullPath);
       log(`  ✕ skills/${name}/ (removed)`, 'dim');
       removed++;
     }
@@ -374,20 +374,22 @@ function cleanupDeprecated(skillsDir) {
 // are in place. An optional skill found under an old spelling is installed under its new name
 // before the old copy goes, so an interrupted migration never loses it. An unedited 0.6.0-0.7.1
 // copy is refreshed in place. Any other folder under a 4.0 name is the user's own; `-y` leaves it.
-function retireRenamedSkills(skillsDir) {
+function retireRenamedSkills(skillsDir, written) {
   const optional = new Set(OPTIONAL_ADDONS.filter((addon) => addon.type === 'local').map((addon) => addon.name));
   const refreshed = [];
   for (const [oldName, newName] of Object.entries(RENAMED_SKILLS)) {
     const found = legacySkillPaths(skillsDir, oldName).filter((fullPath) => fs.existsSync(fullPath));
     if (found.length > 0 && optional.has(newName)) {
-      installOptionalSkillInto(skillsDir, newName);
+      installOptionalSkillInto(skillsDir, newName, written);
       refreshed.push(newName);
     } else if (isShippedCopy(path.join(skillsDir, newName), PRE_STANDARD_SKILL_MD_SHA256)) {
       refreshPreStandardCopy(skillsDir, newName);
+      written.push(path.join(skillsDir, newName));
       refreshed.push(newName);
     }
     for (const fullPath of found) {
       fs.rmSync(fullPath, { recursive: true, force: true });
+      written.push(fullPath);
       log(`  ✕ ${path.basename(fullPath)}/ (renamed to ${newName})`, 'dim');
     }
   }
@@ -612,40 +614,49 @@ function singleSelect(message, items, initial) {
   });
 }
 
-// After install(), whose preflight already cleared every selected addon before any change.
-function installLocalSkill(skillName, roots) {
+// After preflight has cleared every selected addon before any change.
+function installLocalSkill(skillName, roots, written = []) {
   if (!fs.existsSync(path.join(OPTIONAL_SKILLS_SOURCE, skillName))) {
     log(`   ⚠️  Skill "${skillName}" not found`, 'yellow');
     return false;
   }
   log(`\n🛠️  Installing ${skillName}...`, 'cyan');
   for (const root of roots) {
-    installOptionalSkillInto(root, skillName);
+    installOptionalSkillInto(root, skillName, written);
     writeInstallMarker(root, [skillName], readInstallManifest(root));
+    written.push(path.join(root, DEVLYN_INSTALL_MARKER));
   }
   return true;
 }
 
 // One optional skill into one skill-loader directory, replacing any older copy of it. A
 // copy under its name before the 4.0.0 rename goes only once the new one is complete.
-function installOptionalSkillInto(target, skillName) {
+function installOptionalSkillInto(target, skillName, written) {
   const dest = path.join(target, skillName);
   fs.rmSync(dest, { recursive: true, force: true });
   copyRecursive(path.join(OPTIONAL_SKILLS_SOURCE, skillName), dest, target);
   assertCompleteSkillInstall(OPTIONAL_SKILLS_SOURCE, target, [skillName]);
+  written.push(dest);
   const oldName = Object.keys(RENAMED_SKILLS).find((name) => RENAMED_SKILLS[name] === skillName);
   for (const fullPath of oldName ? legacySkillPaths(target, oldName) : []) {
+    if (!fs.existsSync(fullPath)) continue;
     fs.rmSync(fullPath, { recursive: true, force: true });
+    written.push(fullPath);
   }
 }
 
-// A 0.6.0-0.7.1 copy is one SKILL.md, the file that identifies it. Renaming the new one over it is
-// atomic, so an interrupted run leaves the old copy, which the retry finds again, or the new.
+// A 0.6.0-0.7.1 copy is one SKILL.md, the file that identifies it. A failed swap leaves
+// that copy for the retry; a successful refresh discards its generated metadata too.
 function refreshPreStandardCopy(target, skillName) {
-  const skill = path.join(target, skillName, 'SKILL.md');
+  const dir = path.join(target, skillName);
+  const skill = path.join(dir, 'SKILL.md');
   const staged = `${skill}.${process.pid}.tmp`;
   try {
     fs.copyFileSync(path.join(OPTIONAL_SKILLS_SOURCE, skillName, 'SKILL.md'), staged);
+    for (const name of fs.readdirSync(dir)) {
+      const file = path.join(dir, name);
+      if (isIgnoredEntry(file)) fs.rmSync(file, { recursive: true });
+    }
     fs.renameSync(staged, skill);
   } finally {
     fs.rmSync(staged, { force: true });
@@ -676,10 +687,7 @@ function installSkillPack(packName) {
   }
 }
 
-function installAddon(addon, roots) {
-  if (addon.type === 'local') {
-    return installLocalSkill(addon.name, roots);
-  }
+function installAddon(addon) {
   if (addon.type === 'mcp') {
     return installMcpServer(addon.name, addon.command);
   }
@@ -688,13 +696,13 @@ function installAddon(addon, roots) {
 
 // The core skills into one skill root, replacing older copies and retired skills, then the
 // marker that records a complete install.
-function installCoreSkills(skillsDir) {
+function installCoreSkills(skillsDir, written = []) {
   const sourceSkillsDir = path.join(CONFIG_SOURCE, 'skills');
   log(`\n📁 Installing devlyn skills to ${skillsDir.replace(os.homedir(), '~')}`, 'green');
   fs.mkdirSync(skillsDir, { recursive: true });
   const previous = readInstallManifest(skillsDir);
   clearInstallMarker(skillsDir);
-  const removed = cleanupDeprecated(skillsDir);
+  const removed = cleanupDeprecated(skillsDir, written);
   if (removed > 0) {
     log(`\n🧹 Cleaned up ${removed} deprecated file${removed > 1 ? 's' : ''}`, 'yellow');
   }
@@ -705,28 +713,66 @@ function installCoreSkills(skillsDir) {
     // Full replace: copyRecursive is an overlay, so stale files would otherwise persist.
     fs.rmSync(dest, { recursive: true, force: true });
     copyRecursive(src, dest, skillsDir);
+    written.push(dest);
   }
   assertCompleteSkillInstall(sourceSkillsDir, skillsDir, DEVLYN_CORE_SKILLS);
-  const refreshed = retireRenamedSkills(skillsDir);
+  const refreshed = retireRenamedSkills(skillsDir, written);
   writeInstallMarker(skillsDir, [...DEVLYN_CORE_SKILLS, ...refreshed], previous);
+  written.push(path.join(skillsDir, DEVLYN_INSTALL_MARKER));
 }
 
-// Keep installer-managed pipeline state and install metadata out of git.
-function ignoreInGit(gitignoreEntries) {
+function readProjectGitignore() {
   const gitignorePath = path.join(projectDir(), '.gitignore');
-  let gitignoreContent = fs.existsSync(gitignorePath)
-    ? fs.readFileSync(gitignorePath, 'utf8')
-    : '';
-  const gitignoreLines = gitignoreContent.split('\n').map((line) => line.trim());
-  const missingGitignoreEntries = gitignoreEntries.filter((entry) =>
-    !gitignoreLines.includes(entry) && !(entry === '.devlyn/' && gitignoreLines.includes('.devlyn')));
-  if (missingGitignoreEntries.length > 0) {
-    const prefix = gitignoreContent && !gitignoreContent.endsWith('\n') ? '\n' : '';
-    const hasManagedHeader = gitignoreLines.includes('# devlyn-cli pipeline state');
-    const header = hasManagedHeader ? '' : gitignoreContent ? '\n# devlyn-cli pipeline state\n' : '# devlyn-cli pipeline state\n';
-    fs.writeFileSync(gitignorePath, gitignoreContent + prefix + header + missingGitignoreEntries.join('\n') + '\n');
-    log(`  → .gitignore (added ${missingGitignoreEntries.join(', ')})`, 'dim');
+  const stat = fs.lstatSync(gitignorePath, { throwIfNoEntry: false });
+  // Refuse symlinks and hardlinks even when no rules need changing, before any installation write.
+  if (stat && (!stat.isFile() || stat.nlink !== 1)) {
+    throw new InstructionError(`Cannot update ${gitignorePath}: not a regular file with a single link (links are refused).`);
   }
+  return stat ? fs.readFileSync(gitignorePath) : Buffer.alloc(0);
+}
+
+// Ignore runtime state; let the project's install marker travel with its skills.
+function updateProjectGitignore(markerEntry) {
+  const gitignorePath = path.join(projectDir(), '.gitignore');
+  const original = readProjectGitignore();
+  const marker = Buffer.from(markerEntry);
+  const managedHeader = Buffer.from('# devlyn-cli pipeline state');
+  const runtimeRules = [Buffer.from('.devlyn/'), Buffer.from('.devlyn')];
+  const lines = [];
+  for (let start = 0; start < original.length;) {
+    const lf = original.indexOf(0x0a, start);
+    const end = lf === -1 ? original.length : lf + 1;
+    const patternEnd = lf === -1 ? end : original[lf - 1] === 0x0d ? lf - 1 : lf;
+    lines.push({ raw: original.subarray(start, end), pattern: original.subarray(start, patternEnd) });
+    start = end;
+  }
+  const kept = lines.filter(({ pattern }, index) => {
+    if (pattern.equals(marker)) return false;
+    if (!pattern.equals(managedHeader)) return true;
+    // A header owns contiguous patterns until a blank/comment; remove it only when marker removal empties that block.
+    const entries = [];
+    for (let next = index + 1; next < lines.length; next++) {
+      const entry = lines[next].pattern;
+      if (!entry.length || entry[0] === 0x23) break;
+      entries.push(entry);
+    }
+    return !entries.some((entry) => entry.equals(marker)) || entries.some((entry) => !entry.equals(marker));
+  });
+  let gitignoreContent = Buffer.concat(kept.map((line) => line.raw));
+  if (!kept.some(({ pattern }) => runtimeRules.some((rule) => pattern.equals(rule)))) {
+    const lf = original.indexOf(0x0a);
+    const eol = lf > 0 && original[lf - 1] === 0x0d ? '\r\n' : '\n';
+    const prefix = gitignoreContent.length && gitignoreContent.at(-1) !== 0x0a ? eol : '';
+    const header = kept.some(({ pattern }) => pattern.equals(managedHeader))
+      ? '' : `${gitignoreContent.length ? eol : ''}${managedHeader}${eol}`;
+    gitignoreContent = Buffer.concat([gitignoreContent, Buffer.from(`${prefix}${header}.devlyn/${eol}`)]);
+  }
+  if (!gitignoreContent.equals(original)) {
+    fs.writeFileSync(gitignorePath, gitignoreContent);
+    log('  → .gitignore (updated project install rules)', 'dim');
+    return true;
+  }
+  return false;
 }
 
 // With the Claude target in the same run, an AGENTS.md that links to this project's CLAUDE.md (a
@@ -747,16 +793,18 @@ function agentsMdIsClaudeMd() {
 }
 
 function installAgentsProject(withClaude) {
+  const written = [];
   if (!agentsMdIsClaudeMd()) {
-    updateInstructions('AGENTS.md');
+    if (updateInstructions('AGENTS.md')) written.push('AGENTS.md');
   } else if (withClaude) {
     log('  → AGENTS.md is CLAUDE.md here, so it gets the devlyn block written there', 'dim');
   } else {
     throw new InstructionError('AGENTS.md is CLAUDE.md under another name here. Choose CLAUDE.md as well '
       + '(npx devlyn-cli -y --claude) so the devlyn block is written once, into CLAUDE.md.');
   }
-  installCoreSkills(skillRoots('agents', false)[0]);
-  ignoreInGit(['.devlyn/', '.agents/skills/.devlyn-install.json']);
+  installCoreSkills(skillRoots('agents', false)[0], written);
+  if (updateProjectGitignore('.agents/skills/.devlyn-install.json')) written.push('.gitignore');
+  return written;
 }
 
 // Whether Claude Code reads the devlyn defaults of AGENTS.md through an `@AGENTS.md` import in this CLAUDE.md text.
@@ -780,8 +828,9 @@ function installClaudeInstructions() {
     throw new InstructionError('Claude Code reads AGENTS.md here, and its devlyn defaults need an update. Codex, omp, Pi and Grok '
       + 'read them too, with .agents/skills, so choose AGENTS.md as well (npx devlyn-cli -y --claude) to update both together.');
   }
-  updateInstructions('CLAUDE.md', initial, !imported);
+  const changed = updateInstructions('CLAUDE.md', initial, !imported);
   if (imported) log('  → CLAUDE.md imports AGENTS.md, which holds the devlyn block', 'dim');
+  return changed;
 }
 
 // Project CLAUDE.md and .claude/: skills and settings.
@@ -808,16 +857,17 @@ function installClaudeCore() {
       && (!settings.env || typeof settings.env !== 'object' || Array.isArray(settings.env))) {
     throw unmergeable('env must be a JSON object');
   }
-  installClaudeInstructions();
+  const written = installClaudeInstructions() ? ['CLAUDE.md'] : [];
   for (const relPath of DEPRECATED_FILES) {
     const fullPath = path.join(targetDir, relPath);
     if (fs.existsSync(fullPath)) {
       fs.unlinkSync(fullPath);
       log(`  ✕ ${relPath} (deprecated)`, 'dim');
+      written.push(`.claude/${relPath}`);
     }
   }
-  installCoreSkills(skillsDir);
-  ignoreInGit(['.devlyn/', '.claude/skills/.devlyn-install.json']);
+  installCoreSkills(skillsDir, written);
+  if (updateProjectGitignore('.claude/skills/.devlyn-install.json')) written.push('.gitignore');
 
   // One-hour foreground Bash calls and one-hour prompt caching serve a drain host that waits in the foreground.
   let settingsChanged = false;
@@ -848,6 +898,7 @@ function installClaudeCore() {
   if (settingsChanged) {
     fs.writeFileSync(settingsPath, JSON.stringify(settings, null, 2) + '\n');
     log('  → settings.json', 'dim');
+    written.push('.claude/settings.json');
   }
   // Their ownership cannot be established, so the other retired settings stay; name the ones present.
   const retired = [
@@ -857,6 +908,7 @@ function installClaudeCore() {
   if (retired.length > 0) {
     log(`  Retired devlyn settings may remain in .claude/settings.json: ${retired.join(', ')} — delete those you did not add yourself.`, 'yellow');
   }
+  return written;
 }
 
 // Installs the targets in one scope; returns the skill roots written.
@@ -871,20 +923,62 @@ function install(targets, global, optionalNames = []) {
       + 'would apply to every project. Run from a project folder, or use --global for skills only.');
   }
   const roots = targets.flatMap((target) => skillRoots(target, global));
+  const written = [];
+  if (!global) readProjectGitignore();
   preflightSkills(roots, optionalNames,
     !global && targets.includes('claude') ? path.dirname(skillRoots('claude', false)[0]) : null);
   // AGENTS.md first, whatever order the menu gave: a new CLAUDE.md holds the block only when AGENTS.md does not.
   for (const target of ['agents', 'claude'].filter((name) => targets.includes(name))) {
     if (global) skillRoots(target, true).forEach((root) => installCoreSkills(root));
-    else if (target === 'agents') installAgentsProject(targets.includes('claude'));
-    else installClaudeCore();
+    else if (target === 'agents') written.push(...installAgentsProject(targets.includes('claude')));
+    else written.push(...installClaudeCore());
   }
+  for (const name of optionalNames) installLocalSkill(name, roots, written);
   log(`\n✅ devlyn ${PKG.version} installed`, 'green');
   if (global) log('The principles block installs per project: run npx devlyn-cli in the project without --global.');
+  else noticeProjectChanges(written);
   noticeGlobalDrift(roots);
   return roots;
 }
 
+// Advisory only: a successful install stays successful when Git is unavailable or fails.
+function noticeProjectChanges(paths) {
+  if (!paths.length) return;
+  const cwd = projectDir();
+  paths = [...new Set(paths.map((name) => path.relative(cwd, path.resolve(cwd, name)).split(path.sep).join('/')))];
+  const env = { ...gitEnvironment(), GIT_OPTIONAL_LOCKS: '0' };
+  const git = (args) => spawnSync('git', ['-C', cwd, ...args], { encoding: 'utf8', env });
+  const repo = git(['rev-parse', '--show-toplevel']);
+  if (repo.error || repo.status !== 0) return;
+  const status = git(['status', '--porcelain=v1', '-z', '--untracked-files=all', '--no-renames',
+    '--', ...paths.map((name) => `:(icase,literal)${name}`)]);
+  if (status.error || status.status !== 0) return;
+  // Porcelain paths are repository-relative, even when installing in a nested project.
+  const changed = status.stdout.split('\0').filter(Boolean).map((entry) =>
+    path.relative(cwd, path.resolve(repo.stdout.replace(/\r?\n$/, ''), entry.slice(3))).split(path.sep).join('/'));
+  // Keep the installed folder/file scope, using Git's spelling on case-insensitive volumes.
+  const pending = [...new Set(paths.flatMap((name) => [...new Set(changed
+    .map((file) => file.split('/').slice(0, name.split('/').length).join('/')))]
+    .filter((file) => {
+      if (file === name) return true;
+      if (file.toLowerCase() !== name.toLowerCase()) return false;
+      // Case folding alone can include independently edited files on case-sensitive volumes.
+      // Removed paths have no identity left to compare, so require their exact spelling.
+      try {
+        const written = fs.lstatSync(path.resolve(cwd, name), { bigint: true, throwIfNoEntry: false });
+        const reported = fs.lstatSync(path.resolve(cwd, file), { bigint: true, throwIfNoEntry: false });
+        return written && reported && written.dev === reported.dev && written.ino === reported.ino;
+      } catch (error) {
+        log(`Cannot compare Git path ${file} with installed path ${name}: ${error.message}`, 'yellow');
+        return false;
+      }
+    })))];
+  if (!pending.length) return;
+  const quote = (name) => /^[a-zA-Z0-9_./-]+$/.test(name) ? name : `'${name.replace(/'/g, "'\\''")}'`;
+  log('Commit these changes for teammates and /devlyn-ideate drains to use them:', 'yellow');
+  log(`  git add -- ${pending.map(quote).join(' ')} && git commit -m "chore(devlyn): update devlyn-cli to ${PKG.version}"`, 'dim');
+}
+
 // A devlyn install in a user root this run does not refresh drifts and can shadow the
 // project's copy; name it without touching it.
 function noticeGlobalDrift(installed) {
@@ -944,11 +1038,11 @@ async function init({ yes, claude, global }) {
   const scope = await singleSelect('Where', ['This project', 'Global — every project on this machine'], global ? 1 : 0);
   // Ask about optional addons (local skills + external packs; MCP servers belong to Claude Code)
   const selectedAddons = await multiSelect('Optional skills & packs', OPTIONAL_ADDONS.filter((addon) => addon.type !== 'mcp' || targets.includes('claude')));
-  const roots = install(targets, scope === 1, selectedAddons.filter((addon) => addon.type === 'local').map((addon) => addon.name));
+  install(targets, scope === 1, selectedAddons.filter((addon) => addon.type === 'local').map((addon) => addon.name));
 
   if (selectedAddons.length > 0) {
-    for (const addon of selectedAddons) {
-      installAddon(addon, roots);
+    for (const addon of selectedAddons.filter((addon) => addon.type !== 'local')) {
+      installAddon(addon);
     }
   } else {
     log('💡 No optional addons selected', 'dim');

package/bin/skill-history.json

@@ -1,77 +1,613 @@
 {
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+  "source": "skills: config/skills/* and optional-skills/* trees from every first-parent HEAD commit touching those paths and every local tag, derived by scripts/update-skill-history.js using bin/skill-ownership.js normalization (LF, install-path stamps, OS metadata and Python bytecode); deprecated commands: commands/ and optional-commands/*/ files of devlyn-cli 0.0.1-0.5.8 (every published version that shipped them), LF-normalized SHA-256",
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     ],
     "ui-implementation-standards": [
-      "0fbaad2b7d77462916d9364b97b921354ffbf945a68e9e0d422b3a88d36d2569"
+      "0fbaad2b7d77462916d9364b97b921354ffbf945a68e9e0d422b3a88d36d2569",
+      "2472fc5b598a6ba3e2692cf1d9f775b27b4b6669d51c8282d0be3273c7b4a9c4",
+      "3cbfd9ec0ece1c196fc5aaf4558fa0b40926ac957fbc0c426732f92d7827a491",
+      "8c162e0d8b44a69b22b5d17e0c305ce027c7323cb535d947f767bf339c8cc054",
+      "a8f768fb0ac838c44221c4656eb8c3ebb12a29f13c8ee9b34aef9180c27ea775"
+    ],
+    "vercel-composition-patterns": [
+      "9f73c0e78ca790c0d964aba5a40aff93c1f745a3c5481e6a1e356f09f3931075"
+    ],
+    "vercel-react-best-practices": [
+      "18153870565cabc4f1d134820732c975694533e3f8634ad16d113795f5f562e5"
+    ],
+    "vercel-react-native-skills": [
+      "acfb861607a25acc76a20da9e4f26b766a3b72c5d7522de2e8f2fbabb231af1c"
+    ],
+    "web-design-guidelines": [
+      "288ad79d921362a232c491e2df598c5e1dd544e3f3969b0f42d605ffa81f7dad"
+    ],
+    "workflow-routing": [
+      "711cd2633df2062104f12d50037a07a1012a90ab18c422cb5fdf665fcb9dc987",
+      "d6a98c105a0d1952de90c39ca0734cb70cbdd116e6b4a4d45507d796bd2a9e88"
     ]
   },
   "commands": {

package/bin/skill-ownership.js

@@ -3,21 +3,33 @@ const fs = require('fs');
 const path = require('path');
 const { spawnSync } = require('child_process');
 
-// A folder-metadata file the OS writes on its own (Finder, Explorer); never user content.
-// Only a regular file: a folder or link under that name is still the user's.
-function isOsMetadata(full) {
-  return ['.DS_Store', 'Thumbs.db'].includes(path.basename(full))
-    && fs.lstatSync(full, { throwIfNoEntry: false })?.isFile() === true;
+// CPython caches contain only regular *.pyc files. A mixed directory is ordinary
+// content; the fingerprint walker below still refuses links and special files.
+// No published version shipped standalone *.pyc files, so those count as edits.
+function isIgnoredEntry(full) {
+  const stat = fs.lstatSync(full, { throwIfNoEntry: false });
+  const name = path.basename(full);
+  if (stat?.isFile()) return ['.DS_Store', 'Thumbs.db'].includes(name);
+  if (name !== '__pycache__' || !stat?.isDirectory()) return false;
+  return fs.readdirSync(full).every((child) =>
+    child.endsWith('.pyc') && fs.lstatSync(path.join(full, child)).isFile());
 }
 
 // SHA-256 of a file with CRLF read as LF: Git for Windows checks text out with CRLF by
-// default, and an unedited clone must still match its shipped copy.
+// default. 2.8.0-4.0.0 stamped only the exact assignment sentinel in .md files.
+// Accept only shellDoubleQuoteDefault's escapes and an absolute original path.
 function contentHash(file) {
-  const bytes = fs.readFileSync(file).toString('latin1').replace(/\r\n/g, '\n');
+  let bytes = fs.readFileSync(file).toString('latin1').replace(/\r\n/g, '\n');
+  if (path.extname(file) === '.md') {
+    bytes = bytes.replace(/\$\{CLAUDE_SKILL_DIR:-((?:\\[\\$"`}]|[^\\$"`}\n])+)\}/g, (match, escaped) => {
+      const original = escaped.replace(/\\([\\$"`}])/g, '$1');
+      return /^(?:\/|[A-Za-z]:\\|\\\\)/.test(original) ? '${CLAUDE_SKILL_DIR:-__DEVLYN_SKILL_DIR__}' : match;
+    });
+  }
   return crypto.createHash('sha256').update(bytes, 'latin1').digest('hex');
 }
 
-// Hash every entry, including empty directories and dotfiles, except OS metadata. Links and
+// Hash every entry, including empty directories and dotfiles, except generated metadata. Links and
 // special files are never installer-owned.
 function fingerprint(dir) {
   const entries = [];
@@ -26,7 +38,7 @@ function fingerprint(dir) {
     if (stat.isDirectory()) {
       entries.push([relative, 'directory']);
       for (const name of fs.readdirSync(full).sort()) {
-        if (isOsMetadata(path.join(full, name))) continue;
+        if (isIgnoredEntry(path.join(full, name))) continue;
         visit(path.join(full, name), relative ? `${relative}/${name}` : name);
       }
     } else if (stat.isFile()) {
@@ -40,15 +52,20 @@ function fingerprint(dir) {
   return crypto.createHash('sha256').update(JSON.stringify(entries)).digest('hex');
 }
 
+function gitEnvironment() {
+  const env = { ...process.env, LC_ALL: 'C' };
+  for (const key of ['GIT_DIR', 'GIT_WORK_TREE', 'GIT_INDEX_FILE', 'GIT_COMMON_DIR',
+    'GIT_LITERAL_PATHSPECS', 'GIT_GLOB_PATHSPECS', 'GIT_NOGLOB_PATHSPECS', 'GIT_ICASE_PATHSPECS',
+    'GIT_CEILING_DIRECTORIES', 'GIT_DISCOVERY_ACROSS_FILESYSTEM']) delete env[key];
+  return env;
+}
+
 // Use the index, not status: even files deleted locally need ownership checks.
 // Inspect the repository containing this root, including global dotfiles repos.
 function trackedPaths(root) {
   let cwd = root;
   while (!fs.existsSync(cwd)) cwd = path.dirname(cwd);
-  const env = { ...process.env, LC_ALL: 'C' };
-  for (const key of ['GIT_DIR', 'GIT_WORK_TREE', 'GIT_INDEX_FILE', 'GIT_COMMON_DIR',
-    'GIT_LITERAL_PATHSPECS', 'GIT_GLOB_PATHSPECS', 'GIT_NOGLOB_PATHSPECS', 'GIT_ICASE_PATHSPECS',
-    'GIT_CEILING_DIRECTORIES', 'GIT_DISCOVERY_ACROSS_FILESYSTEM']) delete env[key];
+  const env = gitEnvironment();
   const git = (args) => spawnSync('git', ['-C', cwd, ...args], { encoding: 'utf8', env });
   const repo = git(['rev-parse', '--show-toplevel']);
   if (repo.error?.code === 'ENOENT') return [];
@@ -64,4 +81,4 @@ function trackedPaths(root) {
   return files.stdout.split('\0').filter(Boolean).map((file) => path.resolve(repo.stdout.trim(), file));
 }
 
-module.exports = { contentHash, fingerprint, isOsMetadata, trackedPaths };
+module.exports = { contentHash, fingerprint, gitEnvironment, isIgnoredEntry, trackedPaths };

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "devlyn-cli",
-  "version": "4.2.6",
+  "version": "4.2.8",
   "description": "Loop & harness engineering for AI coding agents (Claude Code, Codex, and any AGENTS.md-driven agent) — core engineering principles for CLAUDE.md/AGENTS.md and a loop designer that splits one intent into tasks agents drain hands-free",
   "homepage": "https://github.com/fysoul17/devlyn-cli#readme",
   "bin": {