fix: flatten Claude skill installs (#2582)

Flatten managed Claude skill destinations, preserve user-owned conflicts, and migrate legacy nested installs through the lifecycle tooling.

README.md

@@ -375,6 +375,14 @@ npx ecc-install --profile minimal --target claude
 
 This profile intentionally excludes `hooks-runtime`.
 
+Claude manual installs place each skill directly under
+`~/.claude/skills/<skill-name>/` (or `.claude/skills/<skill-name>/` for
+`claude-project`) so Claude Code can discover it. When upgrading an older ECC
+manual install, the installer migrates only nested `skills/ecc/` files recorded
+in ECC install-state. If a flat skill directory is user-owned, ECC preserves it,
+prints a conflict warning, and keeps any older managed copy tracked for a safe
+uninstall instead of overwriting user files.
+
 If you want the normal core profile but need hooks off, use:
 
 ```bash

docs/es/README.md

@@ -757,16 +757,13 @@ cp -r rules/golang ~/.claude/rules/ecc/
 cp -r rules/php ~/.claude/rules/ecc/
 cp -r rules/arkts ~/.claude/rules/ecc/
 
-# Copiar skills primero (superficie principal de flujo de trabajo)
-# Recomendado (nuevos usuarios): solo skills generales/básicas
-mkdir -p ~/.claude/skills/ecc
-cp -r .agents/skills/* ~/.claude/skills/ecc/
-cp -r skills/search-first ~/.claude/skills/ecc/
+# Instalar skills con el instalador consciente de migraciones.
+# Conserva skills del usuario, informa conflictos y evita sobrescribirlos.
+node scripts/install-apply.js --target claude --modules workflow-quality
 
-# Opcional: añadir skills específicas de framework solo cuando las necesites
-# for s in django-patterns django-tdd laravel-patterns springboot-patterns quarkus-patterns; do
-# cp -r skills/$s ~/.claude/skills/ecc/
-# done
+# Opcional: instalar skills concretas solo cuando las necesites.
+node scripts/install-apply.js --target claude --skills search-first
+# node scripts/install-apply.js --target claude --skills django-patterns,django-tdd
 
 # Opcional: mantener compatibilidad con entradas slash durante la migración
 mkdir -p ~/.claude/commands

scripts/install-apply.js

@@ -32,8 +32,8 @@ Usage: install.sh [--target <${LEGACY_INSTALL_TARGETS.join('|')}>] [--dry-run] [
        install.sh [--dry-run] [--json] --config <path>
 
 Targets:
-  claude       (default) - Install ECC into ~/.claude/ with managed rules/skills under rules/ecc and skills/ecc
-  claude-project - Install ECC into ./.claude/ (per-project) with managed rules/skills under rules/ecc and skills/ecc
+  claude       (default) - Install ECC into ~/.claude/ with managed rules under rules/ecc and flat skills under skills/
+  claude-project - Install ECC into ./.claude/ (per-project) with managed rules under rules/ecc and flat skills under skills/
   cursor       - Install rules, hooks, and bundled Cursor configs to ./.cursor/
   antigravity  - Install rules, workflows, skills, and agents to ./.agent/
   codex        - Install shared agents/config into ~/.codex/
@@ -102,7 +102,10 @@ function printHumanPlan(plan, dryRun) {
       console.log(`Excluded modules: ${plan.excludedModuleIds.join(', ')}`);
     }
   }
-  console.log(`Operations: ${plan.operations.length}`);
+  console.log(`${dryRun ? 'Operations' : 'Applied operations'}: ${plan.operations.length}`);
+  if (Array.isArray(plan.skippedOperations) && plan.skippedOperations.length > 0) {
+    console.log(`Skipped operations: ${plan.skippedOperations.length}`);
+  }
 
   if (plan.warnings.length > 0) {
     console.log('\nWarnings:');
@@ -111,11 +114,18 @@ function printHumanPlan(plan, dryRun) {
     }
   }
 
-  console.log('\nPlanned file operations:');
+  console.log(`\n${dryRun ? 'Planned' : 'Applied'} file operations:`);
   for (const operation of plan.operations) {
     console.log(`- ${operation.sourceRelativePath} -> ${operation.destinationPath}`);
   }
 
+  if (Array.isArray(plan.skippedOperations) && plan.skippedOperations.length > 0) {
+    console.log('\nSkipped file operations:');
+    for (const operation of plan.skippedOperations) {
+      console.log(`- ${operation.sourceRelativePath} -> ${operation.destinationPath}`);
+    }
+  }
+
   if (!dryRun) {
     console.log(`\nDone. Install-state written to ${plan.installStatePath}`);
   }
@@ -135,7 +145,10 @@ function main() {
       findDefaultInstallConfigPath,
       loadInstallConfig,
     } = require('./lib/install/config');
-    const { applyInstallPlan } = require('./lib/install-executor');
+    const {
+      applyInstallPlan,
+      previewInstallPlan,
+    } = require('./lib/install-executor');
     const { createInstallPlanFromRequest } = require('./lib/install/runtime');
     const defaultConfigPath = options.configPath || options.languages.length > 0
       ? null
@@ -147,13 +160,14 @@ function main() {
       ...options,
       config,
     });
-    const plan = createInstallPlanFromRequest(request, {
+    const rawPlan = createInstallPlanFromRequest(request, {
       projectRoot: process.cwd(),
       homeDir: process.env.HOME || os.homedir(),
       claudeRulesDir: process.env.CLAUDE_RULES_DIR || null,
     });
 
     if (options.dryRun) {
+      const plan = previewInstallPlan(rawPlan);
       if (options.json) {
         console.log(JSON.stringify({ dryRun: true, plan }, null, 2));
       } else {
@@ -162,7 +176,7 @@ function main() {
       return;
     }
 
-    const result = applyInstallPlan(plan);
+    const result = applyInstallPlan(rawPlan);
     if (options.json) {
       console.log(JSON.stringify({ dryRun: false, result }, null, 2));
     } else {

scripts/lib/install-executor.js

@@ -123,6 +123,11 @@ function applyInstallPlan(plan) {
   return applyPlan(plan);
 }
 
+function previewInstallPlan(plan) {
+  const { previewInstallPlan: previewPlan } = require('./install/apply');
+  return previewPlan(plan);
+}
+
 function buildCopyFileOperation({ moduleId, sourcePath, sourceRelativePath, destinationPath, strategy }) {
   return {
     kind: 'copy-file',
@@ -802,6 +807,7 @@ module.exports = {
   SUPPORTED_INSTALL_TARGETS,
   LEGACY_INSTALL_TARGETS,
   applyInstallPlan,
+  previewInstallPlan,
   createLegacyCompatInstallPlan,
   createManifestInstallPlan,
   createLegacyInstallPlan,

scripts/lib/install-lifecycle.js

@@ -7,6 +7,10 @@ const { resolveInstallPlan, loadInstallManifests } = require('./install-manifest
 const { readInstallState, writeInstallState } = require('./install-state');
 const { assertWithinTrustedRoot } = require('./path-safety');
 const { createManifestInstallPlan } = require('./install-executor');
+const {
+  prepareClaudeSkillMigration,
+  removeLegacyClaudeSkillFiles,
+} = require('./install/claude-skill-migration');
 const { getInstallTargetAdapter, listInstallTargetAdapters } = require('./install-targets/registry');
 const OPENCODE_BUILD_ARTIFACT = path.join('.opencode', 'dist');
 const OPENCODE_BUILD_SCRIPT = path.join('scripts', 'build-opencode.js');
@@ -951,6 +955,22 @@ function createRepairPlanFromRecord(record, context, options = {}) {
   };
 }
 
+function prepareRepairMigration(plan) {
+  const migration = prepareClaudeSkillMigration(plan);
+  return {
+    migration,
+    plan: {
+      ...plan,
+      operations: migration.finalState.operations,
+      statePreview: migration.finalState,
+      warnings: [
+        ...(Array.isArray(plan.warnings) ? plan.warnings : []),
+        ...migration.warnings,
+      ],
+    },
+  };
+}
+
 function repairInstalledStates(options = {}) {
   const repoRoot = options.repoRoot || DEFAULT_REPO_ROOT;
   const manifests = loadInstallManifests({ repoRoot });
@@ -988,9 +1008,10 @@ function repairInstalledStates(options = {}) {
       const opencodeBuildRepairPath = path.join(context.repoRoot, OPENCODE_BUILD_ARTIFACT);
 
       if (needsOpencodeBuild && options.dryRun) {
-        const desiredPlan = createRepairPlanFromRecord(record, context, {
+        const rawPlan = createRepairPlanFromRecord(record, context, {
           exemptValidationCodes: [OPENCODE_PLUGIN_NOT_BUILT_CODE],
         });
+        const { plan: desiredPlan } = prepareRepairMigration(rawPlan);
         const operationHealth = summarizeManagedOperationHealth(context.repoRoot, desiredPlan.operations);
         const repairOperations = [...operationHealth.missing.map(entry => ({ ...entry.operation })), ...operationHealth.drifted.map(entry => ({ ...entry.operation }))];
         const plannedRepairs = [opencodeBuildRepairPath, ...repairOperations.map(operation => operation.destinationPath)];
@@ -1002,6 +1023,7 @@ function repairInstalledStates(options = {}) {
           repairedPaths: [],
           plannedRepairs,
           stateRefreshed: false,
+          warnings: desiredPlan.warnings,
           error: null
         };
       }
@@ -1021,7 +1043,11 @@ function repairInstalledStates(options = {}) {
         }
       }
 
-      const desiredPlan = createRepairPlanFromRecord(record, context);
+      const rawPlan = createRepairPlanFromRecord(record, context);
+      const {
+        migration,
+        plan: desiredPlan,
+      } = prepareRepairMigration(rawPlan);
       const operationHealth = summarizeManagedOperationHealth(context.repoRoot, desiredPlan.operations);
 
       if (operationHealth.missingSource.length > 0) {
@@ -1031,14 +1057,20 @@ function repairInstalledStates(options = {}) {
           installStatePath: record.installStatePath,
           repairedPaths: [],
           plannedRepairs: [],
+          warnings: desiredPlan.warnings,
           error: `Missing source file(s): ${operationHealth.missingSource.map(entry => entry.sourcePath).join(', ')}`
         };
       }
 
       const repairOperations = [...operationHealth.missing.map(entry => ({ ...entry.operation })), ...operationHealth.drifted.map(entry => ({ ...entry.operation }))];
-      const plannedRepairs = needsOpencodeBuild
-        ? [opencodeBuildRepairPath, ...repairOperations.map(operation => operation.destinationPath)]
-        : repairOperations.map(operation => operation.destinationPath);
+      const legacyMigrationPaths = migration.legacyOperationsToRemove.map(
+        operation => operation.destinationPath
+      );
+      const plannedRepairs = [...new Set([
+        ...(needsOpencodeBuild ? [opencodeBuildRepairPath] : []),
+        ...repairOperations.map(operation => operation.destinationPath),
+        ...legacyMigrationPaths,
+      ])];
 
       if (options.dryRun) {
         return {
@@ -1048,26 +1080,36 @@ function repairInstalledStates(options = {}) {
           repairedPaths: [],
           plannedRepairs,
           stateRefreshed: plannedRepairs.length === 0,
+          warnings: desiredPlan.warnings,
           error: null
         };
       }
 
+      const hasLegacyMigration = migration.legacyOperationsToRemove.length > 0;
+      if (migration.requiresBridgeState && (repairOperations.length > 0 || hasLegacyMigration)) {
+        writeInstallState(desiredPlan.installStatePath, migration.bridgeState);
+      }
+
       if (repairOperations.length > 0) {
         for (const operation of repairOperations) {
           executeRepairOperation(context.repoRoot, operation, record.targetRoot);
         }
-        writeInstallState(desiredPlan.installStatePath, desiredPlan.statePreview);
-      } else {
-        writeInstallState(desiredPlan.installStatePath, desiredPlan.statePreview);
       }
+      if (hasLegacyMigration) {
+        removeLegacyClaudeSkillFiles(migration, desiredPlan.targetRoot);
+      }
+      writeInstallState(desiredPlan.installStatePath, desiredPlan.statePreview);
 
       return {
         adapter: record.adapter,
-        status: (repairOperations.length > 0 || needsOpencodeBuild) ? 'repaired' : 'ok',
+        status: (repairOperations.length > 0 || needsOpencodeBuild || hasLegacyMigration)
+          ? 'repaired'
+          : 'ok',
         installStatePath: record.installStatePath,
         repairedPaths: plannedRepairs,
         plannedRepairs: [],
         stateRefreshed: true,
+        warnings: desiredPlan.warnings,
         error: null
       };
     } catch (error) {

scripts/lib/install-targets/claude-home.js

@@ -27,14 +27,13 @@ function getClaudeManagedDestinationPath(adapter, sourceRelativePath, input) {
   }
 
   if (normalizedSourcePath === 'skills') {
-    return path.join(targetRoot, 'skills', CLAUDE_ECC_NAMESPACE);
+    return path.join(targetRoot, 'skills');
   }
 
   if (normalizedSourcePath.startsWith('skills/')) {
     return path.join(
       targetRoot,
       'skills',
-      CLAUDE_ECC_NAMESPACE,
       normalizedSourcePath.slice('skills/'.length)
     );
   }

scripts/lib/install-targets/claude-project.js

@@ -27,14 +27,13 @@ function getClaudeManagedDestinationPath(adapter, sourceRelativePath, input) {
   }
 
   if (normalizedSourcePath === 'skills') {
-    return path.join(targetRoot, 'skills', CLAUDE_ECC_NAMESPACE);
+    return path.join(targetRoot, 'skills');
   }
 
   if (normalizedSourcePath.startsWith('skills/')) {
     return path.join(
       targetRoot,
       'skills',
-      CLAUDE_ECC_NAMESPACE,
       normalizedSourcePath.slice('skills/'.length)
     );
   }

scripts/lib/install/apply.js

@@ -5,7 +5,12 @@ const path = require('path');
 
 const { writeInstallState } = require('../install-state');
 const { filterMcpConfig, parseDisabledMcpServers } = require('../mcp-config');
-const { buildInstallIndex, isNamespacedSource, rewriteRelativeLinks } = require('./link-rewrite');
+const {
+  assertSafeClaudeSkillOperation,
+  prepareClaudeSkillMigration,
+  removeLegacyClaudeSkillFiles,
+} = require('./claude-skill-migration');
+const { buildInstallIndex, rewriteRelativeLinks } = require('./link-rewrite');
 
 function isMarkdownPath(filePath) {
   return /\.(md|mdx|markdown)$/i.test(String(filePath || ''));
@@ -139,13 +144,49 @@ function buildResolvedClaudeHooks(plan) {
   };
 }
 
-function applyInstallPlan(plan) {
-  const resolvedClaudeHooksPlan = buildResolvedClaudeHooks(plan);
-  const disabledServers = parseDisabledMcpServers(process.env.ECC_DISABLED_MCPS);
-  const linkIndex = buildLinkIndexForPlan(plan);
+function previewInstallPlan(plan) {
+  const migration = prepareClaudeSkillMigration(plan);
+  return {
+    ...plan,
+    statePreview: migration.finalState,
+    plannedOperations: [...plan.operations],
+    operations: migration.appliedOperations,
+    skippedOperations: migration.skippedOperations,
+    warnings: [
+      ...(Array.isArray(plan.warnings) ? plan.warnings : []),
+      ...migration.warnings,
+    ],
+    applied: false,
+  };
+}
 
-  for (const operation of plan.operations) {
+function applyInstallPlan(plan, dependencies = {}) {
+  const persistInstallState = dependencies.writeInstallState || writeInstallState;
+  const migration = prepareClaudeSkillMigration(plan);
+  const appliedPlan = {
+    ...plan,
+    operations: migration.appliedOperations,
+  };
+  const resolvedClaudeHooksPlan = buildResolvedClaudeHooks(appliedPlan);
+  const disabledServers = parseDisabledMcpServers(process.env.ECC_DISABLED_MCPS);
+  const linkIndex = buildLinkIndexForPlan(appliedPlan);
+  const hasLegacyMigration = migration.legacyOperationsToRemove.length > 0;
+
+  if (migration.requiresBridgeState) {
+    // Own every operation that may be written during a flat-skill migration
+    // before the first copy. A later failure is retryable and uninstall can
+    // clean the entire partial install, including non-skill files. During
+    // legacy migration the bridge also retains the prior managed operations.
+    persistInstallState(plan.installStatePath, migration.bridgeState);
+  }
+
+  for (const operation of appliedPlan.operations) {
+    assertSafeClaudeSkillOperation(appliedPlan, operation);
     fs.mkdirSync(path.dirname(operation.destinationPath), { recursive: true });
+    // Recheck directories that were absent during the first validation. This
+    // narrows the symlink-swap window around mkdirSync, but path checks cannot
+    // eliminate a later TOCTOU race before the file write.
+    assertSafeClaudeSkillOperation(appliedPlan, operation);
 
     if (operation.kind === 'merge-json') {
       const payload = cloneJsonValue(operation.mergePayload);
@@ -174,16 +215,14 @@ function applyInstallPlan(plan) {
       continue;
     }
 
-    // Namespaced markdown (e.g. skills/<id> -> skills/ecc/<id>) needs its
-    // relative cross-directory links rewritten so they resolve after install
-    // (issue #2340). Files whose install path is unchanged (no namespace
-    // injected) and all non-markdown files stay on the byte-for-byte copy path.
+    // Markdown may reference files whose installed paths move, such as rules
+    // copied under rules/ecc. Rewrite only links that point at installed targets;
+    // untouched links and non-markdown files stay on the byte-for-byte path.
     if (
       linkIndex
       && operation.kind === 'copy-file'
       && operation.sourceRelativePath
       && isMarkdownPath(operation.destinationPath)
-      && isNamespacedSource(operation.sourceRelativePath, linkIndex)
     ) {
       const rewritten = rewriteRelativeLinks(
         fs.readFileSync(operation.sourcePath, 'utf8'),
@@ -205,14 +244,26 @@ function applyInstallPlan(plan) {
     );
   }
 
-  writeInstallState(plan.installStatePath, plan.statePreview);
+  if (hasLegacyMigration) {
+    removeLegacyClaudeSkillFiles(migration, plan.targetRoot);
+  }
+  persistInstallState(plan.installStatePath, migration.finalState);
 
   return {
     ...plan,
+    statePreview: migration.finalState,
+    plannedOperations: [...plan.operations],
+    operations: migration.appliedOperations,
+    skippedOperations: migration.skippedOperations,
+    warnings: [
+      ...(Array.isArray(plan.warnings) ? plan.warnings : []),
+      ...migration.warnings,
+    ],
     applied: true,
   };
 }
 
 module.exports = {
   applyInstallPlan,
+  previewInstallPlan,
 };

scripts/lib/install/claude-skill-migration.js

@@ -0,0 +1,415 @@
+'use strict';
+
+const fs = require('fs');
+const path = require('path');
+
+const { readInstallState } = require('../install-state');
+const { assertWithinTrustedRoot } = require('../path-safety');
+
+const CLAUDE_TARGETS = new Set(['claude', 'claude-project']);
+
+function pathExists(filePath) {
+  try {
+    fs.lstatSync(filePath);
+    return true;
+  } catch (error) {
+    if (error && error.code === 'ENOENT') {
+      return false;
+    }
+    throw error;
+  }
+}
+
+function normalizeSourceRelativePath(sourceRelativePath) {
+  const slashNormalized = String(sourceRelativePath || '').replace(/\\/g, '/');
+  const normalized = path.posix.normalize(slashNormalized).replace(/^\.\//, '');
+  if (
+    !normalized
+    || normalized === '.'
+    || normalized === '..'
+    || normalized.startsWith('../')
+    || path.posix.isAbsolute(normalized)
+  ) {
+    return null;
+  }
+  return normalized;
+}
+
+function comparablePath(filePath) {
+  const resolvedPath = path.resolve(filePath);
+  return process.platform === 'win32' ? resolvedPath.toLowerCase() : resolvedPath;
+}
+
+function samePath(leftPath, rightPath) {
+  return comparablePath(leftPath) === comparablePath(rightPath);
+}
+
+function assertSafeSkillPath(targetPath, targetRoot, action) {
+  const resolvedRoot = path.resolve(targetRoot);
+  const resolvedTarget = path.resolve(targetPath);
+  const relativePath = path.relative(resolvedRoot, resolvedTarget);
+  if (
+    relativePath === ''
+    || relativePath.startsWith('..')
+    || path.isAbsolute(relativePath)
+  ) {
+    throw new Error(
+      `Refusing to ${action} outside the install root: '${targetPath}' is not within '${targetRoot}'.`
+    );
+  }
+
+  let currentPath = resolvedRoot;
+  for (const segment of relativePath.split(path.sep)) {
+    currentPath = path.join(currentPath, segment);
+    let stats;
+    try {
+      stats = fs.lstatSync(currentPath);
+    } catch (error) {
+      if (error && error.code === 'ENOENT') {
+        break;
+      }
+      throw error;
+    }
+    if (stats.isSymbolicLink()) {
+      throw new Error(
+        `Refusing to ${action} through symlinked Claude skill path: '${currentPath}'.`
+      );
+    }
+  }
+
+  if (pathExists(targetRoot)) {
+    assertWithinTrustedRoot(targetPath, targetRoot, action);
+  }
+}
+
+function describeClaudeSkillOperation(targetRoot, operation) {
+  if (!operation || operation.kind !== 'copy-file') {
+    return null;
+  }
+
+  const sourceRelativePath = normalizeSourceRelativePath(operation.sourceRelativePath);
+  if (!sourceRelativePath) {
+    return null;
+  }
+
+  const sourceParts = sourceRelativePath.split('/');
+  if (sourceParts[0] !== 'skills' || sourceParts.length < 3 || !sourceParts[1]) {
+    return null;
+  }
+
+  const skillName = sourceParts[1];
+  const relativeParts = sourceParts.slice(2);
+  const flatSkillRoot = path.join(targetRoot, 'skills', skillName);
+  const legacySkillRoot = path.join(targetRoot, 'skills', 'ecc', skillName);
+
+  return {
+    sourceKey: sourceRelativePath,
+    skillName,
+    flatSkillRoot,
+    flatDestinationPath: path.join(flatSkillRoot, ...relativeParts),
+    legacySkillRoot,
+    legacyDestinationPath: path.join(legacySkillRoot, ...relativeParts),
+  };
+}
+
+function assertSafeClaudeSkillOperation(plan, operation) {
+  const target = plan && plan.adapter && plan.adapter.target;
+  if (!CLAUDE_TARGETS.has(target)) {
+    return;
+  }
+  const descriptor = describeClaudeSkillOperation(plan.targetRoot, operation);
+  if (!descriptor || !samePath(operation.destinationPath, descriptor.flatDestinationPath)) {
+    return;
+  }
+  assertSafeSkillPath(
+    operation.destinationPath,
+    plan.targetRoot,
+    'install Claude skill'
+  );
+}
+
+function isManagedOperation(operation) {
+  return operation && operation.ownership === 'managed';
+}
+
+function uniqueOperations(operations) {
+  const seen = new Set();
+  return operations.filter(operation => {
+    const key = [
+      operation.kind,
+      normalizeSourceRelativePath(operation.sourceRelativePath) || operation.sourceRelativePath,
+      comparablePath(operation.destinationPath),
+    ].join('\0');
+    if (seen.has(key)) {
+      return false;
+    }
+    seen.add(key);
+    return true;
+  });
+}
+
+function buildState(statePreview, operations) {
+  return {
+    ...statePreview,
+    operations: uniqueOperations(operations).map(operation => ({ ...operation })),
+  };
+}
+
+function groupCurrentSkillOperations(plan) {
+  const groups = new Map();
+  for (const operation of plan.operations) {
+    const descriptor = describeClaudeSkillOperation(plan.targetRoot, operation);
+    if (!descriptor || !samePath(operation.destinationPath, descriptor.flatDestinationPath)) {
+      continue;
+    }
+
+    assertSafeSkillPath(
+      operation.destinationPath,
+      plan.targetRoot,
+      'install Claude skill'
+    );
+
+    const current = groups.get(descriptor.flatSkillRoot) || [];
+    current.push({ operation, descriptor });
+    groups.set(descriptor.flatSkillRoot, current);
+  }
+  return groups;
+}
+
+function classifyPreviousOperations(plan, previousState) {
+  const flatByDestination = new Map();
+  const legacyBySource = new Map();
+  const legacyBySkillRoot = new Map();
+
+  for (const operation of (previousState && previousState.operations) || []) {
+    if (!isManagedOperation(operation)) {
+      continue;
+    }
+    const descriptor = describeClaudeSkillOperation(plan.targetRoot, operation);
+    if (!descriptor) {
+      continue;
+    }
+
+    if (samePath(operation.destinationPath, descriptor.flatDestinationPath)) {
+      assertSafeSkillPath(
+        operation.destinationPath,
+        plan.targetRoot,
+        'inspect managed Claude skill'
+      );
+      flatByDestination.set(comparablePath(operation.destinationPath), operation);
+      continue;
+    }
+
+    if (!samePath(operation.destinationPath, descriptor.legacyDestinationPath)) {
+      continue;
+    }
+
+    assertSafeSkillPath(
+      operation.destinationPath,
+      plan.targetRoot,
+      'migrate managed Claude skill'
+    );
+    legacyBySource.set(descriptor.sourceKey, operation);
+    const current = legacyBySkillRoot.get(descriptor.legacySkillRoot) || [];
+    current.push({ operation, descriptor });
+    legacyBySkillRoot.set(descriptor.legacySkillRoot, current);
+  }
+
+  return {
+    flatByDestination,
+    legacyBySource,
+    legacyBySkillRoot,
+  };
+}
+
+function createConflictWarning(skillName, flatSkillRoot, retainsLegacy) {
+  const legacySuffix = retainsLegacy
+    ? ' The existing ECC-managed nested copy was retained and remains tracked for uninstall.'
+    : '';
+  return `Skipped Claude skill '${skillName}' at ${flatSkillRoot}: the flat skill directory is user-owned because it is not recorded in ECC install-state.${legacySuffix}`;
+}
+
+function createFileConflictWarning(destinationPath, retainsLegacy) {
+  const legacySuffix = retainsLegacy
+    ? ' The matching ECC-managed nested file was retained and remains tracked for uninstall.'
+    : '';
+  return `Skipped user-owned Claude skill file ${destinationPath}: the existing file is not recorded in ECC install-state.${legacySuffix}`;
+}
+
+function createDisabledMigration(plan) {
+  return {
+    enabled: false,
+    appliedOperations: [...plan.operations],
+    skippedOperations: [],
+    warnings: [],
+    bridgeState: plan.statePreview,
+    finalState: plan.statePreview,
+    legacyOperationsToRemove: [],
+    requiresBridgeState: false,
+  };
+}
+
+function collectRetainedLegacyOperations(currentGroups, previous) {
+  const currentSourceKeys = new Set(
+    [...currentGroups.values()]
+      .flat()
+      .map(({ descriptor }) => descriptor.sourceKey)
+  );
+  return (
+    [...previous.legacyBySource.entries()]
+      .filter(([sourceKey]) => !currentSourceKeys.has(sourceKey))
+      .map(([_sourceKey, operation]) => operation)
+  );
+}
+
+function classifySkillGroup(flatSkillRoot, entries, previous) {
+  const hasManagedFlatFile = entries.some(({ operation }) => (
+    previous.flatByDestination.has(comparablePath(operation.destinationPath))
+  ));
+  const legacyEntries = previous.legacyBySkillRoot.get(
+    entries[0].descriptor.legacySkillRoot
+  ) || [];
+
+  if (pathExists(flatSkillRoot) && !hasManagedFlatFile) {
+    return {
+      skippedOperations: entries.map(({ operation }) => operation),
+      warnings: [createConflictWarning(
+        entries[0].descriptor.skillName,
+        flatSkillRoot,
+        legacyEntries.length > 0
+      )],
+      retainedLegacyOperations: legacyEntries.map(({ operation }) => operation),
+    };
+  }
+
+  const conflicts = entries.filter(({ operation }) => (
+    pathExists(operation.destinationPath)
+    && !previous.flatByDestination.has(comparablePath(operation.destinationPath))
+  ));
+  return {
+    skippedOperations: conflicts.map(({ operation }) => operation),
+    warnings: conflicts.map(({ operation, descriptor }) => createFileConflictWarning(
+      operation.destinationPath,
+      previous.legacyBySource.has(descriptor.sourceKey)
+    )),
+    retainedLegacyOperations: conflicts
+      .map(({ descriptor }) => previous.legacyBySource.get(descriptor.sourceKey))
+      .filter(Boolean),
+  };
+}
+
+function classifySkillConflicts(currentGroups, previous) {
+  const groupClassifications = [...currentGroups.entries()]
+    .map(([flatSkillRoot, entries]) => classifySkillGroup(
+      flatSkillRoot,
+      entries,
+      previous
+    ));
+  const skippedOperations = groupClassifications
+    .flatMap(classification => classification.skippedOperations);
+  return {
+    skippedOperations,
+    skippedDestinations: new Set(
+      skippedOperations.map(operation => comparablePath(operation.destinationPath))
+    ),
+    warnings: groupClassifications.flatMap(classification => classification.warnings),
+    retainedLegacyOperations: new Set([
+      ...collectRetainedLegacyOperations(currentGroups, previous),
+      ...groupClassifications.flatMap(
+        classification => classification.retainedLegacyOperations
+      ),
+    ]),
+  };
+}
+
+function buildMigrationStates(plan, previousState, previous, classification) {
+  const { skippedDestinations, retainedLegacyOperations } = classification;
+  const appliedOperations = plan.operations.filter(operation => (
+    !skippedDestinations.has(comparablePath(operation.destinationPath))
+  ));
+  const legacyOperations = [...previous.legacyBySource.values()];
+  const legacyOperationsToRemove = legacyOperations.filter(operation => (
+    !retainedLegacyOperations.has(operation)
+  ));
+  const finalOperations = [
+    ...plan.statePreview.operations.filter(operation => (
+      !skippedDestinations.has(comparablePath(operation.destinationPath))
+    )),
+    ...retainedLegacyOperations,
+  ];
+  const bridgeOperations = [
+    ...((previousState && previousState.operations) || []),
+    ...appliedOperations,
+  ];
+
+  return {
+    appliedOperations,
+    bridgeState: buildState(plan.statePreview, bridgeOperations),
+    finalState: buildState(plan.statePreview, finalOperations),
+    legacyOperationsToRemove,
+    requiresBridgeState: appliedOperations.length > 0,
+  };
+}
+
+function prepareClaudeSkillMigration(plan) {
+  const target = plan && plan.adapter && plan.adapter.target;
+  if (!CLAUDE_TARGETS.has(target)) {
+    return createDisabledMigration(plan);
+  }
+
+  const previousState = pathExists(plan.installStatePath)
+    ? readInstallState(plan.installStatePath)
+    : null;
+  const currentGroups = groupCurrentSkillOperations(plan);
+  const previous = classifyPreviousOperations(plan, previousState);
+  const classification = classifySkillConflicts(currentGroups, previous);
+  const states = buildMigrationStates(
+    plan,
+    previousState,
+    previous,
+    classification
+  );
+
+  return {
+    enabled: true,
+    appliedOperations: states.appliedOperations,
+    skippedOperations: classification.skippedOperations,
+    warnings: classification.warnings,
+    bridgeState: states.bridgeState,
+    finalState: states.finalState,
+    legacyOperationsToRemove: states.legacyOperationsToRemove,
+    requiresBridgeState: states.requiresBridgeState,
+  };
+}
+
+function cleanupEmptyLegacyParents(filePath, targetRoot) {
+  const skillsRoot = path.join(targetRoot, 'skills');
+  let currentPath = path.dirname(filePath);
+
+  while (!samePath(currentPath, skillsRoot)) {
+    assertSafeSkillPath(currentPath, targetRoot, 'clean Claude skill migration');
+    if (!pathExists(currentPath) || fs.readdirSync(currentPath).length > 0) {
+      return;
+    }
+    fs.rmdirSync(currentPath);
+    currentPath = path.dirname(currentPath);
+  }
+}
+
+function removeLegacyClaudeSkillFiles(migration, targetRoot) {
+  for (const operation of migration.legacyOperationsToRemove) {
+    assertSafeSkillPath(
+      operation.destinationPath,
+      targetRoot,
+      'migrate managed Claude skill'
+    );
+    fs.rmSync(operation.destinationPath, { force: true });
+    cleanupEmptyLegacyParents(operation.destinationPath, targetRoot);
+  }
+}
+
+module.exports = {
+  assertSafeClaudeSkillOperation,
+  prepareClaudeSkillMigration,
+  removeLegacyClaudeSkillFiles,
+};

scripts/lib/install/link-rewrite.js

@@ -22,7 +22,7 @@ function stripTrailingSlash(value) {
 // `fileMappings` is a list of { sourceRel, destRel } where both are paths
 // relative to the repo root and the install root respectively. The directory
 // map is derived by walking shared ancestors of each source/dest pair, which is
-// exact for prefix-insertion namespacing (e.g. `skills/x` -> `skills/ecc/x`):
+// exact for prefix-insertion namespacing (e.g. `rules/x` -> `rules/ecc/x`):
 // the path suffix below the inserted segment is preserved, so ancestor `k`
 // of the source maps to the dest with the matching number of trailing
 // segments removed.
@@ -94,27 +94,16 @@ function resolveInstalledTarget(target, sourceDir, index) {
   return null;
 }
 
-// True when the plan installs `sourceRel` at a different relative path than the
-// source (i.e. a namespace segment was injected, e.g. skills/x -> skills/ecc/x).
-// Callers use this to keep non-namespaced files on the byte-for-byte copy path.
-function isNamespacedSource(sourceRel, index) {
-  const normalizedSource = toPosix(sourceRel);
-  const installedSource = index && index.byFile.get(normalizedSource);
-  return Boolean(installedSource) && installedSource !== normalizedSource;
-}
-
-// Rewrite relative links in a single namespaced markdown file so they resolve
-// to the file's installed location. Returns the content unchanged when the
-// file itself was not namespaced or when no link needs adjustment. Pure: no IO.
+// Rewrite relative links in a markdown file so they resolve to installed target
+// locations. The source file may itself install at the same relative path; links
+// can still need changes when their targets move, such as rules -> rules/ecc.
+// Pure: no IO.
 function rewriteRelativeLinks(content, options) {
   const { sourceRel, index } = options || {};
   const normalizedSource = toPosix(sourceRel);
   const installedSource = index && index.byFile.get(normalizedSource);
 
-  // Only rewrite when the file's own install path gained/changed a namespace
-  // segment. If it lands at the same relative path, every link recomputes to
-  // itself, so there is nothing to do.
-  if (!installedSource || installedSource === normalizedSource) {
+  if (!installedSource) {
     return content;
   }
 
@@ -174,6 +163,5 @@ function rewriteRelativeLinks(content, options) {
 
 module.exports = {
   buildInstallIndex,
-  isNamespacedSource,
   rewriteRelativeLinks,
 };

tests/lib/install-claude-skill-migration.test.js

@@ -0,0 +1,811 @@
+'use strict';
+
+const assert = require('assert');
+const fs = require('fs');
+const os = require('os');
+const path = require('path');
+
+const { applyInstallPlan } = require('../../scripts/lib/install/apply');
+const { readInstallState, writeInstallState } = require('../../scripts/lib/install-state');
+const { uninstallInstalledStates } = require('../../scripts/lib/install-lifecycle');
+
+function createTempDir(prefix) {
+  return fs.mkdtempSync(path.join(os.tmpdir(), prefix));
+}
+
+function cleanup(dirPath) {
+  fs.rmSync(dirPath, { recursive: true, force: true });
+}
+
+function createOperation(moduleId, sourceRoot, sourceRelativePath, destinationPath) {
+  return {
+    kind: 'copy-file',
+    moduleId,
+    sourcePath: path.join(sourceRoot, sourceRelativePath),
+    sourceRelativePath,
+    destinationPath,
+    strategy: 'preserve-relative-path',
+    ownership: 'managed',
+    scaffoldOnly: false,
+  };
+}
+
+function createFixture(options = {}) {
+  const tempDir = createTempDir('claude-skill-migration-');
+  const homeDir = path.join(tempDir, 'home');
+  const projectRoot = path.join(tempDir, 'project');
+  const sourceRoot = path.join(tempDir, 'source');
+  const target = options.target || 'claude';
+  const targetRoot = target === 'claude'
+    ? path.join(homeDir, '.claude')
+    : path.join(projectRoot, '.claude');
+  const installStatePath = path.join(targetRoot, 'ecc', 'install-state.json');
+  const skillFiles = options.skillFiles || {
+    'SKILL.md': '# Current ECC skill\n',
+    'references/guide.md': '# Current ECC guide\n',
+  };
+
+  for (const [relativePath, content] of Object.entries(skillFiles)) {
+    const sourcePath = path.join(sourceRoot, 'skills', 'demo-skill', relativePath);
+    fs.mkdirSync(path.dirname(sourcePath), { recursive: true });
+    fs.writeFileSync(sourcePath, content);
+  }
+
+  const operations = Object.keys(skillFiles).map(relativePath => createOperation(
+    'workflow-quality',
+    sourceRoot,
+    path.join('skills', 'demo-skill', relativePath),
+    path.join(targetRoot, 'skills', 'demo-skill', relativePath)
+  ));
+  const statePreview = {
+    schemaVersion: 'ecc.install.v1',
+    installedAt: new Date().toISOString(),
+    target: {
+      id: target === 'claude' ? 'claude-home' : 'claude-project',
+      target,
+      kind: target === 'claude' ? 'home' : 'project',
+      root: targetRoot,
+      installStatePath,
+    },
+    request: {
+      profile: null,
+      modules: ['workflow-quality'],
+      includeComponents: [],
+      excludeComponents: [],
+      legacyLanguages: [],
+      legacyMode: false,
+    },
+    resolution: {
+      selectedModules: ['workflow-quality'],
+      skippedModules: [],
+    },
+    source: {
+      repoVersion: null,
+      repoCommit: null,
+      manifestVersion: 1,
+    },
+    operations: operations.map(operation => ({ ...operation })),
+  };
+
+  return {
+    tempDir,
+    homeDir,
+    projectRoot,
+    sourceRoot,
+    target,
+    targetRoot,
+    installStatePath,
+    operations,
+    plan: {
+      mode: 'manifest',
+      target,
+      adapter: {
+        id: target === 'claude' ? 'claude-home' : 'claude-project',
+        target,
+        kind: target === 'claude' ? 'home' : 'project',
+      },
+      targetRoot,
+      installRoot: targetRoot,
+      installStatePath,
+      operations,
+      statePreview,
+      warnings: [],
+    },
+  };
+}
+
+function legacyDestinationPath(targetRoot, operation) {
+  const sourceParts = operation.sourceRelativePath.split(path.sep);
+  return path.join(targetRoot, 'skills', 'ecc', ...sourceParts.slice(1));
+}
+
+function seedLegacyInstall(fixture, options = {}) {
+  const legacyOperations = fixture.operations.map((operation, index) => {
+    const destinationPath = legacyDestinationPath(fixture.targetRoot, operation);
+    fs.mkdirSync(path.dirname(destinationPath), { recursive: true });
+    fs.writeFileSync(destinationPath, `# Legacy managed file ${index}\n`);
+    return {
+      ...operation,
+      sourceRelativePath: options.windowsSourcePaths
+        ? operation.sourceRelativePath.split(path.sep).join('\\')
+        : operation.sourceRelativePath,
+      destinationPath,
+    };
+  });
+
+  writeInstallState(fixture.installStatePath, {
+    ...fixture.plan.statePreview,
+    operations: legacyOperations,
+  });
+  return legacyOperations;
+}
+
+function runUninstall(fixture) {
+  return uninstallInstalledStates({
+    homeDir: fixture.homeDir,
+    projectRoot: fixture.projectRoot,
+    targets: [fixture.target],
+  });
+}
+
+function test(name, fn) {
+  try {
+    fn();
+    console.log(`  \u2713 ${name}`);
+    return true;
+  } catch (error) {
+    console.log(`  \u2717 ${name}`);
+    console.log(`    Error: ${error.stack || error.message}`);
+    return false;
+  }
+}
+
+function runTests() {
+  console.log('\n=== Testing Claude flat-skill migration ===\n');
+  let passed = 0;
+  let failed = 0;
+
+  for (const target of ['claude', 'claude-project']) {
+    if (test(`migrates state-managed nested skills for ${target} without deleting untracked files`, () => {
+      const fixture = createFixture({ target });
+      try {
+        const legacyOperations = seedLegacyInstall(fixture, {
+          windowsSourcePaths: target === 'claude-project',
+        });
+        const untrackedPath = path.join(
+          fixture.targetRoot,
+          'skills',
+          'ecc',
+          'demo-skill',
+          'user-notes.md'
+        );
+        fs.writeFileSync(untrackedPath, '# User notes\n');
+
+        applyInstallPlan(fixture.plan);
+
+        for (const operation of fixture.operations) {
+          assert.strictEqual(
+            fs.readFileSync(operation.destinationPath, 'utf8'),
+            fs.readFileSync(operation.sourcePath, 'utf8')
+          );
+        }
+        for (const operation of legacyOperations) {
+          assert.ok(!fs.existsSync(operation.destinationPath), operation.destinationPath);
+        }
+        assert.strictEqual(fs.readFileSync(untrackedPath, 'utf8'), '# User notes\n');
+
+        const state = readInstallState(fixture.installStatePath);
+        assert.ok(state.operations.some(operation => (
+          operation.destinationPath === fixture.operations[0].destinationPath
+        )));
+        assert.ok(!state.operations.some(operation => (
+          operation.destinationPath.includes(path.join('skills', 'ecc', 'demo-skill'))
+        )));
+
+        const rerun = applyInstallPlan(fixture.plan);
+        assert.deepStrictEqual(rerun.skippedOperations, []);
+        assert.strictEqual(fs.readFileSync(untrackedPath, 'utf8'), '# User notes\n');
+
+        const uninstall = runUninstall(fixture);
+        assert.strictEqual(uninstall.summary.errorCount, 0);
+        assert.ok(!fs.existsSync(fixture.operations[0].destinationPath));
+        assert.strictEqual(fs.readFileSync(untrackedPath, 'utf8'), '# User notes\n');
+      } finally {
+        cleanup(fixture.tempDir);
+      }
+    })) passed++; else failed++;
+  }
+
+  if (test('selective migration preserves unrelated legacy skills and uninstall ownership', () => {
+    const fixture = createFixture();
+    try {
+      const legacyOperations = seedLegacyInstall(fixture);
+      const otherSourceRelativePath = path.join('skills', 'other-skill', 'SKILL.md');
+      const otherSourcePath = path.join(fixture.sourceRoot, otherSourceRelativePath);
+      const otherLegacyPath = path.join(
+        fixture.targetRoot,
+        'skills',
+        'ecc',
+        'other-skill',
+        'SKILL.md'
+      );
+      fs.mkdirSync(path.dirname(otherSourcePath), { recursive: true });
+      fs.mkdirSync(path.dirname(otherLegacyPath), { recursive: true });
+      fs.writeFileSync(otherSourcePath, '# Other source\n');
+      fs.writeFileSync(otherLegacyPath, '# Other legacy managed skill\n');
+      const otherLegacyOperation = createOperation(
+        'other-module',
+        fixture.sourceRoot,
+        otherSourceRelativePath,
+        otherLegacyPath
+      );
+      writeInstallState(fixture.installStatePath, {
+        ...fixture.plan.statePreview,
+        operations: [...legacyOperations, otherLegacyOperation],
+      });
+
+      applyInstallPlan(fixture.plan);
+
+      assert.ok(legacyOperations.every(operation => !fs.existsSync(operation.destinationPath)));
+      assert.strictEqual(
+        fs.readFileSync(otherLegacyPath, 'utf8'),
+        '# Other legacy managed skill\n'
+      );
+      const state = readInstallState(fixture.installStatePath);
+      assert.ok(state.operations.some(operation => (
+        operation.destinationPath === otherLegacyPath
+      )));
+
+      const uninstall = runUninstall(fixture);
+      assert.strictEqual(uninstall.summary.errorCount, 0);
+      assert.ok(!fs.existsSync(otherLegacyPath));
+    } finally {
+      cleanup(fixture.tempDir);
+    }
+  })) passed++; else failed++;
+
+  if (test('reruns a completed migration idempotently and remains uninstallable', () => {
+    const fixture = createFixture();
+    try {
+      const legacyOperations = seedLegacyInstall(fixture);
+      applyInstallPlan(fixture.plan);
+      const stateAfterMigration = readInstallState(fixture.installStatePath);
+
+      const rerun = applyInstallPlan(fixture.plan);
+      const stateAfterRerun = readInstallState(fixture.installStatePath);
+
+      assert.deepStrictEqual(rerun.skippedOperations, []);
+      assert.ok(!rerun.warnings.some(warning => (
+        warning.includes('user-owned') || warning.includes('nested copy')
+      )));
+      assert.deepStrictEqual(stateAfterRerun, stateAfterMigration);
+      assert.ok(fixture.operations.every(operation => (
+        fs.readFileSync(operation.destinationPath, 'utf8')
+          === fs.readFileSync(operation.sourcePath, 'utf8')
+      )));
+      assert.ok(legacyOperations.every(operation => !fs.existsSync(operation.destinationPath)));
+      assert.ok(!fs.existsSync(path.join(fixture.targetRoot, 'skills', 'ecc')));
+
+      const uninstall = runUninstall(fixture);
+      assert.strictEqual(uninstall.summary.errorCount, 0);
+      assert.ok(fixture.operations.every(operation => !fs.existsSync(operation.destinationPath)));
+    } finally {
+      cleanup(fixture.tempDir);
+    }
+  })) passed++; else failed++;
+
+  if (test('preserves a user-owned flat skill and keeps legacy ownership for uninstall', () => {
+    const fixture = createFixture();
+    try {
+      const legacyOperations = seedLegacyInstall(fixture);
+      const userSkillPath = fixture.operations[0].destinationPath;
+      fs.mkdirSync(path.dirname(userSkillPath), { recursive: true });
+      fs.writeFileSync(userSkillPath, '# User-owned flat skill\n');
+
+      const result = applyInstallPlan(fixture.plan);
+
+      assert.strictEqual(fs.readFileSync(userSkillPath, 'utf8'), '# User-owned flat skill\n');
+      assert.ok(legacyOperations.every(operation => fs.existsSync(operation.destinationPath)));
+      assert.ok(result.warnings.some(warning => (
+        warning.includes('demo-skill') && warning.includes('user-owned')
+      )), JSON.stringify(result.warnings));
+      assert.strictEqual(result.operations.length, 0);
+      assert.strictEqual(result.skippedOperations.length, fixture.operations.length);
+
+      const state = readInstallState(fixture.installStatePath);
+      assert.ok(legacyOperations.every(legacyOperation => (
+        state.operations.some(operation => operation.destinationPath === legacyOperation.destinationPath)
+      )));
+      assert.ok(!state.operations.some(operation => (
+        operation.destinationPath === fixture.operations[0].destinationPath
+      )));
+
+      const uninstall = runUninstall(fixture);
+      assert.strictEqual(uninstall.summary.errorCount, 0);
+      assert.strictEqual(fs.readFileSync(userSkillPath, 'utf8'), '# User-owned flat skill\n');
+      assert.ok(legacyOperations.every(operation => !fs.existsSync(operation.destinationPath)));
+    } finally {
+      cleanup(fixture.tempDir);
+    }
+  })) passed++; else failed++;
+
+  if (test('does not claim or merge into a user-owned flat skill on first install', () => {
+    const fixture = createFixture();
+    try {
+      const userSkillPath = fixture.operations[0].destinationPath;
+      fs.mkdirSync(path.dirname(userSkillPath), { recursive: true });
+      fs.writeFileSync(userSkillPath, '# User-owned flat skill\n');
+
+      const result = applyInstallPlan(fixture.plan);
+
+      assert.strictEqual(fs.readFileSync(userSkillPath, 'utf8'), '# User-owned flat skill\n');
+      assert.ok(!fs.existsSync(fixture.operations[1].destinationPath));
+      assert.ok(result.warnings.some(warning => warning.includes('user-owned')));
+      assert.strictEqual(result.operations.length, 0);
+      assert.strictEqual(result.skippedOperations.length, fixture.operations.length);
+      assert.deepStrictEqual(readInstallState(fixture.installStatePath).operations, []);
+
+      const uninstall = runUninstall(fixture);
+      assert.strictEqual(uninstall.summary.errorCount, 0);
+      assert.strictEqual(fs.readFileSync(userSkillPath, 'utf8'), '# User-owned flat skill\n');
+    } finally {
+      cleanup(fixture.tempDir);
+    }
+  })) passed++; else failed++;
+
+  if (test('updates recorded flat files but preserves conflicting unrecorded files', () => {
+    const initial = createFixture({
+      skillFiles: {
+        'SKILL.md': '# Initial ECC skill\n',
+      },
+    });
+    let expanded;
+    try {
+      applyInstallPlan(initial.plan);
+      expanded = createFixture({
+        skillFiles: {
+          'SKILL.md': '# Updated ECC skill\n',
+          'references/guide.md': '# ECC guide\n',
+          'references/new.md': '# New managed file\n',
+        },
+      });
+      const expandedOriginalTargetRoot = expanded.targetRoot;
+      expanded.homeDir = initial.homeDir;
+      expanded.projectRoot = initial.projectRoot;
+      expanded.targetRoot = initial.targetRoot;
+      expanded.installStatePath = initial.installStatePath;
+      expanded.operations = expanded.operations.map(operation => ({
+        ...operation,
+        destinationPath: path.join(
+          initial.targetRoot,
+          path.relative(expandedOriginalTargetRoot, operation.destinationPath)
+        ),
+      }));
+      expanded.plan = {
+        ...expanded.plan,
+        targetRoot: initial.targetRoot,
+        installRoot: initial.targetRoot,
+        installStatePath: initial.installStatePath,
+        operations: expanded.operations,
+        statePreview: {
+          ...expanded.plan.statePreview,
+          target: {
+            ...expanded.plan.statePreview.target,
+            root: initial.targetRoot,
+            installStatePath: initial.installStatePath,
+          },
+          operations: expanded.operations,
+        },
+      };
+
+      const userGuidePath = expanded.operations[1].destinationPath;
+      fs.mkdirSync(path.dirname(userGuidePath), { recursive: true });
+      fs.writeFileSync(userGuidePath, '# User guide\n');
+
+      const result = applyInstallPlan(expanded.plan);
+
+      assert.strictEqual(
+        fs.readFileSync(expanded.operations[0].destinationPath, 'utf8'),
+        '# Updated ECC skill\n'
+      );
+      assert.strictEqual(fs.readFileSync(userGuidePath, 'utf8'), '# User guide\n');
+      assert.strictEqual(
+        fs.readFileSync(expanded.operations[2].destinationPath, 'utf8'),
+        '# New managed file\n'
+      );
+      assert.ok(result.warnings.some(warning => warning.includes('guide.md')));
+
+      const state = readInstallState(initial.installStatePath);
+      assert.ok(state.operations.some(operation => (
+        operation.destinationPath === expanded.operations[0].destinationPath
+      )));
+      assert.ok(!state.operations.some(operation => (
+        operation.destinationPath === userGuidePath
+      )));
+      assert.ok(state.operations.some(operation => (
+        operation.destinationPath === expanded.operations[2].destinationPath
+      )));
+    } finally {
+      cleanup(initial.tempDir);
+      if (expanded) {
+        cleanup(expanded.tempDir);
+      }
+    }
+  })) passed++; else failed++;
+
+  if (test('tracks a partial migration so retry and uninstall remain safe', () => {
+    const fixture = createFixture();
+    try {
+      const legacyOperations = seedLegacyInstall(fixture);
+      const missingSourcePlan = {
+        ...fixture.plan,
+        operations: fixture.operations.map((operation, index) => (
+          index === 1
+            ? { ...operation, sourcePath: path.join(fixture.sourceRoot, 'missing.md') }
+            : operation
+        )),
+      };
+
+      assert.throws(() => applyInstallPlan(missingSourcePlan), /ENOENT/);
+      assert.ok(legacyOperations.every(operation => fs.existsSync(operation.destinationPath)));
+      assert.ok(fs.existsSync(fixture.operations[0].destinationPath));
+      assert.ok(!fs.existsSync(fixture.operations[1].destinationPath));
+      const bridgeState = readInstallState(fixture.installStatePath);
+      assert.ok(legacyOperations.every(legacyOperation => (
+        bridgeState.operations.some(operation => (
+          operation.destinationPath === legacyOperation.destinationPath
+        ))
+      )));
+      assert.ok(fixture.operations.every(flatOperation => (
+        bridgeState.operations.some(operation => (
+          operation.destinationPath === flatOperation.destinationPath
+        ))
+      )));
+
+      const retry = applyInstallPlan(fixture.plan);
+      assert.deepStrictEqual(retry.skippedOperations, []);
+      assert.ok(fixture.operations.every(operation => fs.existsSync(operation.destinationPath)));
+      assert.ok(legacyOperations.every(operation => !fs.existsSync(operation.destinationPath)));
+
+      const uninstall = runUninstall(fixture);
+      assert.strictEqual(uninstall.summary.errorCount, 0);
+      assert.ok(fixture.operations.every(operation => !fs.existsSync(operation.destinationPath)));
+    } finally {
+      cleanup(fixture.tempDir);
+    }
+  })) passed++; else failed++;
+
+  if (test('tracks a partial first install so retry does not misclassify it as user-owned', () => {
+    const fixture = createFixture();
+    try {
+      const missingSourcePlan = {
+        ...fixture.plan,
+        operations: fixture.operations.map((operation, index) => (
+          index === 1
+            ? { ...operation, sourcePath: path.join(fixture.sourceRoot, 'missing.md') }
+            : operation
+        )),
+      };
+
+      assert.throws(() => applyInstallPlan(missingSourcePlan), /ENOENT/);
+      assert.ok(fs.existsSync(fixture.operations[0].destinationPath));
+      assert.ok(!fs.existsSync(fixture.operations[1].destinationPath));
+      const bridgeState = readInstallState(fixture.installStatePath);
+      assert.ok(fixture.operations.every(flatOperation => (
+        bridgeState.operations.some(operation => (
+          operation.destinationPath === flatOperation.destinationPath
+        ))
+      )));
+
+      const retry = applyInstallPlan(fixture.plan);
+      assert.deepStrictEqual(retry.skippedOperations, []);
+      assert.ok(!retry.warnings.some(warning => warning.includes('user-owned')));
+      assert.ok(fixture.operations.every(operation => fs.existsSync(operation.destinationPath)));
+
+      const uninstall = runUninstall(fixture);
+      assert.strictEqual(uninstall.summary.errorCount, 0);
+      assert.ok(fixture.operations.every(operation => !fs.existsSync(operation.destinationPath)));
+    } finally {
+      cleanup(fixture.tempDir);
+    }
+  })) passed++; else failed++;
+
+  if (test('tracks non-skill files written before a partial flat-skill install fails', () => {
+    const fixture = createFixture();
+    try {
+      const ruleSourceRelativePath = path.join('rules', 'common', 'coding.md');
+      const ruleSourcePath = path.join(fixture.sourceRoot, ruleSourceRelativePath);
+      const ruleDestinationPath = path.join(
+        fixture.targetRoot,
+        'rules',
+        'ecc',
+        'common',
+        'coding.md'
+      );
+      fs.mkdirSync(path.dirname(ruleSourcePath), { recursive: true });
+      fs.writeFileSync(ruleSourcePath, '# Managed rule\n');
+
+      const ruleOperation = createOperation(
+        'workflow-quality',
+        fixture.sourceRoot,
+        ruleSourceRelativePath,
+        ruleDestinationPath
+      );
+      const missingOperation = createOperation(
+        'workflow-quality',
+        fixture.sourceRoot,
+        path.join('commands', 'missing.md'),
+        path.join(fixture.targetRoot, 'commands', 'missing.md')
+      );
+      const operations = [
+        fixture.operations[0],
+        ruleOperation,
+        missingOperation,
+      ];
+      const partialPlan = {
+        ...fixture.plan,
+        operations,
+        statePreview: {
+          ...fixture.plan.statePreview,
+          operations: operations.map(operation => ({ ...operation })),
+        },
+      };
+
+      assert.throws(() => applyInstallPlan(partialPlan), /ENOENT/);
+      assert.ok(fs.existsSync(ruleDestinationPath));
+
+      const bridgeState = readInstallState(fixture.installStatePath);
+      assert.ok(bridgeState.operations.some(operation => (
+        operation.destinationPath === ruleDestinationPath
+      )));
+
+      const uninstall = runUninstall(fixture);
+      assert.strictEqual(uninstall.summary.errorCount, 0);
+      assert.ok(!fs.existsSync(ruleDestinationPath));
+    } finally {
+      cleanup(fixture.tempDir);
+    }
+  })) passed++; else failed++;
+
+  if (test('tracks partial non-skill writes when every flat skill is user-owned', () => {
+    const fixture = createFixture();
+    try {
+      const userSkillPath = fixture.operations[0].destinationPath;
+      fs.mkdirSync(path.dirname(userSkillPath), { recursive: true });
+      fs.writeFileSync(userSkillPath, '# User skill\n');
+
+      const ruleSourceRelativePath = path.join('rules', 'common', 'coding.md');
+      const ruleSourcePath = path.join(fixture.sourceRoot, ruleSourceRelativePath);
+      const ruleDestinationPath = path.join(
+        fixture.targetRoot,
+        'rules',
+        'ecc',
+        'common',
+        'coding.md'
+      );
+      fs.mkdirSync(path.dirname(ruleSourcePath), { recursive: true });
+      fs.writeFileSync(ruleSourcePath, '# Managed rule\n');
+
+      const ruleOperation = createOperation(
+        'workflow-quality',
+        fixture.sourceRoot,
+        ruleSourceRelativePath,
+        ruleDestinationPath
+      );
+      const missingOperation = createOperation(
+        'workflow-quality',
+        fixture.sourceRoot,
+        path.join('commands', 'missing.md'),
+        path.join(fixture.targetRoot, 'commands', 'missing.md')
+      );
+      const operations = [
+        ...fixture.operations,
+        ruleOperation,
+        missingOperation,
+      ];
+      const partialPlan = {
+        ...fixture.plan,
+        operations,
+        statePreview: {
+          ...fixture.plan.statePreview,
+          operations: operations.map(operation => ({ ...operation })),
+        },
+      };
+
+      assert.throws(() => applyInstallPlan(partialPlan), /ENOENT/);
+      assert.strictEqual(fs.readFileSync(userSkillPath, 'utf8'), '# User skill\n');
+      assert.ok(fs.existsSync(ruleDestinationPath));
+
+      const bridgeState = readInstallState(fixture.installStatePath);
+      assert.ok(!bridgeState.operations.some(operation => (
+        operation.destinationPath === userSkillPath
+      )));
+      assert.ok(bridgeState.operations.some(operation => (
+        operation.destinationPath === ruleDestinationPath
+      )));
+
+      const uninstall = runUninstall(fixture);
+      assert.strictEqual(uninstall.summary.errorCount, 0);
+      assert.strictEqual(fs.readFileSync(userSkillPath, 'utf8'), '# User skill\n');
+      assert.ok(!fs.existsSync(ruleDestinationPath));
+    } finally {
+      cleanup(fixture.tempDir);
+    }
+  })) passed++; else failed++;
+
+  if (test('keeps legacy files tracked when the bridge state write fails', () => {
+    const fixture = createFixture();
+    try {
+      const legacyOperations = seedLegacyInstall(fixture);
+      const failingStateWriter = filePath => {
+        assert.strictEqual(
+          path.resolve(filePath),
+          path.resolve(fixture.installStatePath)
+        );
+        throw new Error('injected install-state write failure');
+      };
+
+      assert.throws(
+        () => applyInstallPlan(fixture.plan, { writeInstallState: failingStateWriter }),
+        /injected install-state write failure/
+      );
+
+      assert.ok(legacyOperations.every(operation => fs.existsSync(operation.destinationPath)));
+      assert.ok(fixture.operations.every(operation => !fs.existsSync(operation.destinationPath)));
+      const state = readInstallState(fixture.installStatePath);
+      assert.ok(state.operations.every(operation => (
+        operation.destinationPath.includes(path.join('skills', 'ecc', 'demo-skill'))
+      )));
+
+      const retry = applyInstallPlan(fixture.plan);
+      assert.deepStrictEqual(retry.skippedOperations, []);
+      const uninstall = runUninstall(fixture);
+      assert.strictEqual(uninstall.summary.errorCount, 0);
+      assert.ok(fixture.operations.every(operation => !fs.existsSync(operation.destinationPath)));
+    } finally {
+      cleanup(fixture.tempDir);
+    }
+  })) passed++; else failed++;
+
+  if (test('keeps both layouts represented if the final state write fails', () => {
+    const fixture = createFixture();
+    let stateWriteCount = 0;
+    try {
+      const legacyOperations = seedLegacyInstall(fixture);
+      const failFinalStateWrite = (filePath, state) => {
+        assert.strictEqual(
+          path.resolve(filePath),
+          path.resolve(fixture.installStatePath)
+        );
+        stateWriteCount += 1;
+        if (stateWriteCount === 2) {
+          throw new Error('injected final install-state write failure');
+        }
+        return writeInstallState(fixture.installStatePath, state);
+      };
+
+      assert.throws(
+        () => applyInstallPlan(fixture.plan, { writeInstallState: failFinalStateWrite }),
+        /injected final install-state write failure/
+      );
+      assert.ok(fixture.operations.every(operation => fs.existsSync(operation.destinationPath)));
+      assert.ok(legacyOperations.every(operation => !fs.existsSync(operation.destinationPath)));
+
+      const bridgeState = readInstallState(fixture.installStatePath);
+      assert.ok(fixture.operations.every(flatOperation => (
+        bridgeState.operations.some(operation => (
+          operation.destinationPath === flatOperation.destinationPath
+        ))
+      )));
+      assert.ok(bridgeState.operations.some(operation => (
+        operation.destinationPath.includes(path.join('skills', 'ecc', 'demo-skill'))
+      )));
+
+      const uninstall = runUninstall(fixture);
+      assert.strictEqual(uninstall.summary.errorCount, 0);
+      assert.ok(fixture.operations.every(operation => !fs.existsSync(operation.destinationPath)));
+    } finally {
+      cleanup(fixture.tempDir);
+    }
+  })) passed++; else failed++;
+
+  if (test('rejects a flat skill symlink that escapes the Claude install root', () => {
+    if (process.platform === 'win32') {
+      console.log('    ↷ skipped on Windows: symlink privileges vary');
+      return;
+    }
+
+    const fixture = createFixture();
+    try {
+      const outsideRoot = path.join(fixture.tempDir, 'outside');
+      fs.mkdirSync(outsideRoot, { recursive: true });
+      const flatSkillRoot = path.join(fixture.targetRoot, 'skills', 'demo-skill');
+      fs.mkdirSync(path.dirname(flatSkillRoot), { recursive: true });
+      fs.symlinkSync(outsideRoot, flatSkillRoot, 'dir');
+
+      assert.throws(
+        () => applyInstallPlan(fixture.plan),
+        /symlinked Claude skill path/
+      );
+      assert.deepStrictEqual(fs.readdirSync(outsideRoot), []);
+      assert.ok(!fs.existsSync(fixture.installStatePath));
+    } finally {
+      cleanup(fixture.tempDir);
+    }
+  })) passed++; else failed++;
+
+  if (test('rechecks skill directories created between validation and copy', () => {
+    if (process.platform === 'win32') {
+      console.log('    ↷ skipped on Windows: symlink privileges vary');
+      return;
+    }
+
+    const fixture = createFixture({
+      skillFiles: {
+        'SKILL.md': '# Current ECC skill\n',
+      },
+    });
+    const destinationDirectory = path.dirname(fixture.operations[0].destinationPath);
+    const outsideRoot = path.join(fixture.tempDir, 'outside');
+    const originalMkdirSync = fs.mkdirSync;
+
+    try {
+      originalMkdirSync(outsideRoot, { recursive: true });
+      let injectedSymlink = false;
+      fs.mkdirSync = function mkdirAndReplaceWithSymlink(directoryPath, options) {
+        const result = originalMkdirSync(directoryPath, options);
+        if (!injectedSymlink && path.resolve(directoryPath) === path.resolve(destinationDirectory)) {
+          fs.rmSync(destinationDirectory, { recursive: true, force: true });
+          fs.symlinkSync(outsideRoot, destinationDirectory, 'dir');
+          injectedSymlink = true;
+        }
+        return result;
+      };
+
+      assert.throws(
+        () => applyInstallPlan(fixture.plan, { writeInstallState() {} }),
+        /symlinked Claude skill path/
+      );
+      assert.strictEqual(injectedSymlink, true);
+      assert.deepStrictEqual(fs.readdirSync(outsideRoot), []);
+    } finally {
+      fs.mkdirSync = originalMkdirSync;
+      cleanup(fixture.tempDir);
+    }
+  })) passed++; else failed++;
+
+  if (test('rejects a dangling destination symlink before copying a Claude skill file', () => {
+    if (process.platform === 'win32') {
+      console.log('    ↷ skipped on Windows: symlink privileges vary');
+      return;
+    }
+
+    const fixture = createFixture({
+      skillFiles: {
+        'SKILL.md': '# Current ECC skill\n',
+      },
+    });
+    try {
+      const outsideRoot = path.join(fixture.tempDir, 'outside');
+      const outsideTarget = path.join(outsideRoot, 'not-created.md');
+      fs.mkdirSync(outsideRoot, { recursive: true });
+      fs.mkdirSync(path.dirname(fixture.operations[0].destinationPath), { recursive: true });
+      fs.symlinkSync(outsideTarget, fixture.operations[0].destinationPath, 'file');
+      assert.strictEqual(fs.existsSync(fixture.operations[0].destinationPath), false);
+
+      assert.throws(
+        () => applyInstallPlan(fixture.plan),
+        /symlinked Claude skill path/
+      );
+      assert.ok(!fs.existsSync(outsideTarget));
+      assert.ok(!fs.existsSync(fixture.installStatePath));
+    } finally {
+      cleanup(fixture.tempDir);
+    }
+  })) passed++; else failed++;
+
+  console.log(`\nResults: Passed: ${passed}, Failed: ${failed}`);
+  process.exit(failed > 0 ? 1 : 0);
+}
+
+runTests();

tests/lib/install-executor.test.js

@@ -362,7 +362,7 @@ function runTests() {
       )));
       assert.ok(plan.operations.some(operation => (
         operation.sourceRelativePath === path.join('skills', 'demo', 'SKILL.md')
-        && operation.destinationPath === path.join(homeDir, '.claude', 'skills', 'ecc', 'demo', 'SKILL.md')
+        && operation.destinationPath === path.join(homeDir, '.claude', 'skills', 'demo', 'SKILL.md')
       )));
       assert.deepStrictEqual(plan.warnings, ['fixture warning']);
       assert.strictEqual(plan.statePreview.request.profile, 'minimal');
@@ -416,7 +416,7 @@ function runTests() {
 
       assert.strictEqual(applied.applied, true);
       assert.ok(fs.existsSync(path.join(homeDir, '.claude', 'rules', 'ecc', 'common', 'coding-style.md')));
-      assert.ok(fs.existsSync(path.join(homeDir, '.claude', 'skills', 'ecc', 'demo', 'SKILL.md')));
+      assert.ok(fs.existsSync(path.join(homeDir, '.claude', 'skills', 'demo', 'SKILL.md')));
       assert.ok(fs.existsSync(path.join(homeDir, '.claude', 'src', 'app.js')));
       assert.ok(fs.existsSync(path.join(homeDir, '.claude', 'standalone.txt')));
       assert.ok(fs.existsSync(path.join(homeDir, '.claude', 'plugin.json')));

tests/lib/install-lifecycle.test.js

@@ -634,6 +634,103 @@ function runTests() {
     }
   })) passed++; else failed++;
 
+  if (test('Claude repair and dry-run preserve user-owned flat skills during legacy migration', () => {
+    const homeDir = createTempDir('install-lifecycle-home-');
+    const projectRoot = createTempDir('install-lifecycle-project-');
+
+    try {
+      const targetRoot = path.join(homeDir, '.claude');
+      const installStatePath = path.join(targetRoot, 'ecc', 'install-state.json');
+      const flatSkillPath = path.join(targetRoot, 'skills', 'tdd-workflow', 'SKILL.md');
+      const legacySkillPath = path.join(
+        targetRoot,
+        'skills',
+        'ecc',
+        'tdd-workflow',
+        'SKILL.md'
+      );
+      fs.mkdirSync(path.dirname(flatSkillPath), { recursive: true });
+      fs.mkdirSync(path.dirname(legacySkillPath), { recursive: true });
+      fs.writeFileSync(flatSkillPath, '# User-owned flat skill\n');
+      fs.writeFileSync(legacySkillPath, '# Previously managed nested skill\n');
+
+      writeState(installStatePath, {
+        adapter: { id: 'claude-home', target: 'claude', kind: 'home' },
+        targetRoot,
+        installStatePath,
+        request: {
+          profile: null,
+          modules: ['workflow-quality'],
+          includeComponents: [],
+          excludeComponents: [],
+          legacyLanguages: [],
+          legacyMode: false,
+        },
+        resolution: {
+          selectedModules: ['platform-configs', 'workflow-quality'],
+          skippedModules: [],
+        },
+        operations: [{
+          kind: 'copy-file',
+          moduleId: 'workflow-quality',
+          sourcePath: path.join(REPO_ROOT, 'skills', 'tdd-workflow', 'SKILL.md'),
+          sourceRelativePath: path.join('skills', 'tdd-workflow', 'SKILL.md'),
+          destinationPath: legacySkillPath,
+          strategy: 'preserve-relative-path',
+          ownership: 'managed',
+          scaffoldOnly: false,
+        }],
+        source: {
+          repoVersion: CURRENT_PACKAGE_VERSION,
+          repoCommit: 'abc123',
+          manifestVersion: CURRENT_MANIFEST_VERSION,
+        },
+      });
+
+      const dryRun = repairInstalledStates({
+        repoRoot: REPO_ROOT,
+        homeDir,
+        projectRoot,
+        targets: ['claude'],
+        dryRun: true,
+      });
+      assert.ok(!dryRun.results[0].plannedRepairs.includes(flatSkillPath));
+      assert.ok(dryRun.results[0].warnings.some(warning => warning.includes('user-owned')));
+      assert.strictEqual(fs.readFileSync(flatSkillPath, 'utf8'), '# User-owned flat skill\n');
+      assert.strictEqual(
+        fs.readFileSync(legacySkillPath, 'utf8'),
+        '# Previously managed nested skill\n'
+      );
+
+      const repaired = repairInstalledStates({
+        repoRoot: REPO_ROOT,
+        homeDir,
+        projectRoot,
+        targets: ['claude'],
+      });
+      assert.strictEqual(repaired.results[0].status, 'repaired');
+      assert.ok(repaired.results[0].warnings.some(warning => warning.includes('user-owned')));
+      assert.strictEqual(fs.readFileSync(flatSkillPath, 'utf8'), '# User-owned flat skill\n');
+      assert.strictEqual(
+        fs.readFileSync(legacySkillPath, 'utf8'),
+        fs.readFileSync(
+          path.join(REPO_ROOT, 'skills', 'tdd-workflow', 'SKILL.md'),
+          'utf8'
+        )
+      );
+      const repairedState = JSON.parse(fs.readFileSync(installStatePath, 'utf8'));
+      assert.ok(repairedState.operations.some(operation => (
+        operation.destinationPath === legacySkillPath
+      )));
+      assert.ok(!repairedState.operations.some(operation => (
+        operation.destinationPath === flatSkillPath
+      )));
+    } finally {
+      cleanup(homeDir);
+      cleanup(projectRoot);
+    }
+  })) passed++; else failed++;
+
   if (test('repair copies missing managed files from recorded source paths', () => {
     const homeDir = createTempDir('install-lifecycle-home-');
     const projectRoot = createTempDir('install-lifecycle-project-');

tests/lib/install-link-rewrite.test.js

@@ -10,20 +10,19 @@ const path = require('path');
 
 const {
   buildInstallIndex,
-  isNamespacedSource,
   rewriteRelativeLinks,
 } = require('../../scripts/lib/install/link-rewrite');
 const { createManifestInstallPlan } = require('../../scripts/lib/install-executor');
 
 const REPO_ROOT = path.resolve(__dirname, '..', '..');
 
-// A claude-style namespace placement: skills/<id> -> skills/ecc/<id> and
+// A claude-style namespace placement: skills/<id> -> skills/<id> and
 // rules/<x> -> rules/ecc/<x>. Mirrors what the real adapter emits.
 function claudeNamespaceMappings() {
   return [
-    { sourceRel: 'skills/react-patterns/SKILL.md', destRel: 'skills/ecc/react-patterns/SKILL.md' },
-    { sourceRel: 'skills/react-patterns/other.md', destRel: 'skills/ecc/react-patterns/other.md' },
-    { sourceRel: 'skills/react-patterns/sub/NOTE.md', destRel: 'skills/ecc/react-patterns/sub/NOTE.md' },
+    { sourceRel: 'skills/react-patterns/SKILL.md', destRel: 'skills/react-patterns/SKILL.md' },
+    { sourceRel: 'skills/react-patterns/other.md', destRel: 'skills/react-patterns/other.md' },
+    { sourceRel: 'skills/react-patterns/sub/NOTE.md', destRel: 'skills/react-patterns/sub/NOTE.md' },
     { sourceRel: 'rules/react/hooks.md', destRel: 'rules/ecc/react/hooks.md' },
     { sourceRel: 'rules/react/testing.md', destRel: 'rules/ecc/react/testing.md' },
     { sourceRel: 'rules/react/coding-style.md', destRel: 'rules/ecc/react/coding-style.md' },
@@ -64,17 +63,17 @@ function runTests() {
   for (const skill of ['react-patterns', 'react-performance', 'react-testing']) {
     if (test(`rewrites ../../rules file link for ${skill}`, () => {
       const idx = buildInstallIndex([
-        { sourceRel: `skills/${skill}/SKILL.md`, destRel: `skills/ecc/${skill}/SKILL.md` },
+        { sourceRel: `skills/${skill}/SKILL.md`, destRel: `skills/${skill}/SKILL.md` },
         { sourceRel: 'rules/react/hooks.md', destRel: 'rules/ecc/react/hooks.md' },
       ]);
       const before = 'See [rules](../../rules/react/hooks.md) for details.';
       const after = rewriteRelativeLinks(before, { sourceRel: `skills/${skill}/SKILL.md`, index: idx });
       assert.notStrictEqual(after, before, 'rewrite must change the broken link (not vacuous)');
       assert.ok(
-        after.includes('](../../../rules/ecc/react/hooks.md)'),
+        after.includes('](../../rules/ecc/react/hooks.md)'),
         `expected corrected link, got: ${after}`
       );
-      assert.ok(!after.includes('](../../rules/'), 'broken depth must be gone');
+      assert.ok(!after.includes('](../../rules/react/'), 'un-namespaced rules link must be gone');
     })) passed++; else failed++;
   }
 
@@ -82,7 +81,7 @@ function runTests() {
     const before = '- Rules: [rules/react/](../../rules/react/)';
     const after = rewriteRelativeLinks(before, { sourceRel: 'skills/react-patterns/SKILL.md', index });
     assert.notStrictEqual(after, before);
-    assert.ok(after.includes('](../../../rules/ecc/react/)'), `got: ${after}`);
+    assert.ok(after.includes('](../../rules/ecc/react/)'), `got: ${after}`);
   })) passed++; else failed++;
 
   if (test('leaves an intra-skill sibling link unchanged', () => {
@@ -111,7 +110,7 @@ function runTests() {
   if (test('preserves a #fragment on a rewritten link', () => {
     const before = '[hooks](../../rules/react/hooks.md#use-effect)';
     const after = rewriteRelativeLinks(before, { sourceRel: 'skills/react-patterns/SKILL.md', index });
-    assert.ok(after.includes('](../../../rules/ecc/react/hooks.md#use-effect)'), `got: ${after}`);
+    assert.ok(after.includes('](../../rules/ecc/react/hooks.md#use-effect)'), `got: ${after}`);
   })) passed++; else failed++;
 
   if (test('does not rewrite links inside fenced code blocks', () => {
@@ -123,16 +122,16 @@ function runTests() {
     ].join('\n');
     const after = rewriteRelativeLinks(before, { sourceRel: 'skills/react-patterns/SKILL.md', index });
     assert.ok(after.includes('[code](../../rules/react/hooks.md)'), 'code-fence link must be untouched');
-    assert.ok(after.includes('[prose](../../../rules/ecc/react/hooks.md)'), 'prose link must be rewritten');
+    assert.ok(after.includes('[prose](../../rules/ecc/react/hooks.md)'), 'prose link must be rewritten');
   })) passed++; else failed++;
 
   if (test('computes depth from path math for a nested skill file', () => {
-    // skills/react-patterns/sub/NOTE.md -> skills/ecc/react-patterns/sub/NOTE.md
+    // skills/react-patterns/sub/NOTE.md -> skills/react-patterns/sub/NOTE.md
     // Source link is ../../../rules/react/hooks.md (3 up from sub/).
     const before = '[r](../../../rules/react/hooks.md)';
     const after = rewriteRelativeLinks(before, { sourceRel: 'skills/react-patterns/sub/NOTE.md', index });
     assert.notStrictEqual(after, before, 'nested depth must be recomputed, not hardcoded');
-    assert.ok(after.includes('](../../../../rules/ecc/react/hooks.md)'), `got: ${after}`);
+    assert.ok(after.includes('](../../../rules/ecc/react/hooks.md)'), `got: ${after}`);
   })) passed++; else failed++;
 
   if (test('is a no-op for a non-namespacing (identity) placement', () => {
@@ -148,24 +147,6 @@ function runTests() {
     assert.strictEqual(after, before);
   })) passed++; else failed++;
 
-  // Guards the apply-layer gate: only namespaced files leave the byte-copy
-  // path, so non-namespaced markdown is still copied verbatim.
-  if (test('isNamespacedSource flags only files whose install path changed', () => {
-    assert.strictEqual(
-      isNamespacedSource('skills/react-patterns/SKILL.md', index), true,
-      'a namespaced skill file must be flagged'
-    );
-    const identity = buildInstallIndex(identityMappings());
-    assert.strictEqual(
-      isNamespacedSource('skills/react-patterns/SKILL.md', identity), false,
-      'an identity-mapped file must stay on the byte-copy path'
-    );
-    assert.strictEqual(
-      isNamespacedSource('skills/not-in-plan/SKILL.md', index), false,
-      'a file the plan does not install is not namespaced'
-    );
-  })) passed++; else failed++;
-
   // Integration: real repo content + real claude plan. Every rewritten link in
   // the three React skills must resolve to a destination the SAME plan installs.
   if (test('real React skills: rewritten rules links resolve to installed targets', () => {
@@ -201,13 +182,16 @@ function runTests() {
       const content = fs.readFileSync(path.join(REPO_ROOT, sourceRel), 'utf8');
       assert.ok(content.includes('](../../rules/'), `${sourceRel} should have a broken link pre-fix`);
       const rewritten = rewriteRelativeLinks(content, { sourceRel, index: realIndex });
-      assert.ok(!rewritten.includes('](../../rules/'), `${sourceRel} still has the broken depth`);
+      assert.ok(
+        !rewritten.includes('](../../rules/react/'),
+        `${sourceRel} still links to un-namespaced rules`
+      );
 
       // Only links we actually changed are validated here; cross-skill links to
       // skills outside this module subset are legitimately left untouched.
       const before = extractLinks(content);
       const after = extractLinks(rewritten);
-      const installedSkillDir = path.posix.dirname(`skills/ecc/${skill}/SKILL.md`);
+      const installedSkillDir = path.posix.dirname(`skills/${skill}/SKILL.md`);
       for (let i = 0; i < after.length; i += 1) {
         if (after[i] === before[i]) {
           continue;

tests/lib/install-targets.test.js

@@ -71,7 +71,7 @@ function runTests() {
     assert.strictEqual(statePath, path.join(homeDir, '.claude', 'ecc', 'install-state.json'));
   })) passed++; else failed++;
 
-  if (test('plans claude rules and skills under ECC-managed subdirectories', () => {
+  if (test('plans namespaced Claude rules and flat discoverable skills', () => {
     const repoRoot = path.join(__dirname, '..', '..');
     const homeDir = '/Users/example';
 
@@ -101,9 +101,9 @@ function runTests() {
     assert.ok(
       plan.operations.some(operation => (
         normalizedRelativePath(operation.sourceRelativePath) === 'skills/tdd-workflow'
-        && operation.destinationPath === path.join(homeDir, '.claude', 'skills', 'ecc', 'tdd-workflow')
+        && operation.destinationPath === path.join(homeDir, '.claude', 'skills', 'tdd-workflow')
       )),
-      'Should install bundled Claude skills under skills/ecc'
+      'Should install bundled Claude skills under skills'
     );
   })) passed++; else failed++;
 
@@ -884,7 +884,7 @@ function runTests() {
     assert.ok(byTarget.supports('claude-project'));
   })) passed++; else failed++;
 
-  if (test('plans claude-project rules and skills under project-scope ECC-managed subdirectories', () => {
+  if (test('plans project-scoped namespaced Claude rules and flat skills', () => {
     const repoRoot = path.join(__dirname, '..', '..');
     const projectRoot = '/workspace/app';
 
@@ -917,9 +917,9 @@ function runTests() {
     assert.ok(
       plan.operations.some(operation => (
         normalizedRelativePath(operation.sourceRelativePath) === 'skills/tdd-workflow'
-        && operation.destinationPath === path.join(projectRoot, '.claude', 'skills', 'ecc', 'tdd-workflow')
+        && operation.destinationPath === path.join(projectRoot, '.claude', 'skills', 'tdd-workflow')
       )),
-      'Should install bundled skills under project-scope skills/ecc'
+      'Should install bundled skills under project-scope skills'
     );
   })) passed++; else failed++;
 

tests/lib/locale-install.test.js

@@ -205,7 +205,7 @@ function runTests() {
         'Should install Japanese README under docs/ja-JP'
       );
       assert.ok(
-        !fs.existsSync(path.join(claudeRoot, 'skills', 'ecc', 'configure-ecc', 'SKILL.md')),
+        !fs.existsSync(path.join(claudeRoot, 'skills', 'configure-ecc', 'SKILL.md')),
         'Locale-only install should not install English skills'
       );
 

tests/lib/selective-install.test.js

@@ -658,7 +658,7 @@ function runTests() {
 
       const claudeRoot = path.join(homeDir, '.claude');
       // Security skill should be installed (from --with)
-      assert.ok(fs.existsSync(path.join(claudeRoot, 'skills', 'ecc', 'security-review', 'SKILL.md')),
+      assert.ok(fs.existsSync(path.join(claudeRoot, 'skills', 'security-review', 'SKILL.md')),
         'Should install security-review skill from --with');
       // Core profile modules should be installed
       assert.ok(fs.existsSync(path.join(claudeRoot, 'rules', 'ecc', 'common', 'coding-style.md')),
@@ -697,12 +697,12 @@ function runTests() {
 
       const claudeRoot = path.join(homeDir, '.claude');
       // Orchestration skills should NOT be installed (from --without)
-      assert.ok(!fs.existsSync(path.join(claudeRoot, 'skills', 'ecc', 'dmux-workflows', 'SKILL.md')),
+      assert.ok(!fs.existsSync(path.join(claudeRoot, 'skills', 'dmux-workflows', 'SKILL.md')),
         'Should not install orchestration skills');
       // Developer profile base modules should be installed
       assert.ok(fs.existsSync(path.join(claudeRoot, 'rules', 'ecc', 'common', 'coding-style.md')),
         'Should install core rules');
-      assert.ok(fs.existsSync(path.join(claudeRoot, 'skills', 'ecc', 'tdd-workflow', 'SKILL.md')),
+      assert.ok(fs.existsSync(path.join(claudeRoot, 'skills', 'tdd-workflow', 'SKILL.md')),
         'Should install workflow skills');
 
       const statePath = path.join(claudeRoot, 'ecc', 'install-state.json');
@@ -735,7 +735,7 @@ function runTests() {
 
       const claudeRoot = path.join(homeDir, '.claude');
       // framework-language skill (from lang:typescript) should be installed
-      assert.ok(fs.existsSync(path.join(claudeRoot, 'skills', 'ecc', 'coding-standards', 'SKILL.md')),
+      assert.ok(fs.existsSync(path.join(claudeRoot, 'skills', 'coding-standards', 'SKILL.md')),
         'Should install framework-language skills');
       // Its dependencies should be installed
       assert.ok(fs.existsSync(path.join(claudeRoot, 'rules', 'ecc', 'common', 'coding-style.md')),
@@ -771,11 +771,11 @@ function runTests() {
 
       const claudeRoot = path.join(homeDir, '.claude');
       assert.ok(
-        fs.existsSync(path.join(claudeRoot, 'skills', 'ecc', 'continuous-learning-v2', 'SKILL.md')),
+        fs.existsSync(path.join(claudeRoot, 'skills', 'continuous-learning-v2', 'SKILL.md')),
         'Should install continuous-learning-v2'
       );
       assert.ok(
-        !fs.existsSync(path.join(claudeRoot, 'skills', 'ecc', 'tdd-workflow', 'SKILL.md')),
+        !fs.existsSync(path.join(claudeRoot, 'skills', 'tdd-workflow', 'SKILL.md')),
         'Should not install unrelated workflow-quality skills'
       );
 

tests/scripts/install-apply.test.js

@@ -100,8 +100,8 @@ function runTests() {
       assert.ok(fs.existsSync(path.join(claudeRoot, 'commands', 'plan.md')));
       assert.ok(fs.existsSync(path.join(claudeRoot, 'scripts', 'hooks', 'session-end.js')));
       assert.ok(fs.existsSync(path.join(claudeRoot, 'scripts', 'lib', 'utils.js')));
-      assert.ok(fs.existsSync(path.join(claudeRoot, 'skills', 'ecc', 'tdd-workflow', 'SKILL.md')));
-      assert.ok(fs.existsSync(path.join(claudeRoot, 'skills', 'ecc', 'coding-standards', 'SKILL.md')));
+      assert.ok(fs.existsSync(path.join(claudeRoot, 'skills', 'tdd-workflow', 'SKILL.md')));
+      assert.ok(fs.existsSync(path.join(claudeRoot, 'skills', 'coding-standards', 'SKILL.md')));
       assert.ok(fs.existsSync(path.join(claudeRoot, 'plugin.json')));
 
       const statePath = path.join(homeDir, '.claude', 'ecc', 'install-state.json');
@@ -133,23 +133,23 @@ function runTests() {
       assert.strictEqual(result.code, 0, result.stderr);
 
       const claudeRoot = path.join(homeDir, '.claude');
-      const skillPath = path.join(claudeRoot, 'skills', 'ecc', 'react-patterns', 'SKILL.md');
+      const skillPath = path.join(claudeRoot, 'skills', 'react-patterns', 'SKILL.md');
       assert.ok(fs.existsSync(skillPath), 'react-patterns SKILL.md should be installed');
 
       const content = fs.readFileSync(skillPath, 'utf8');
       assert.ok(
-        content.includes('../../../rules/ecc/react/'),
+        content.includes('../../rules/ecc/react/'),
         'source-relative rules link should be rewritten for the ecc/ namespace'
       );
       assert.ok(
-        !content.includes('](../../rules/'),
-        'no un-namespaced ](../../rules/ links should remain'
+        !content.includes('](../../rules/react/'),
+        'no un-namespaced ](../../rules/react/ links should remain'
       );
 
       // The rewritten link must resolve to a file that actually exists on disk.
       const linkTarget = path.join(
         path.dirname(skillPath),
-        '../../../rules/ecc/react/hooks.md'
+        '../../rules/ecc/react/hooks.md'
       );
       assert.ok(fs.existsSync(linkTarget), 'rewritten link target should exist');
     } finally {
@@ -468,11 +468,101 @@ function runTests() {
 
       const result = run(['--profile', 'core'], { cwd: projectDir, homeDir });
       assert.strictEqual(result.code, 0, result.stderr);
+      assert.ok(result.stdout.includes('user-owned'), result.stdout);
+      assert.ok(result.stdout.includes('Skipped operations:'), result.stdout);
 
       assert.strictEqual(fs.readFileSync(userRulePath, 'utf8'), '# User custom rule\n');
       assert.strictEqual(fs.readFileSync(userSkillPath, 'utf8'), '# User custom skill\n');
       assert.ok(fs.existsSync(path.join(claudeRoot, 'rules', 'ecc', 'common', 'coding-style.md')));
-      assert.ok(fs.existsSync(path.join(claudeRoot, 'skills', 'ecc', 'tdd-workflow', 'SKILL.md')));
+      assert.ok(fs.existsSync(path.join(claudeRoot, 'skills', 'verification-loop', 'SKILL.md')));
+      const state = readJson(path.join(claudeRoot, 'ecc', 'install-state.json'));
+      assert.ok(!state.operations.some(operation => (
+        operation.destinationPath.startsWith(path.join(claudeRoot, 'skills', 'tdd-workflow'))
+      )));
+    } finally {
+      cleanup(homeDir);
+      cleanup(projectDir);
+    }
+  })) passed++; else failed++;
+
+  if (test('reports applied and skipped user-owned Claude skill operations in JSON', () => {
+    const homeDir = createTempDir('install-apply-home-');
+    const projectDir = createTempDir('install-apply-project-');
+
+    try {
+      const userSkillPath = path.join(
+        homeDir,
+        '.claude',
+        'skills',
+        'tdd-workflow',
+        'SKILL.md'
+      );
+      fs.mkdirSync(path.dirname(userSkillPath), { recursive: true });
+      fs.writeFileSync(userSkillPath, '# User custom skill\n');
+
+      const result = run(['--skills', 'tdd-workflow', '--json'], {
+        cwd: projectDir,
+        homeDir,
+      });
+      assert.strictEqual(result.code, 0, result.stderr);
+
+      const payload = JSON.parse(result.stdout);
+      assert.strictEqual(payload.dryRun, false);
+      assert.ok(payload.result.plannedOperations.length > 0);
+      assert.ok(payload.result.operations.length > 0);
+      assert.ok(payload.result.skippedOperations.length > 0);
+      assert.strictEqual(
+        payload.result.operations.length + payload.result.skippedOperations.length,
+        payload.result.plannedOperations.length
+      );
+      assert.ok(payload.result.skippedOperations.every(operation => (
+        operation.destinationPath.startsWith(path.dirname(userSkillPath))
+      )));
+      assert.ok(!payload.result.operations.some(operation => (
+        operation.destinationPath.startsWith(path.dirname(userSkillPath))
+      )));
+      assert.ok(payload.result.warnings.some(warning => warning.includes('user-owned')));
+      assert.strictEqual(fs.readFileSync(userSkillPath, 'utf8'), '# User custom skill\n');
+    } finally {
+      cleanup(homeDir);
+      cleanup(projectDir);
+    }
+  })) passed++; else failed++;
+
+  if (test('dry-run reports the same user-owned Claude skill conflicts as apply', () => {
+    const homeDir = createTempDir('install-apply-home-');
+    const projectDir = createTempDir('install-apply-project-');
+
+    try {
+      const userSkillRoot = path.join(
+        homeDir,
+        '.claude',
+        'skills',
+        'tdd-workflow'
+      );
+      const userSkillPath = path.join(userSkillRoot, 'SKILL.md');
+      fs.mkdirSync(userSkillRoot, { recursive: true });
+      fs.writeFileSync(userSkillPath, '# User custom skill\n');
+
+      const result = run(
+        ['--skills', 'tdd-workflow', '--dry-run', '--json'],
+        { cwd: projectDir, homeDir }
+      );
+      assert.strictEqual(result.code, 0, result.stderr);
+
+      const payload = JSON.parse(result.stdout);
+      assert.strictEqual(payload.dryRun, true);
+      assert.ok(payload.plan.plannedOperations.length > 0);
+      assert.ok(payload.plan.skippedOperations.length > 0);
+      assert.ok(payload.plan.warnings.some(warning => warning.includes('user-owned')));
+      assert.ok(payload.plan.skippedOperations.every(operation => (
+        operation.destinationPath.startsWith(userSkillRoot)
+      )));
+      assert.ok(!payload.plan.operations.some(operation => (
+        operation.destinationPath.startsWith(userSkillRoot)
+      )));
+      assert.strictEqual(fs.readFileSync(userSkillPath, 'utf8'), '# User custom skill\n');
+      assert.ok(!fs.existsSync(path.join(homeDir, '.claude', 'ecc', 'install-state.json')));
     } finally {
       cleanup(homeDir);
       cleanup(projectDir);
@@ -893,8 +983,8 @@ function runTests() {
       const result = run(['--config', configPath], { cwd: projectDir, homeDir });
       assert.strictEqual(result.code, 0, result.stderr);
 
-      assert.ok(fs.existsSync(path.join(homeDir, '.claude', 'skills', 'ecc', 'security-review', 'SKILL.md')));
-      assert.ok(!fs.existsSync(path.join(homeDir, '.claude', 'skills', 'ecc', 'dmux-workflows', 'SKILL.md')));
+      assert.ok(fs.existsSync(path.join(homeDir, '.claude', 'skills', 'security-review', 'SKILL.md')));
+      assert.ok(!fs.existsSync(path.join(homeDir, '.claude', 'skills', 'dmux-workflows', 'SKILL.md')));
 
       const state = readJson(path.join(homeDir, '.claude', 'ecc', 'install-state.json'));
       assert.strictEqual(state.request.profile, 'developer');
@@ -925,8 +1015,8 @@ function runTests() {
       const result = run([], { cwd: projectDir, homeDir });
       assert.strictEqual(result.code, 0, result.stderr);
 
-      assert.ok(fs.existsSync(path.join(homeDir, '.claude', 'skills', 'ecc', 'security-review', 'SKILL.md')));
-      assert.ok(!fs.existsSync(path.join(homeDir, '.claude', 'skills', 'ecc', 'dmux-workflows', 'SKILL.md')));
+      assert.ok(fs.existsSync(path.join(homeDir, '.claude', 'skills', 'security-review', 'SKILL.md')));
+      assert.ok(!fs.existsSync(path.join(homeDir, '.claude', 'skills', 'dmux-workflows', 'SKILL.md')));
 
       const state = readJson(path.join(homeDir, '.claude', 'ecc', 'install-state.json'));
       assert.strictEqual(state.request.profile, 'developer');