fix: flatten Claude skill installs (#2582)

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

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');