diff --git a/docs/cs/how-to/non-interactive-installation.md b/docs/cs/how-to/non-interactive-installation.md
index 12ea31eb3..4d784f923 100644
--- a/docs/cs/how-to/non-interactive-installation.md
+++ b/docs/cs/how-to/non-interactive-installation.md
@@ -60,7 +60,7 @@ Dostupná ID nástrojů pro příznak `--tools`:
 
 **Preferované:** `claude-code`, `cursor`
 
-Spusťte `npx bmad-method install` interaktivně jednou pro zobrazení aktuálního seznamu podporovaných nástrojů, nebo zkontrolujte [konfiguraci kódů platforem](https://github.com/bmad-code-org/BMAD-METHOD/blob/main/tools/cli/installers/lib/ide/platform-codes.yaml).
+Spusťte `npx bmad-method install` interaktivně jednou pro zobrazení aktuálního seznamu podporovaných nástrojů, nebo zkontrolujte [konfiguraci kódů platforem](https://github.com/bmad-code-org/BMAD-METHOD/blob/main/tools/installer/ide/platform-codes.yaml).
 
 ## Režimy instalace
 
diff --git a/test/test-installation-components.js b/test/test-installation-components.js
index 58d6c7d8f..4827afcbf 100644
--- a/test/test-installation-components.js
+++ b/test/test-installation-components.js
@@ -139,19 +139,10 @@ async function runTests() {
     const platformCodes = await loadPlatformCodes();
     const windsurfInstaller = platformCodes.platforms.windsurf?.installer;
 
-    assert(windsurfInstaller?.target_dir === '.windsurf/skills', 'Windsurf target_dir uses native skills path');
-
-    assert(
-      Array.isArray(windsurfInstaller?.legacy_targets) && windsurfInstaller.legacy_targets.includes('.windsurf/workflows'),
-      'Windsurf installer cleans legacy workflow output',
-    );
+    assert(windsurfInstaller?.target_dir === '.agents/skills', 'Windsurf target_dir uses native skills path');
 
     const tempProjectDir = await fs.mkdtemp(path.join(os.tmpdir(), 'bmad-windsurf-test-'));
     const installedBmadDir = await createTestBmadFixture();
-    const legacyDir = path.join(tempProjectDir, '.windsurf', 'workflows', 'bmad-legacy-dir');
-    await fs.ensureDir(legacyDir);
-    await fs.writeFile(path.join(tempProjectDir, '.windsurf', 'workflows', 'bmad-legacy.md'), 'legacy\n');
-    await fs.writeFile(path.join(legacyDir, 'SKILL.md'), 'legacy\n');
 
     const ideManager = new IdeManager();
     await ideManager.ensureInitialized();
@@ -162,11 +153,9 @@ async function runTests() {
 
     assert(result.success === true, 'Windsurf setup succeeds against temp project');
 
-    const skillFile = path.join(tempProjectDir, '.windsurf', 'skills', 'bmad-master', 'SKILL.md');
+    const skillFile = path.join(tempProjectDir, '.agents', 'skills', 'bmad-master', 'SKILL.md');
     assert(await fs.pathExists(skillFile), 'Windsurf install writes SKILL.md directory output');
 
-    assert(!(await fs.pathExists(path.join(tempProjectDir, '.windsurf', 'workflows'))), 'Windsurf setup removes legacy workflows dir');
-
     await fs.remove(tempProjectDir);
     await fs.remove(path.dirname(installedBmadDir));
   } catch (error) {
@@ -187,17 +176,8 @@ async function runTests() {
 
     assert(kiroInstaller?.target_dir === '.kiro/skills', 'Kiro target_dir uses native skills path');
 
-    assert(
-      Array.isArray(kiroInstaller?.legacy_targets) && kiroInstaller.legacy_targets.includes('.kiro/steering'),
-      'Kiro installer cleans legacy steering output',
-    );
-
     const tempProjectDir = await fs.mkdtemp(path.join(os.tmpdir(), 'bmad-kiro-test-'));
     const installedBmadDir = await createTestBmadFixture();
-    const legacyDir = path.join(tempProjectDir, '.kiro', 'steering', 'bmad-legacy-dir');
-    await fs.ensureDir(legacyDir);
-    await fs.writeFile(path.join(tempProjectDir, '.kiro', 'steering', 'bmad-legacy.md'), 'legacy\n');
-    await fs.writeFile(path.join(legacyDir, 'SKILL.md'), 'legacy\n');
 
     const ideManager = new IdeManager();
     await ideManager.ensureInitialized();
@@ -211,8 +191,6 @@ async function runTests() {
     const skillFile = path.join(tempProjectDir, '.kiro', 'skills', 'bmad-master', 'SKILL.md');
     assert(await fs.pathExists(skillFile), 'Kiro install writes SKILL.md directory output');
 
-    assert(!(await fs.pathExists(path.join(tempProjectDir, '.kiro', 'steering'))), 'Kiro setup removes legacy steering dir');
-
     await fs.remove(tempProjectDir);
     await fs.remove(path.dirname(installedBmadDir));
   } catch (error) {
@@ -233,17 +211,8 @@ async function runTests() {
 
     assert(antigravityInstaller?.target_dir === '.agent/skills', 'Antigravity target_dir uses native skills path');
 
-    assert(
-      Array.isArray(antigravityInstaller?.legacy_targets) && antigravityInstaller.legacy_targets.includes('.agent/workflows'),
-      'Antigravity installer cleans legacy workflow output',
-    );
-
     const tempProjectDir = await fs.mkdtemp(path.join(os.tmpdir(), 'bmad-antigravity-test-'));
     const installedBmadDir = await createTestBmadFixture();
-    const legacyDir = path.join(tempProjectDir, '.agent', 'workflows', 'bmad-legacy-dir');
-    await fs.ensureDir(legacyDir);
-    await fs.writeFile(path.join(tempProjectDir, '.agent', 'workflows', 'bmad-legacy.md'), 'legacy\n');
-    await fs.writeFile(path.join(legacyDir, 'SKILL.md'), 'legacy\n');
 
     const ideManager = new IdeManager();
     await ideManager.ensureInitialized();
@@ -257,8 +226,6 @@ async function runTests() {
     const skillFile = path.join(tempProjectDir, '.agent', 'skills', 'bmad-master', 'SKILL.md');
     assert(await fs.pathExists(skillFile), 'Antigravity install writes SKILL.md directory output');
 
-    assert(!(await fs.pathExists(path.join(tempProjectDir, '.agent', 'workflows'))), 'Antigravity setup removes legacy workflows dir');
-
     await fs.remove(tempProjectDir);
     await fs.remove(path.dirname(installedBmadDir));
   } catch (error) {
@@ -277,12 +244,7 @@ async function runTests() {
     const platformCodes = await loadPlatformCodes();
     const auggieInstaller = platformCodes.platforms.auggie?.installer;
 
-    assert(auggieInstaller?.target_dir === '.augment/skills', 'Auggie target_dir uses native skills path');
-
-    assert(
-      Array.isArray(auggieInstaller?.legacy_targets) && auggieInstaller.legacy_targets.includes('.augment/commands'),
-      'Auggie installer cleans legacy command output',
-    );
+    assert(auggieInstaller?.target_dir === '.agents/skills', 'Auggie target_dir uses native skills path');
 
     assert(
       auggieInstaller?.ancestor_conflict_check !== true,
@@ -291,10 +253,6 @@ async function runTests() {
 
     const tempProjectDir = await fs.mkdtemp(path.join(os.tmpdir(), 'bmad-auggie-test-'));
     const installedBmadDir = await createTestBmadFixture();
-    const legacyDir = path.join(tempProjectDir, '.augment', 'commands', 'bmad-legacy-dir');
-    await fs.ensureDir(legacyDir);
-    await fs.writeFile(path.join(tempProjectDir, '.augment', 'commands', 'bmad-legacy.md'), 'legacy\n');
-    await fs.writeFile(path.join(legacyDir, 'SKILL.md'), 'legacy\n');
 
     const ideManager = new IdeManager();
     await ideManager.ensureInitialized();
@@ -305,11 +263,9 @@ async function runTests() {
 
     assert(result.success === true, 'Auggie setup succeeds against temp project');
 
-    const skillFile = path.join(tempProjectDir, '.augment', 'skills', 'bmad-master', 'SKILL.md');
+    const skillFile = path.join(tempProjectDir, '.agents', 'skills', 'bmad-master', 'SKILL.md');
     assert(await fs.pathExists(skillFile), 'Auggie install writes SKILL.md directory output');
 
-    assert(!(await fs.pathExists(path.join(tempProjectDir, '.augment', 'commands'))), 'Auggie setup removes legacy commands dir');
-
     await fs.remove(tempProjectDir);
     await fs.remove(path.dirname(installedBmadDir));
   } catch (error) {
@@ -328,30 +284,10 @@ async function runTests() {
     const platformCodes = await loadPlatformCodes();
     const opencodeInstaller = platformCodes.platforms.opencode?.installer;
 
-    assert(opencodeInstaller?.target_dir === '.opencode/skills', 'OpenCode target_dir uses native skills path');
-
-    assert(
-      Array.isArray(opencodeInstaller?.legacy_targets) &&
-        ['.opencode/agents', '.opencode/commands', '.opencode/agent', '.opencode/command'].every((legacyTarget) =>
-          opencodeInstaller.legacy_targets.includes(legacyTarget),
-        ),
-      'OpenCode installer cleans split legacy agent and command output',
-    );
+    assert(opencodeInstaller?.target_dir === '.agents/skills', 'OpenCode target_dir uses native skills path');
 
     const tempProjectDir = await fs.mkdtemp(path.join(os.tmpdir(), 'bmad-opencode-test-'));
     const installedBmadDir = await createTestBmadFixture();
-    const legacyDirs = [
-      path.join(tempProjectDir, '.opencode', 'agents', 'bmad-legacy-agent'),
-      path.join(tempProjectDir, '.opencode', 'commands', 'bmad-legacy-command'),
-      path.join(tempProjectDir, '.opencode', 'agent', 'bmad-legacy-agent-singular'),
-      path.join(tempProjectDir, '.opencode', 'command', 'bmad-legacy-command-singular'),
-    ];
-
-    for (const legacyDir of legacyDirs) {
-      await fs.ensureDir(legacyDir);
-      await fs.writeFile(path.join(legacyDir, 'SKILL.md'), 'legacy\n');
-      await fs.writeFile(path.join(path.dirname(legacyDir), `${path.basename(legacyDir)}.md`), 'legacy\n');
-    }
 
     const ideManager = new IdeManager();
     await ideManager.ensureInitialized();
@@ -362,16 +298,9 @@ async function runTests() {
 
     assert(result.success === true, 'OpenCode setup succeeds against temp project');
 
-    const skillFile = path.join(tempProjectDir, '.opencode', 'skills', 'bmad-master', 'SKILL.md');
+    const skillFile = path.join(tempProjectDir, '.agents', 'skills', 'bmad-master', 'SKILL.md');
     assert(await fs.pathExists(skillFile), 'OpenCode install writes SKILL.md directory output');
 
-    for (const legacyDir of ['agents', 'commands', 'agent', 'command']) {
-      assert(
-        !(await fs.pathExists(path.join(tempProjectDir, '.opencode', legacyDir))),
-        `OpenCode setup removes legacy .opencode/${legacyDir} dir`,
-      );
-    }
-
     await fs.remove(tempProjectDir);
     await fs.remove(path.dirname(installedBmadDir));
   } catch (error) {
@@ -392,16 +321,8 @@ async function runTests() {
 
     assert(claudeInstaller?.target_dir === '.claude/skills', 'Claude Code target_dir uses native skills path');
 
-    assert(
-      Array.isArray(claudeInstaller?.legacy_targets) && claudeInstaller.legacy_targets.includes('.claude/commands'),
-      'Claude Code installer cleans legacy command output',
-    );
-
     const tempProjectDir9 = await fs.mkdtemp(path.join(os.tmpdir(), 'bmad-claude-code-test-'));
     const installedBmadDir9 = await createTestBmadFixture();
-    const legacyDir9 = path.join(tempProjectDir9, '.claude', 'commands');
-    await fs.ensureDir(legacyDir9);
-    await fs.writeFile(path.join(legacyDir9, 'bmad-legacy.md'), 'legacy\n');
 
     const ideManager9 = new IdeManager();
     await ideManager9.ensureInitialized();
@@ -420,8 +341,6 @@ async function runTests() {
     const nameMatch9 = skillContent9.match(/^name:\s*(.+)$/m);
     assert(nameMatch9 && nameMatch9[1].trim() === 'bmad-master', 'Claude Code skill name frontmatter matches directory name exactly');
 
-    assert(!(await fs.pathExists(legacyDir9)), 'Claude Code setup removes legacy commands dir');
-
     await fs.remove(tempProjectDir9);
     await fs.remove(path.dirname(installedBmadDir9));
   } catch (error) {
@@ -444,16 +363,8 @@ async function runTests() {
 
     assert(codexInstaller?.target_dir === '.agents/skills', 'Codex target_dir uses native skills path');
 
-    assert(
-      Array.isArray(codexInstaller?.legacy_targets) && codexInstaller.legacy_targets.includes('.codex/prompts'),
-      'Codex installer cleans legacy prompt output',
-    );
-
     const tempProjectDir11 = await fs.mkdtemp(path.join(os.tmpdir(), 'bmad-codex-test-'));
     const installedBmadDir11 = await createTestBmadFixture();
-    const legacyDir11 = path.join(tempProjectDir11, '.codex', 'prompts');
-    await fs.ensureDir(legacyDir11);
-    await fs.writeFile(path.join(legacyDir11, 'bmad-legacy.md'), 'legacy\n');
 
     const ideManager11 = new IdeManager();
     await ideManager11.ensureInitialized();
@@ -472,8 +383,6 @@ async function runTests() {
     const nameMatch11 = skillContent11.match(/^name:\s*(.+)$/m);
     assert(nameMatch11 && nameMatch11[1].trim() === 'bmad-master', 'Codex skill name frontmatter matches directory name exactly');
 
-    assert(!(await fs.pathExists(legacyDir11)), 'Codex setup removes legacy prompts dir');
-
     await fs.remove(tempProjectDir11);
     await fs.remove(path.dirname(installedBmadDir11));
   } catch (error) {
@@ -494,20 +403,12 @@ async function runTests() {
     const platformCodes13 = await loadPlatformCodes();
     const cursorInstaller = platformCodes13.platforms.cursor?.installer;
 
-    assert(cursorInstaller?.target_dir === '.cursor/skills', 'Cursor target_dir uses native skills path');
-
-    assert(
-      Array.isArray(cursorInstaller?.legacy_targets) && cursorInstaller.legacy_targets.includes('.cursor/commands'),
-      'Cursor installer cleans legacy command output',
-    );
+    assert(cursorInstaller?.target_dir === '.agents/skills', 'Cursor target_dir uses native skills path');
 
     assert(!cursorInstaller?.ancestor_conflict_check, 'Cursor installer does not enable ancestor conflict checks');
 
     const tempProjectDir13c = await fs.mkdtemp(path.join(os.tmpdir(), 'bmad-cursor-test-'));
     const installedBmadDir13c = await createTestBmadFixture();
-    const legacyDir13c = path.join(tempProjectDir13c, '.cursor', 'commands');
-    await fs.ensureDir(legacyDir13c);
-    await fs.writeFile(path.join(legacyDir13c, 'bmad-legacy.md'), 'legacy\n');
 
     const ideManager13c = new IdeManager();
     await ideManager13c.ensureInitialized();
@@ -518,7 +419,7 @@ async function runTests() {
 
     assert(result13c.success === true, 'Cursor setup succeeds against temp project');
 
-    const skillFile13c = path.join(tempProjectDir13c, '.cursor', 'skills', 'bmad-master', 'SKILL.md');
+    const skillFile13c = path.join(tempProjectDir13c, '.agents', 'skills', 'bmad-master', 'SKILL.md');
     assert(await fs.pathExists(skillFile13c), 'Cursor install writes SKILL.md directory output');
 
     // Verify name frontmatter matches directory name
@@ -526,8 +427,6 @@ async function runTests() {
     const nameMatch13c = skillContent13c.match(/^name:\s*(.+)$/m);
     assert(nameMatch13c && nameMatch13c[1].trim() === 'bmad-master', 'Cursor skill name frontmatter matches directory name exactly');
 
-    assert(!(await fs.pathExists(legacyDir13c)), 'Cursor setup removes legacy commands dir');
-
     await fs.remove(tempProjectDir13c);
     await fs.remove(path.dirname(installedBmadDir13c));
   } catch (error) {
@@ -546,19 +445,10 @@ async function runTests() {
     const platformCodes13 = await loadPlatformCodes();
     const rooInstaller = platformCodes13.platforms.roo?.installer;
 
-    assert(rooInstaller?.target_dir === '.roo/skills', 'Roo target_dir uses native skills path');
-
-    assert(
-      Array.isArray(rooInstaller?.legacy_targets) && rooInstaller.legacy_targets.includes('.roo/commands'),
-      'Roo installer cleans legacy command output',
-    );
+    assert(rooInstaller?.target_dir === '.agents/skills', 'Roo target_dir uses native skills path');
 
     const tempProjectDir13 = await fs.mkdtemp(path.join(os.tmpdir(), 'bmad-roo-test-'));
     const installedBmadDir13 = await createTestBmadFixture();
-    const legacyDir13 = path.join(tempProjectDir13, '.roo', 'commands', 'bmad-legacy-dir');
-    await fs.ensureDir(legacyDir13);
-    await fs.writeFile(path.join(tempProjectDir13, '.roo', 'commands', 'bmad-legacy.md'), 'legacy\n');
-    await fs.writeFile(path.join(legacyDir13, 'SKILL.md'), 'legacy\n');
 
     const ideManager13 = new IdeManager();
     await ideManager13.ensureInitialized();
@@ -569,7 +459,7 @@ async function runTests() {
 
     assert(result13.success === true, 'Roo setup succeeds against temp project');
 
-    const skillFile13 = path.join(tempProjectDir13, '.roo', 'skills', 'bmad-master', 'SKILL.md');
+    const skillFile13 = path.join(tempProjectDir13, '.agents', 'skills', 'bmad-master', 'SKILL.md');
     assert(await fs.pathExists(skillFile13), 'Roo install writes SKILL.md directory output');
 
     // Verify name frontmatter matches directory name (Roo constraint: lowercase alphanumeric + hyphens)
@@ -580,8 +470,6 @@ async function runTests() {
       'Roo skill name frontmatter matches directory name exactly (lowercase alphanumeric + hyphens)',
     );
 
-    assert(!(await fs.pathExists(path.join(tempProjectDir13, '.roo', 'commands'))), 'Roo setup removes legacy commands dir');
-
     // Reinstall/upgrade: run setup again over existing skills output
     const result13b = await ideManager13.setup('roo', tempProjectDir13, installedBmadDir13, {
       silent: true,
@@ -615,31 +503,13 @@ async function runTests() {
     const platformCodes17 = await loadPlatformCodes();
     const copilotInstaller = platformCodes17.platforms['github-copilot']?.installer;
 
-    assert(copilotInstaller?.target_dir === '.github/skills', 'GitHub Copilot target_dir uses native skills path');
-
-    assert(
-      Array.isArray(copilotInstaller?.legacy_targets) && copilotInstaller.legacy_targets.includes('.github/agents'),
-      'GitHub Copilot installer cleans legacy agents output',
-    );
-
-    assert(
-      Array.isArray(copilotInstaller?.legacy_targets) && copilotInstaller.legacy_targets.includes('.github/prompts'),
-      'GitHub Copilot installer cleans legacy prompts output',
-    );
+    assert(copilotInstaller?.target_dir === '.agents/skills', 'GitHub Copilot target_dir uses native skills path');
 
     const tempProjectDir17 = await fs.mkdtemp(path.join(os.tmpdir(), 'bmad-copilot-test-'));
     const installedBmadDir17 = await createTestBmadFixture();
 
-    // Create legacy .github/agents/ and .github/prompts/ files
-    const legacyAgentsDir17 = path.join(tempProjectDir17, '.github', 'agents');
-    const legacyPromptsDir17 = path.join(tempProjectDir17, '.github', 'prompts');
-    await fs.ensureDir(legacyAgentsDir17);
-    await fs.ensureDir(legacyPromptsDir17);
-    await fs.writeFile(path.join(legacyAgentsDir17, 'bmad-legacy.agent.md'), 'legacy agent\n');
-    await fs.writeFile(path.join(legacyPromptsDir17, 'bmad-legacy.prompt.md'), 'legacy prompt\n');
-
-    // Create legacy copilot-instructions.md with BMAD markers
     const copilotInstructionsPath17 = path.join(tempProjectDir17, '.github', 'copilot-instructions.md');
+    await fs.ensureDir(path.dirname(copilotInstructionsPath17));
     await fs.writeFile(
       copilotInstructionsPath17,
       'User content before\n<!-- BMAD:START -->\nBMAD generated content\n<!-- BMAD:END -->\nUser content after\n',
@@ -654,7 +524,7 @@ async function runTests() {
 
     assert(result17.success === true, 'GitHub Copilot setup succeeds against temp project');
 
-    const skillFile17 = path.join(tempProjectDir17, '.github', 'skills', 'bmad-master', 'SKILL.md');
+    const skillFile17 = path.join(tempProjectDir17, '.agents', 'skills', 'bmad-master', 'SKILL.md');
     assert(await fs.pathExists(skillFile17), 'GitHub Copilot install writes SKILL.md directory output');
 
     // Verify name frontmatter matches directory name
@@ -662,10 +532,6 @@ async function runTests() {
     const nameMatch17 = skillContent17.match(/^name:\s*(.+)$/m);
     assert(nameMatch17 && nameMatch17[1].trim() === 'bmad-master', 'GitHub Copilot skill name frontmatter matches directory name exactly');
 
-    assert(!(await fs.pathExists(legacyAgentsDir17)), 'GitHub Copilot setup removes legacy agents dir');
-
-    assert(!(await fs.pathExists(legacyPromptsDir17)), 'GitHub Copilot setup removes legacy prompts dir');
-
     // Verify copilot-instructions.md BMAD markers were stripped but user content preserved
     const cleanedInstructions17 = await fs.readFile(copilotInstructionsPath17, 'utf8');
     assert(
@@ -697,17 +563,8 @@ async function runTests() {
 
     assert(clineInstaller?.target_dir === '.cline/skills', 'Cline target_dir uses native skills path');
 
-    assert(
-      Array.isArray(clineInstaller?.legacy_targets) && clineInstaller.legacy_targets.includes('.clinerules/workflows'),
-      'Cline installer cleans legacy workflow output',
-    );
-
     const tempProjectDir18 = await fs.mkdtemp(path.join(os.tmpdir(), 'bmad-cline-test-'));
     const installedBmadDir18 = await createTestBmadFixture();
-    const legacyDir18 = path.join(tempProjectDir18, '.clinerules', 'workflows', 'bmad-legacy-dir');
-    await fs.ensureDir(legacyDir18);
-    await fs.writeFile(path.join(tempProjectDir18, '.clinerules', 'workflows', 'bmad-legacy.md'), 'legacy\n');
-    await fs.writeFile(path.join(legacyDir18, 'SKILL.md'), 'legacy\n');
 
     const ideManager18 = new IdeManager();
     await ideManager18.ensureInitialized();
@@ -726,8 +583,6 @@ async function runTests() {
     const nameMatch18 = skillContent18.match(/^name:\s*(.+)$/m);
     assert(nameMatch18 && nameMatch18[1].trim() === 'bmad-master', 'Cline skill name frontmatter matches directory name exactly');
 
-    assert(!(await fs.pathExists(path.join(tempProjectDir18, '.clinerules', 'workflows'))), 'Cline setup removes legacy workflows dir');
-
     // Reinstall/upgrade: run setup again over existing skills output
     const result18b = await ideManager18.setup('cline', tempProjectDir18, installedBmadDir18, {
       silent: true,
@@ -757,17 +612,8 @@ async function runTests() {
 
     assert(codebuddyInstaller?.target_dir === '.codebuddy/skills', 'CodeBuddy target_dir uses native skills path');
 
-    assert(
-      Array.isArray(codebuddyInstaller?.legacy_targets) && codebuddyInstaller.legacy_targets.includes('.codebuddy/commands'),
-      'CodeBuddy installer cleans legacy command output',
-    );
-
     const tempProjectDir19 = await fs.mkdtemp(path.join(os.tmpdir(), 'bmad-codebuddy-test-'));
     const installedBmadDir19 = await createTestBmadFixture();
-    const legacyDir19 = path.join(tempProjectDir19, '.codebuddy', 'commands', 'bmad-legacy-dir');
-    await fs.ensureDir(legacyDir19);
-    await fs.writeFile(path.join(tempProjectDir19, '.codebuddy', 'commands', 'bmad-legacy.md'), 'legacy\n');
-    await fs.writeFile(path.join(legacyDir19, 'SKILL.md'), 'legacy\n');
 
     const ideManager19 = new IdeManager();
     await ideManager19.ensureInitialized();
@@ -785,8 +631,6 @@ async function runTests() {
     const nameMatch19 = skillContent19.match(/^name:\s*(.+)$/m);
     assert(nameMatch19 && nameMatch19[1].trim() === 'bmad-master', 'CodeBuddy skill name frontmatter matches directory name exactly');
 
-    assert(!(await fs.pathExists(path.join(tempProjectDir19, '.codebuddy', 'commands'))), 'CodeBuddy setup removes legacy commands dir');
-
     const result19b = await ideManager19.setup('codebuddy', tempProjectDir19, installedBmadDir19, {
       silent: true,
       selectedModules: ['bmm'],
@@ -813,19 +657,10 @@ async function runTests() {
     const platformCodes20 = await loadPlatformCodes();
     const crushInstaller = platformCodes20.platforms.crush?.installer;
 
-    assert(crushInstaller?.target_dir === '.crush/skills', 'Crush target_dir uses native skills path');
-
-    assert(
-      Array.isArray(crushInstaller?.legacy_targets) && crushInstaller.legacy_targets.includes('.crush/commands'),
-      'Crush installer cleans legacy command output',
-    );
+    assert(crushInstaller?.target_dir === '.agents/skills', 'Crush target_dir uses native skills path');
 
     const tempProjectDir20 = await fs.mkdtemp(path.join(os.tmpdir(), 'bmad-crush-test-'));
     const installedBmadDir20 = await createTestBmadFixture();
-    const legacyDir20 = path.join(tempProjectDir20, '.crush', 'commands', 'bmad-legacy-dir');
-    await fs.ensureDir(legacyDir20);
-    await fs.writeFile(path.join(tempProjectDir20, '.crush', 'commands', 'bmad-legacy.md'), 'legacy\n');
-    await fs.writeFile(path.join(legacyDir20, 'SKILL.md'), 'legacy\n');
 
     const ideManager20 = new IdeManager();
     await ideManager20.ensureInitialized();
@@ -836,15 +671,13 @@ async function runTests() {
 
     assert(result20.success === true, 'Crush setup succeeds against temp project');
 
-    const skillFile20 = path.join(tempProjectDir20, '.crush', 'skills', 'bmad-master', 'SKILL.md');
+    const skillFile20 = path.join(tempProjectDir20, '.agents', 'skills', 'bmad-master', 'SKILL.md');
     assert(await fs.pathExists(skillFile20), 'Crush install writes SKILL.md directory output');
 
     const skillContent20 = await fs.readFile(skillFile20, 'utf8');
     const nameMatch20 = skillContent20.match(/^name:\s*(.+)$/m);
     assert(nameMatch20 && nameMatch20[1].trim() === 'bmad-master', 'Crush skill name frontmatter matches directory name exactly');
 
-    assert(!(await fs.pathExists(path.join(tempProjectDir20, '.crush', 'commands'))), 'Crush setup removes legacy commands dir');
-
     const result20b = await ideManager20.setup('crush', tempProjectDir20, installedBmadDir20, {
       silent: true,
       selectedModules: ['bmm'],
@@ -873,16 +706,8 @@ async function runTests() {
 
     assert(traeInstaller?.target_dir === '.trae/skills', 'Trae target_dir uses native skills path');
 
-    assert(
-      Array.isArray(traeInstaller?.legacy_targets) && traeInstaller.legacy_targets.includes('.trae/rules'),
-      'Trae installer cleans legacy rules output',
-    );
-
     const tempProjectDir21 = await fs.mkdtemp(path.join(os.tmpdir(), 'bmad-trae-test-'));
     const installedBmadDir21 = await createTestBmadFixture();
-    const legacyDir21 = path.join(tempProjectDir21, '.trae', 'rules');
-    await fs.ensureDir(legacyDir21);
-    await fs.writeFile(path.join(legacyDir21, 'bmad-legacy.md'), 'legacy\n');
 
     const ideManager21 = new IdeManager();
     await ideManager21.ensureInitialized();
@@ -900,8 +725,6 @@ async function runTests() {
     const nameMatch21 = skillContent21.match(/^name:\s*(.+)$/m);
     assert(nameMatch21 && nameMatch21[1].trim() === 'bmad-master', 'Trae skill name frontmatter matches directory name exactly');
 
-    assert(!(await fs.pathExists(path.join(tempProjectDir21, '.trae', 'rules'))), 'Trae setup removes legacy rules dir');
-
     const result21b = await ideManager21.setup('trae', tempProjectDir21, installedBmadDir21, {
       silent: true,
       selectedModules: ['bmm'],
@@ -930,12 +753,7 @@ async function runTests() {
 
     assert(!kiloConfig22?.suspended, 'KiloCoder is not suspended');
 
-    assert(kiloConfig22?.installer?.target_dir === '.kilocode/skills', 'KiloCoder target_dir uses native skills path');
-
-    assert(
-      Array.isArray(kiloConfig22?.installer?.legacy_targets) && kiloConfig22.installer.legacy_targets.includes('.kilocode/workflows'),
-      'KiloCoder installer cleans legacy workflows output',
-    );
+    assert(kiloConfig22?.installer?.target_dir === '.agents/skills', 'KiloCoder target_dir uses native skills path');
 
     const ideManager22 = new IdeManager();
     await ideManager22.ensureInitialized();
@@ -950,11 +768,6 @@ async function runTests() {
     const tempProjectDir22 = await fs.mkdtemp(path.join(os.tmpdir(), 'bmad-kilo-test-'));
     const installedBmadDir22 = await createTestBmadFixture();
 
-    // Pre-populate legacy Kilo artifacts that should be cleaned up
-    const legacyDir22 = path.join(tempProjectDir22, '.kilocode', 'workflows');
-    await fs.ensureDir(legacyDir22);
-    await fs.writeFile(path.join(legacyDir22, 'bmad-legacy.md'), 'legacy\n');
-
     const result22 = await ideManager22.setup('kilo', tempProjectDir22, installedBmadDir22, {
       silent: true,
       selectedModules: ['bmm'],
@@ -962,15 +775,13 @@ async function runTests() {
 
     assert(result22.success === true, 'KiloCoder setup succeeds against temp project');
 
-    const skillFile22 = path.join(tempProjectDir22, '.kilocode', 'skills', 'bmad-master', 'SKILL.md');
+    const skillFile22 = path.join(tempProjectDir22, '.agents', 'skills', 'bmad-master', 'SKILL.md');
     assert(await fs.pathExists(skillFile22), 'KiloCoder install writes SKILL.md directory output');
 
     const skillContent22 = await fs.readFile(skillFile22, 'utf8');
     const nameMatch22 = skillContent22.match(/^name:\s*(.+)$/m);
     assert(nameMatch22 && nameMatch22[1].trim() === 'bmad-master', 'KiloCoder skill name frontmatter matches directory name exactly');
 
-    assert(!(await fs.pathExists(path.join(tempProjectDir22, '.kilocode', 'workflows'))), 'KiloCoder setup removes legacy workflows dir');
-
     const result22b = await ideManager22.setup('kilo', tempProjectDir22, installedBmadDir22, {
       silent: true,
       selectedModules: ['bmm'],
@@ -997,18 +808,10 @@ async function runTests() {
     const platformCodes23 = await loadPlatformCodes();
     const geminiInstaller = platformCodes23.platforms.gemini?.installer;
 
-    assert(geminiInstaller?.target_dir === '.gemini/skills', 'Gemini target_dir uses native skills path');
-
-    assert(
-      Array.isArray(geminiInstaller?.legacy_targets) && geminiInstaller.legacy_targets.includes('.gemini/commands'),
-      'Gemini installer cleans legacy commands output',
-    );
+    assert(geminiInstaller?.target_dir === '.agents/skills', 'Gemini target_dir uses native skills path');
 
     const tempProjectDir23 = await fs.mkdtemp(path.join(os.tmpdir(), 'bmad-gemini-test-'));
     const installedBmadDir23 = await createTestBmadFixture();
-    const legacyDir23 = path.join(tempProjectDir23, '.gemini', 'commands');
-    await fs.ensureDir(legacyDir23);
-    await fs.writeFile(path.join(legacyDir23, 'bmad-legacy.toml'), 'legacy\n');
 
     const ideManager23 = new IdeManager();
     await ideManager23.ensureInitialized();
@@ -1019,15 +822,13 @@ async function runTests() {
 
     assert(result23.success === true, 'Gemini setup succeeds against temp project');
 
-    const skillFile23 = path.join(tempProjectDir23, '.gemini', 'skills', 'bmad-master', 'SKILL.md');
+    const skillFile23 = path.join(tempProjectDir23, '.agents', 'skills', 'bmad-master', 'SKILL.md');
     assert(await fs.pathExists(skillFile23), 'Gemini install writes SKILL.md directory output');
 
     const skillContent23 = await fs.readFile(skillFile23, 'utf8');
     const nameMatch23 = skillContent23.match(/^name:\s*(.+)$/m);
     assert(nameMatch23 && nameMatch23[1].trim() === 'bmad-master', 'Gemini skill name frontmatter matches directory name exactly');
 
-    assert(!(await fs.pathExists(path.join(tempProjectDir23, '.gemini', 'commands'))), 'Gemini setup removes legacy commands dir');
-
     const result23b = await ideManager23.setup('gemini', tempProjectDir23, installedBmadDir23, {
       silent: true,
       selectedModules: ['bmm'],
@@ -1055,16 +856,9 @@ async function runTests() {
     const iflowInstaller = platformCodes24.platforms.iflow?.installer;
 
     assert(iflowInstaller?.target_dir === '.iflow/skills', 'iFlow target_dir uses native skills path');
-    assert(
-      Array.isArray(iflowInstaller?.legacy_targets) && iflowInstaller.legacy_targets.includes('.iflow/commands'),
-      'iFlow installer cleans legacy commands output',
-    );
 
     const tempProjectDir24 = await fs.mkdtemp(path.join(os.tmpdir(), 'bmad-iflow-test-'));
     const installedBmadDir24 = await createTestBmadFixture();
-    const legacyDir24 = path.join(tempProjectDir24, '.iflow', 'commands');
-    await fs.ensureDir(legacyDir24);
-    await fs.writeFile(path.join(legacyDir24, 'bmad-legacy.md'), 'legacy\n');
 
     const ideManager24 = new IdeManager();
     await ideManager24.ensureInitialized();
@@ -1083,8 +877,6 @@ async function runTests() {
     const nameMatch24 = skillContent24.match(/^name:\s*(.+)$/m);
     assert(nameMatch24 && nameMatch24[1].trim() === 'bmad-master', 'iFlow skill name frontmatter matches directory name exactly');
 
-    assert(!(await fs.pathExists(path.join(tempProjectDir24, '.iflow', 'commands'))), 'iFlow setup removes legacy commands dir');
-
     await fs.remove(tempProjectDir24);
     await fs.remove(path.dirname(installedBmadDir24));
   } catch (error) {
@@ -1104,16 +896,9 @@ async function runTests() {
     const qwenInstaller = platformCodes25.platforms.qwen?.installer;
 
     assert(qwenInstaller?.target_dir === '.qwen/skills', 'QwenCoder target_dir uses native skills path');
-    assert(
-      Array.isArray(qwenInstaller?.legacy_targets) && qwenInstaller.legacy_targets.includes('.qwen/commands'),
-      'QwenCoder installer cleans legacy commands output',
-    );
 
     const tempProjectDir25 = await fs.mkdtemp(path.join(os.tmpdir(), 'bmad-qwen-test-'));
     const installedBmadDir25 = await createTestBmadFixture();
-    const legacyDir25 = path.join(tempProjectDir25, '.qwen', 'commands');
-    await fs.ensureDir(legacyDir25);
-    await fs.writeFile(path.join(legacyDir25, 'bmad-legacy.md'), 'legacy\n');
 
     const ideManager25 = new IdeManager();
     await ideManager25.ensureInitialized();
@@ -1132,8 +917,6 @@ async function runTests() {
     const nameMatch25 = skillContent25.match(/^name:\s*(.+)$/m);
     assert(nameMatch25 && nameMatch25[1].trim() === 'bmad-master', 'QwenCoder skill name frontmatter matches directory name exactly');
 
-    assert(!(await fs.pathExists(path.join(tempProjectDir25, '.qwen', 'commands'))), 'QwenCoder setup removes legacy commands dir');
-
     await fs.remove(tempProjectDir25);
     await fs.remove(path.dirname(installedBmadDir25));
   } catch (error) {
@@ -1152,17 +935,10 @@ async function runTests() {
     const platformCodes26 = await loadPlatformCodes();
     const rovoInstaller = platformCodes26.platforms['rovo-dev']?.installer;
 
-    assert(rovoInstaller?.target_dir === '.rovodev/skills', 'Rovo Dev target_dir uses native skills path');
-    assert(
-      Array.isArray(rovoInstaller?.legacy_targets) && rovoInstaller.legacy_targets.includes('.rovodev/workflows'),
-      'Rovo Dev installer cleans legacy workflows output',
-    );
+    assert(rovoInstaller?.target_dir === '.agents/skills', 'Rovo Dev target_dir uses native skills path');
 
     const tempProjectDir26 = await fs.mkdtemp(path.join(os.tmpdir(), 'bmad-rovodev-test-'));
     const installedBmadDir26 = await createTestBmadFixture();
-    const legacyDir26 = path.join(tempProjectDir26, '.rovodev', 'workflows');
-    await fs.ensureDir(legacyDir26);
-    await fs.writeFile(path.join(legacyDir26, 'bmad-legacy.md'), 'legacy\n');
 
     // Create a prompts.yml with BMAD entries and a user entry
     const yaml26 = require('yaml');
@@ -1173,6 +949,7 @@ async function runTests() {
         { name: 'my-custom-prompt', description: 'User prompt', content_file: 'custom.md' },
       ],
     });
+    await fs.ensureDir(path.dirname(promptsPath26));
     await fs.writeFile(promptsPath26, promptsContent26);
 
     const ideManager26 = new IdeManager();
@@ -1184,7 +961,7 @@ async function runTests() {
 
     assert(result26.success === true, 'Rovo Dev setup succeeds against temp project');
 
-    const skillFile26 = path.join(tempProjectDir26, '.rovodev', 'skills', 'bmad-master', 'SKILL.md');
+    const skillFile26 = path.join(tempProjectDir26, '.agents', 'skills', 'bmad-master', 'SKILL.md');
     assert(await fs.pathExists(skillFile26), 'Rovo Dev install writes SKILL.md directory output');
 
     // Verify name frontmatter matches directory name
@@ -1192,8 +969,6 @@ async function runTests() {
     const nameMatch26 = skillContent26.match(/^name:\s*(.+)$/m);
     assert(nameMatch26 && nameMatch26[1].trim() === 'bmad-master', 'Rovo Dev skill name frontmatter matches directory name exactly');
 
-    assert(!(await fs.pathExists(path.join(tempProjectDir26, '.rovodev', 'workflows'))), 'Rovo Dev setup removes legacy workflows dir');
-
     // Verify prompts.yml cleanup: BMAD entries removed, user entry preserved
     const cleanedPrompts26 = yaml26.parse(await fs.readFile(promptsPath26, 'utf8'));
     assert(
@@ -1295,7 +1070,7 @@ async function runTests() {
     const platformCodes28 = await loadPlatformCodes();
     const piInstaller = platformCodes28.platforms.pi?.installer;
 
-    assert(piInstaller?.target_dir === '.pi/skills', 'Pi target_dir uses native skills path');
+    assert(piInstaller?.target_dir === '.agents/skills', 'Pi target_dir uses native skills path');
 
     tempProjectDir28 = await fs.mkdtemp(path.join(os.tmpdir(), 'bmad-pi-test-'));
     installedBmadDir28 = await createTestBmadFixture();
@@ -1325,7 +1100,7 @@ async function runTests() {
     const detectedAfter28 = await ideManager28.detectInstalledIdes(tempProjectDir28);
     assert(detectedAfter28.includes('pi'), 'Pi is detected after install');
 
-    const skillFile28 = path.join(tempProjectDir28, '.pi', 'skills', 'bmad-master', 'SKILL.md');
+    const skillFile28 = path.join(tempProjectDir28, '.agents', 'skills', 'bmad-master', 'SKILL.md');
     assert(await fs.pathExists(skillFile28), 'Pi install writes SKILL.md directory output');
 
     // Parse YAML frontmatter between --- markers
@@ -1607,7 +1382,7 @@ async function runTests() {
     });
 
     assert(result.success === true, 'Antigravity setup succeeds with overlapping skill names');
-    assert(result.detail === '1 skills', 'Installer detail reports skill count');
+    assert(result.detail === '1 skills → .agent/skills', 'Installer detail reports skill count and target dir');
     assert(result.handlerResult.results.skillDirectories === 1, 'Result exposes unique skill directory count');
     assert(result.handlerResult.results.skills === 1, 'Result retains verbatim skill count');
     assert(
@@ -2847,6 +2622,157 @@ async function runTests() {
 
   console.log('');
 
+  // ============================================================
+  // Test Suite 40: Shared target_dir coordination
+  // ============================================================
+  console.log(`${colors.yellow}Test Suite 40: Shared target_dir coordination${colors.reset}\n`);
+
+  try {
+    // Cursor and Gemini both use .agents/skills — verify they coordinate.
+    clearCache();
+    const platformCodes40 = await loadPlatformCodes();
+    const cursorTarget = platformCodes40.platforms.cursor?.installer?.target_dir;
+    const geminiTarget = platformCodes40.platforms.gemini?.installer?.target_dir;
+    assert(cursorTarget === '.agents/skills' && geminiTarget === '.agents/skills', 'Cursor and Gemini share .agents/skills target_dir');
+
+    const tempProjectDir40 = await fs.mkdtemp(path.join(os.tmpdir(), 'bmad-shared-target-'));
+    const installedBmadDir40 = await createTestBmadFixture();
+
+    const ideManager40 = new IdeManager();
+    await ideManager40.ensureInitialized();
+
+    // Run setupBatch with both platforms — second should skip skill write.
+    const batchResults = await ideManager40.setupBatch(['cursor', 'gemini'], tempProjectDir40, installedBmadDir40, {
+      silent: true,
+      selectedModules: ['core'],
+    });
+
+    assert(batchResults.length === 2, 'setupBatch returns one result per IDE');
+    assert(batchResults[0].success === true, 'First platform (cursor) succeeds');
+    assert(batchResults[1].success === true, 'Second platform (gemini) succeeds');
+    assert(
+      batchResults[1].handlerResult?.results?.sharedTargetHandledByPeer === true,
+      'Second platform marked sharedTargetHandledByPeer (skipped redundant write)',
+    );
+
+    // Skill should be present in the shared dir after batch.
+    const sharedDir = path.join(tempProjectDir40, '.agents', 'skills');
+    const sharedDirEntries = await fs.readdir(sharedDir);
+    assert(sharedDirEntries.includes('bmad-master'), 'Shared .agents/skills/ contains bmad-master after batched install');
+
+    // Now uninstall just cursor while gemini remains. Skills must survive.
+    const cleanupResults = await ideManager40.cleanupByList(tempProjectDir40, ['cursor'], {
+      silent: true,
+      remainingIdes: ['gemini'],
+    });
+    assert(cleanupResults[0].skippedTarget === true, 'Cursor cleanup skips target_dir wipe when Gemini remains');
+    const stillThere = await fs.readdir(sharedDir);
+    assert(stillThere.includes('bmad-master'), 'bmad-master still present after partial uninstall (gemini still installed)');
+
+    // (Cleanup of the last sharing platform requires bmadDir to be inside
+    //  projectDir to compute removalSet; that's the production layout. The
+    //  fixture above keeps bmad in a separate temp dir, so test 41 below
+    //  exercises the in-project layout instead.)
+
+    await fs.remove(tempProjectDir40).catch(() => {});
+    await fs.remove(path.dirname(installedBmadDir40)).catch(() => {});
+  } catch (error) {
+    console.log(`${colors.red}Test Suite 40 setup failed: ${error.message}${colors.reset}`);
+    failed++;
+  }
+
+  console.log('');
+
+  // ============================================================
+  // Test Suite 40b: setupBatch — failed first writer does not poison peers
+  // ============================================================
+  console.log(`${colors.yellow}Test Suite 40b: setupBatch resilience to first-writer failure${colors.reset}\n`);
+
+  try {
+    const tempProjectDir40b = await fs.mkdtemp(path.join(os.tmpdir(), 'bmad-batch-fail-'));
+    const installedBmadDir40b = await createTestBmadFixture();
+
+    const ideManager40b = new IdeManager();
+    await ideManager40b.ensureInitialized();
+
+    // Force cursor's setup() to fail. With the bug, gemini would see the
+    // claimed target and skip — leaving .agents/skills/ empty.
+    const cursorHandler40b = ideManager40b.handlers.get('cursor');
+    const originalSetup = cursorHandler40b.setup.bind(cursorHandler40b);
+    cursorHandler40b.setup = async () => {
+      throw new Error('Simulated cursor failure');
+    };
+
+    const batchResults40b = await ideManager40b.setupBatch(['cursor', 'gemini'], tempProjectDir40b, installedBmadDir40b, {
+      silent: true,
+      selectedModules: ['core'],
+    });
+
+    // Restore so other tests aren't affected.
+    cursorHandler40b.setup = originalSetup;
+
+    assert(batchResults40b[0].success === false, 'Cursor reports failure');
+    assert(batchResults40b[1].success === true, 'Gemini still succeeds despite cursor failure');
+    assert(
+      batchResults40b[1].handlerResult?.results?.sharedTargetHandledByPeer !== true,
+      'Gemini does NOT skip its own write — it becomes the new first writer',
+    );
+
+    const sharedDir40b = path.join(tempProjectDir40b, '.agents', 'skills');
+    const entries40b = await fs.readdir(sharedDir40b);
+    assert(entries40b.includes('bmad-master'), 'Shared dir is populated by gemini after cursor failure');
+
+    await fs.remove(tempProjectDir40b).catch(() => {});
+    await fs.remove(path.dirname(installedBmadDir40b)).catch(() => {});
+  } catch (error) {
+    console.log(`${colors.red}Test Suite 40b setup failed: ${error.message}${colors.reset}`);
+    failed++;
+  }
+
+  console.log('');
+
+  // ============================================================
+  // Test Suite 41: Custom-module skill ownership (non-bmad prefix)
+  // ============================================================
+  console.log(`${colors.yellow}Test Suite 41: Custom-module skill ownership${colors.reset}\n`);
+
+  try {
+    // A custom module can ship a skill with any canonicalId (e.g. "fred-cool-skill").
+    // detect() must recognize it as BMAD-owned via the manifest, not the bmad- prefix.
+    const fixtureRoot41 = await fs.mkdtemp(path.join(os.tmpdir(), 'bmad-custom-prefix-'));
+    const bmadDir41 = path.join(fixtureRoot41, '_bmad');
+    await fs.ensureDir(path.join(bmadDir41, '_config'));
+    await fs.writeFile(
+      path.join(bmadDir41, '_config', 'skill-manifest.csv'),
+      [
+        'canonicalId,name,description,module,path',
+        '"fred-cool-skill","fred-cool-skill","Custom module skill","fred","_bmad/fred/skills/fred-cool-skill/SKILL.md"',
+        '',
+      ].join('\n'),
+    );
+    const fredSkill = path.join(bmadDir41, 'fred', 'skills', 'fred-cool-skill');
+    await fs.ensureDir(fredSkill);
+    await fs.writeFile(
+      path.join(fredSkill, 'SKILL.md'),
+      ['---', 'name: fred-cool-skill', 'description: Custom module skill', '---', '', 'A custom module skill.'].join('\n'),
+    );
+
+    const ideManager41 = new IdeManager();
+    await ideManager41.ensureInitialized();
+    await ideManager41.setup('cursor', fixtureRoot41, bmadDir41, { silent: true, selectedModules: ['fred'] });
+
+    const cursorHandler = ideManager41.handlers.get('cursor');
+    const detected = await cursorHandler.detect(fixtureRoot41);
+    assert(detected === true, 'detect() recognizes non-bmad-prefixed skill as BMAD-owned via skill-manifest.csv');
+
+    await fs.remove(fixtureRoot41).catch(() => {});
+  } catch (error) {
+    console.log(`${colors.red}Test Suite 41 setup failed: ${error.message}${colors.reset}`);
+    failed++;
+  }
+
+  console.log('');
+
   // ============================================================
   // Summary
   // ============================================================
diff --git a/tools/docs/native-skills-migration-checklist.md b/tools/docs/native-skills-migration-checklist.md
index 80c6a9296..e8fa4ad34 100644
--- a/tools/docs/native-skills-migration-checklist.md
+++ b/tools/docs/native-skills-migration-checklist.md
@@ -222,7 +222,6 @@ Support assumption: full Agent Skills support. Gemini CLI docs confirm workspace
 
 - [x] Confirm Gemini CLI native skills path is `.gemini/skills/{skill-name}/SKILL.md` (per [geminicli.com/docs/cli/skills](https://geminicli.com/docs/cli/skills/))
 - [x] Implement native skills output — target_dir `.gemini/skills`, skill_format true, template_type default (replaces TOML templates)
-- [x] Add legacy cleanup for `.gemini/commands` (via `legacy_targets`)
 - [x] Test fresh install — skills written to `.gemini/skills/bmad-master/SKILL.md` with correct frontmatter
 - [x] Test reinstall/upgrade from legacy TOML command output — legacy dir removed, skills installed
 - [x] Confirm no ancestor conflict protection is needed — Gemini CLI uses workspace > user > extension precedence, no ancestor directory inheritance
@@ -236,7 +235,6 @@ Support assumption: full Agent Skills support. iFlow docs confirm workspace skil
 
 - [x] Confirm iFlow native skills path is `.iflow/skills/{skill-name}/SKILL.md`
 - [x] Implement native skills output — target_dir `.iflow/skills`, skill_format true, template_type default
-- [x] Add legacy cleanup for `.iflow/commands` (via `legacy_targets`)
 - [x] Test fresh install — skills written to `.iflow/skills/bmad-master/SKILL.md`
 - [x] Test legacy cleanup — legacy commands dir removed
 - [x] Implement/extend automated tests — 6 assertions in test suite 24
@@ -249,7 +247,6 @@ Support assumption: full Agent Skills support. Qwen Code supports workspace skil
 
 - [x] Confirm QwenCoder native skills path is `.qwen/skills/{skill-name}/SKILL.md`
 - [x] Implement native skills output — target_dir `.qwen/skills`, skill_format true, template_type default
-- [x] Add legacy cleanup for `.qwen/commands` (via `legacy_targets`)
 - [x] Test fresh install — skills written to `.qwen/skills/bmad-master/SKILL.md`
 - [x] Test legacy cleanup — legacy commands dir removed
 - [x] Implement/extend automated tests — 6 assertions in test suite 25
@@ -262,7 +259,6 @@ Support assumption: full Agent Skills support. Rovo Dev now supports workspace s
 
 - [x] Confirm Rovo Dev native skills path is `.rovodev/skills/{skill-name}/SKILL.md` (per Atlassian blog)
 - [x] Replace 257-line custom `rovodev.js` with config-driven entry in `platform-codes.yaml`
-- [x] Add legacy cleanup for `.rovodev/workflows` (via `legacy_targets`) and BMAD entries in `prompts.yml` (via `cleanupRovoDevPrompts()` in `_config-driven.js`)
 - [x] Test fresh install — skills written to `.rovodev/skills/bmad-master/SKILL.md`
 - [x] Test legacy cleanup — legacy workflows dir removed, `prompts.yml` BMAD entries stripped while preserving user entries
 - [x] Implement/extend automated tests — 8 assertions in test suite 26
diff --git a/tools/installer/core/installer.js b/tools/installer/core/installer.js
index ef6e8662f..a68193bc6 100644
--- a/tools/installer/core/installer.js
+++ b/tools/installer/core/installer.js
@@ -14,6 +14,7 @@ const { ExternalModuleManager } = require('../modules/external-manager');
 const { resolveModuleVersion } = require('../modules/version-resolver');
 
 const { ExistingInstall } = require('./existing-install');
+const { warnPreNativeSkillsLegacy } = require('./legacy-warnings');
 
 class Installer {
   constructor() {
@@ -41,6 +42,16 @@ class Installer {
       const officialModules = await OfficialModules.build(config, paths);
       const existingInstall = await ExistingInstall.detect(paths.bmadDir);
 
+      try {
+        await warnPreNativeSkillsLegacy({
+          projectRoot: paths.projectRoot,
+          existingVersion: existingInstall.installed ? existingInstall.version : null,
+        });
+      } catch (error) {
+        // Legacy-dir scan is informational; never let it abort install.
+        await prompts.log.warn(`Warning: Could not check for legacy BMAD entries: ${error.message}`);
+      }
+
       if (existingInstall.installed) {
         await this._removeDeselectedModules(existingInstall, config, paths);
         updateState = await this._prepareUpdateState(paths, config, existingInstall, officialModules);
@@ -183,15 +194,16 @@ class Installer {
 
     if (toRemove.length === 0) return;
 
-    await this.ideManager.ensureInitialized();
-    for (const ide of toRemove) {
-      try {
-        const handler = this.ideManager.handlers.get(ide);
-        if (handler) {
-          await handler.cleanup(paths.projectRoot);
-        }
-      } catch (error) {
-        await prompts.log.warn(`Warning: Failed to remove ${ide}: ${error.message}`);
+    // Pass the newly-selected list as remainingIdes so cleanupByList skips
+    // target_dir wipes for IDEs whose directory is still owned by a peer
+    // (e.g. removing 'cursor' while 'gemini' remains — both share .agents/skills).
+    const results = await this.ideManager.cleanupByList(paths.projectRoot, toRemove, {
+      remainingIdes: [...newlySelected],
+    });
+
+    for (const result of results || []) {
+      if (result && result.success === false) {
+        await prompts.log.warn(`Warning: Failed to remove ${result.ide}: ${result.error || 'unknown error'}`);
       }
     }
   }
@@ -342,13 +354,14 @@ class Installer {
       return;
     }
 
-    for (const ide of validIdes) {
-      const setupResult = await this.ideManager.setup(ide, paths.projectRoot, paths.bmadDir, {
-        selectedModules: allModules || [],
-        verbose: config.verbose,
-        previousSkillIds,
-      });
+    const setupResults = await this.ideManager.setupBatch(validIdes, paths.projectRoot, paths.bmadDir, {
+      selectedModules: allModules || [],
+      verbose: config.verbose,
+      previousSkillIds,
+    });
 
+    for (const setupResult of setupResults) {
+      const ide = setupResult.ide;
       if (setupResult.success) {
         addResult(ide, 'ok', setupResult.detail || '');
       } else {
diff --git a/tools/installer/core/legacy-warnings.js b/tools/installer/core/legacy-warnings.js
new file mode 100644
index 000000000..e3098b82b
--- /dev/null
+++ b/tools/installer/core/legacy-warnings.js
@@ -0,0 +1,151 @@
+const os = require('node:os');
+const path = require('node:path');
+const semver = require('semver');
+const fs = require('../fs-native');
+const prompts = require('../prompts');
+const { BMAD_FOLDER_NAME } = require('../ide/shared/path-utils');
+const { getInstalledCanonicalIds, isBmadOwnedEntry } = require('../ide/shared/installed-skills');
+
+const MIN_NATIVE_SKILLS_VERSION = '6.1.0';
+
+// Pre-v6.1.0 paths: BMAD used to install commands/workflows/etc in tool-specific dirs.
+// In v6.1.0 BMAD switched to native SKILL.md format.
+const LEGACY_COMMAND_PATHS = [
+  '.agent/workflows',
+  '.augment/commands',
+  '.claude/commands',
+  '.clinerules/workflows',
+  '.codex/prompts',
+  '~/.codex/prompts',
+  '.codebuddy/commands',
+  '.crush/commands',
+  '.cursor/commands',
+  '.gemini/commands',
+  '.github/agents',
+  '.github/prompts',
+  '.iflow/commands',
+  '.kilocode/workflows',
+  '.kiro/steering',
+  '.opencode/agents',
+  '.opencode/commands',
+  '.opencode/agent',
+  '.opencode/command',
+  '.qwen/commands',
+  '.roo/commands',
+  '.rovodev/workflows',
+  '.trae/rules',
+  '.windsurf/workflows',
+];
+
+// Skill paths that moved to the cross-tool .agents/skills/ standard.
+// Users upgrading from a prior install may have stale BMAD skills here that
+// the AI tool will load alongside the new ones, causing duplicates.
+const LEGACY_SKILL_PATHS = [
+  '.augment/skills',
+  '~/.augment/skills',
+  '.codex/skills',
+  '.crush/skills',
+  '.cursor/skills',
+  '~/.cursor/skills',
+  '.gemini/skills',
+  '~/.gemini/skills',
+  '.github/skills',
+  '~/.github/skills',
+  '.kilocode/skills',
+  '.kimi/skills',
+  '~/.kimi/skills',
+  '.opencode/skills',
+  '~/.opencode/skills',
+  '.pi/skills',
+  '~/.pi/skills',
+  '.roo/skills',
+  '~/.roo/skills',
+  '.rovodev/skills',
+  '~/.rovodev/skills',
+  '.windsurf/skills',
+  '~/.windsurf/skills',
+  '~/.codeium/windsurf/skills',
+];
+
+const LEGACY_PATHS = [...LEGACY_COMMAND_PATHS, ...LEGACY_SKILL_PATHS];
+
+function expandPath(p) {
+  if (p === '~') return os.homedir();
+  if (p.startsWith('~/')) return path.join(os.homedir(), p.slice(2));
+  return p;
+}
+
+function resolveLegacyPath(projectRoot, p) {
+  if (path.isAbsolute(p) || p.startsWith('~')) return expandPath(p);
+  return path.join(projectRoot, p);
+}
+
+async function findStaleLegacyDirs(projectRoot) {
+  const bmadDir = path.join(projectRoot, BMAD_FOLDER_NAME);
+  const canonicalIds = await getInstalledCanonicalIds(bmadDir);
+
+  const findings = [];
+  for (const legacyPath of LEGACY_PATHS) {
+    const resolved = resolveLegacyPath(projectRoot, legacyPath);
+    if (!(await fs.pathExists(resolved))) continue;
+    try {
+      const entries = await fs.readdir(resolved);
+      const bmadEntries = entries.filter((e) => isBmadOwnedEntry(e, canonicalIds));
+      if (bmadEntries.length > 0) {
+        findings.push({ path: resolved, displayPath: legacyPath, count: bmadEntries.length, entries: bmadEntries });
+      }
+    } catch {
+      // Unreadable dir — skip
+    }
+  }
+  return findings;
+}
+
+function isPreNativeSkillsVersion(version) {
+  if (!version) return false;
+  const coerced = semver.valid(version) || semver.valid(semver.coerce(version));
+  if (!coerced) return false;
+  return semver.lt(coerced, MIN_NATIVE_SKILLS_VERSION);
+}
+
+async function warnPreNativeSkillsLegacy({ projectRoot, existingVersion } = {}) {
+  const versionTriggered = isPreNativeSkillsVersion(existingVersion);
+  const staleDirs = await findStaleLegacyDirs(projectRoot);
+
+  if (!versionTriggered && staleDirs.length === 0) return;
+
+  if (versionTriggered) {
+    await prompts.log.warn(
+      `Detected previous BMAD install v${existingVersion} (pre-${MIN_NATIVE_SKILLS_VERSION}). ` +
+        `BMAD switched to native skills format in v${MIN_NATIVE_SKILLS_VERSION}; old command/workflow directories from your prior install may still be present.`,
+    );
+  }
+
+  if (staleDirs.length > 0) {
+    await prompts.log.warn(
+      `Found stale BMAD entries in ${staleDirs.length} legacy location(s) that the new installer no longer manages. ` +
+        `Your AI tool may load these alongside the new skills, causing duplicates. Remove them manually:`,
+    );
+    for (const finding of staleDirs) {
+      // Print each entry by exact name. A `bmad*` glob would (a) miss
+      // custom-module skills the canonicalId scan now picks up, and
+      // (b) match bmad-os-* utility skills the user should keep.
+      const entries = finding.entries || [];
+      for (const entry of entries) {
+        await prompts.log.message(`    rm -rf "${path.join(finding.path, entry)}"`);
+      }
+    }
+  } else if (versionTriggered) {
+    await prompts.log.message(
+      '  No stale legacy directories detected, but if your AI tool shows duplicate BMAD commands after install, check for old `bmad-*` entries in tool-specific dirs (e.g. .claude/commands, .cursor/commands).',
+    );
+  }
+}
+
+module.exports = {
+  warnPreNativeSkillsLegacy,
+  findStaleLegacyDirs,
+  isPreNativeSkillsVersion,
+  LEGACY_PATHS,
+  MIN_NATIVE_SKILLS_VERSION,
+};
diff --git a/tools/installer/ide/_config-driven.js b/tools/installer/ide/_config-driven.js
index 563818f67..737e10862 100644
--- a/tools/installer/ide/_config-driven.js
+++ b/tools/installer/ide/_config-driven.js
@@ -1,10 +1,10 @@
-const os = require('node:os');
 const path = require('node:path');
 const fs = require('../fs-native');
 const yaml = require('yaml');
 const prompts = require('../prompts');
 const csv = require('csv-parse/sync');
 const { BMAD_FOLDER_NAME } = require('./shared/path-utils');
+const { getInstalledCanonicalIds, isBmadOwnedEntry } = require('./shared/installed-skills');
 
 /**
  * Config-driven IDE setup handler
@@ -16,7 +16,7 @@ const { BMAD_FOLDER_NAME } = require('./shared/path-utils');
  * Features:
  * - Config-driven from platform-codes.yaml
  * - Verbatim skill installation from skill-manifest.csv
- * - Legacy directory cleanup and IDE-specific marker removal
+ * - IDE-specific marker removal (copilot-instructions, kilo modes, rovodev prompts)
  */
 class ConfigDrivenIdeSetup {
   constructor(platformCode, platformConfig) {
@@ -44,16 +44,20 @@ class ConfigDrivenIdeSetup {
   async detect(projectDir) {
     if (!this.configDir) return false;
 
-    const dir = path.join(projectDir || process.cwd(), this.configDir);
-    if (await fs.pathExists(dir)) {
-      try {
-        const entries = await fs.readdir(dir);
-        return entries.some((e) => typeof e === 'string' && e.startsWith('bmad'));
-      } catch {
-        return false;
-      }
+    const root = projectDir || process.cwd();
+    const dir = path.join(root, this.configDir);
+    if (!(await fs.pathExists(dir))) return false;
+
+    let entries;
+    try {
+      entries = await fs.readdir(dir);
+    } catch {
+      return false;
     }
-    return false;
+
+    const bmadDir = await this._findBmadDir(root);
+    const canonicalIds = await getInstalledCanonicalIds(bmadDir);
+    return entries.some((e) => isBmadOwnedEntry(e, canonicalIds));
   }
 
   /**
@@ -92,6 +96,12 @@ class ConfigDrivenIdeSetup {
       return { success: false, reason: 'no-config' };
     }
 
+    // When a peer platform in the same install batch owns this target_dir,
+    // skip the skill write — the peer has already populated it.
+    if (options.skipTarget) {
+      return { success: true, results: { skills: 0, sharedTargetHandledByPeer: true } };
+    }
+
     if (this.installerConfig.target_dir) {
       return this.installToTarget(projectDir, bmadDir, this.installerConfig, options);
     }
@@ -222,27 +232,6 @@ class ConfigDrivenIdeSetup {
       removalSet = new Set();
     }
 
-    // Migrate legacy target directories (e.g. .opencode/agent → .opencode/agents)
-    // Legacy dirs are abandoned entirely, so use prefix matching (null removalSet)
-    if (this.installerConfig?.legacy_targets) {
-      const legacyDirsExist = await Promise.all(
-        this.installerConfig.legacy_targets.map((d) =>
-          this.isGlobalPath(d) ? fs.pathExists(d.replace(/^~/, os.homedir())) : fs.pathExists(path.join(projectDir, d)),
-        ),
-      );
-      if (legacyDirsExist.some(Boolean)) {
-        if (!options.silent) await prompts.log.message('  Migrating legacy directories...');
-        for (const legacyDir of this.installerConfig.legacy_targets) {
-          if (this.isGlobalPath(legacyDir)) {
-            await this.warnGlobalLegacy(legacyDir, options);
-          } else {
-            await this.cleanupTarget(projectDir, legacyDir, options, null);
-            await this.removeEmptyParents(projectDir, legacyDir);
-          }
-        }
-      }
-    }
-
     // Strip BMAD markers from copilot-instructions.md if present
     if (this.name === 'github-copilot') {
       await this.cleanupCopilotInstructions(projectDir, options);
@@ -258,47 +247,17 @@ class ConfigDrivenIdeSetup {
       await this.cleanupRovoDevPrompts(projectDir, options);
     }
 
+    // Skip target_dir cleanup when a peer platform owns this directory
+    // (set during dedup'd install or when uninstalling one of several
+    // platforms that share the same target_dir).
+    if (options.skipTarget) return;
+
     // Clean current target directory
     if (this.installerConfig?.target_dir) {
       await this.cleanupTarget(projectDir, this.installerConfig.target_dir, options, removalSet);
     }
   }
 
-  /**
-   * Check if a path is global (starts with ~ or is absolute)
-   * @param {string} p - Path to check
-   * @returns {boolean}
-   */
-  isGlobalPath(p) {
-    return p.startsWith('~') || path.isAbsolute(p);
-  }
-
-  /**
-   * Warn about stale BMAD files in a global legacy directory (never auto-deletes)
-   * @param {string} legacyDir - Legacy directory path (may start with ~)
-   * @param {Object} options - Options (silent, etc.)
-   */
-  async warnGlobalLegacy(legacyDir, options = {}) {
-    try {
-      const expanded = legacyDir.startsWith('~/')
-        ? path.join(os.homedir(), legacyDir.slice(2))
-        : legacyDir === '~'
-          ? os.homedir()
-          : legacyDir;
-
-      if (!(await fs.pathExists(expanded))) return;
-
-      const entries = await fs.readdir(expanded);
-      const bmadFiles = entries.filter((e) => typeof e === 'string' && e.startsWith('bmad'));
-
-      if (bmadFiles.length > 0 && !options.silent) {
-        await prompts.log.warn(`Found ${bmadFiles.length} stale BMAD file(s) in ${expanded}. Remove manually: rm ${expanded}/bmad-*`);
-      }
-    } catch {
-      // Errors reading global paths are silently ignored
-    }
-  }
-
   /**
    * Find the _bmad directory in a project
    * @param {string} projectDir - Project directory
@@ -426,8 +385,8 @@ class ConfigDrivenIdeSetup {
       // Always preserve bmad-os-* utility skills regardless of cleanup mode
       if (entry.startsWith('bmad-os-')) continue;
 
-      // Surgical removal from set, or legacy prefix matching when set is null
-      const shouldRemove = removalSet ? removalSet.has(entry) : entry.startsWith('bmad');
+      // Surgical removal from set, or fallback to manifest+prefix detection when null
+      const shouldRemove = removalSet ? removalSet.has(entry) : isBmadOwnedEntry(entry, null);
 
       if (shouldRemove) {
         try {
@@ -590,10 +549,9 @@ class ConfigDrivenIdeSetup {
       try {
         if (await fs.pathExists(candidatePath)) {
           const entries = await fs.readdir(candidatePath);
-          const hasBmad = entries.some(
-            (e) => typeof e === 'string' && e.toLowerCase().startsWith('bmad') && !e.toLowerCase().startsWith('bmad-os-'),
-          );
-          if (hasBmad) {
+          const ancestorBmadDir = await this._findBmadDir(current);
+          const canonicalIds = await getInstalledCanonicalIds(ancestorBmadDir);
+          if (entries.some((e) => isBmadOwnedEntry(e, canonicalIds))) {
             return candidatePath;
           }
         }
@@ -605,43 +563,6 @@ class ConfigDrivenIdeSetup {
 
     return null;
   }
-
-  /**
-   * Walk up ancestor directories from relativeDir toward projectDir, removing each if empty
-   * Stops at projectDir boundary — never removes projectDir itself
-   * @param {string} projectDir - Project root (boundary)
-   * @param {string} relativeDir - Relative directory to start from
-   */
-  async removeEmptyParents(projectDir, relativeDir) {
-    const resolvedProject = path.resolve(projectDir);
-    let current = relativeDir;
-    let last = null;
-    while (current && current !== '.' && current !== last) {
-      last = current;
-      const fullPath = path.resolve(projectDir, current);
-      // Boundary guard: never traverse outside projectDir
-      if (!fullPath.startsWith(resolvedProject + path.sep) && fullPath !== resolvedProject) break;
-      try {
-        if (!(await fs.pathExists(fullPath))) {
-          // Dir already gone — advance current; last is reset at top of next iteration
-          current = path.dirname(current);
-          continue;
-        }
-        const remaining = await fs.readdir(fullPath);
-        if (remaining.length > 0) break;
-        await fs.rmdir(fullPath);
-      } catch (error) {
-        // ENOTEMPTY: TOCTOU race (file added between readdir and rmdir) — skip level, continue upward
-        // ENOENT: dir removed by another process between pathExists and rmdir — skip level, continue upward
-        if (error.code === 'ENOTEMPTY' || error.code === 'ENOENT') {
-          current = path.dirname(current);
-          continue;
-        }
-        break; // fatal error (e.g. EACCES) — stop upward walk
-      }
-      current = path.dirname(current);
-    }
-  }
 }
 
 module.exports = { ConfigDrivenIdeSetup };
diff --git a/tools/installer/ide/manager.js b/tools/installer/ide/manager.js
index ac49a8773..6370e4f41 100644
--- a/tools/installer/ide/manager.js
+++ b/tools/installer/ide/manager.js
@@ -160,8 +160,18 @@ class IdeManager {
       let detail = '';
       if (handlerResult && handlerResult.results) {
         const r = handlerResult.results;
-        const count = r.skillDirectories || r.skills || 0;
-        if (count > 0) detail = `${count} skills`;
+        let count = r.skillDirectories || r.skills || 0;
+        // Dedup'd platform: report the count its peer wrote so the user sees
+        // a consistent picture across all platforms sharing the dir.
+        if (count === 0 && r.sharedTargetHandledByPeer && options.sharedSkillCount) {
+          count = options.sharedSkillCount;
+        }
+        const targetDir = handler.installerConfig?.target_dir || null;
+        if (count > 0 && targetDir) {
+          detail = `${count} skills → ${targetDir}`;
+        } else if (count > 0) {
+          detail = `${count} skills`;
+        }
       }
       // Propagate handler's success status (default true for backward compat)
       const success = handlerResult?.success !== false;
@@ -172,6 +182,57 @@ class IdeManager {
     }
   }
 
+  /**
+   * Run setup for multiple IDEs as a single batch.
+   * Dedupes work when several selected platforms share the same target_dir:
+   * the first platform owns the directory write, peers skip it.
+   * @param {Array<string>} ideList - IDE names to set up
+   * @param {string} projectDir
+   * @param {string} bmadDir
+   * @param {Object} [options] - Forwarded to each handler.setup
+   * @returns {Promise<Array>} Per-IDE results
+   */
+  async setupBatch(ideList, projectDir, bmadDir, options = {}) {
+    await this.ensureInitialized();
+    const results = [];
+    // target_dir → { firstIde, skillCount } from the platform that actually wrote it
+    const claimedTargets = new Map();
+
+    for (const ideName of ideList) {
+      const handler = this.handlers.get(ideName.toLowerCase());
+      if (!handler) {
+        results.push(await this.setup(ideName, projectDir, bmadDir, options));
+        continue;
+      }
+
+      const target = handler.installerConfig?.target_dir || null;
+      const claim = target ? claimedTargets.get(target) : null;
+      const skipTarget = !!claim;
+
+      const result = await this.setup(ideName, projectDir, bmadDir, {
+        ...options,
+        skipTarget,
+        sharedWith: claim?.firstIde || null,
+        sharedTarget: target,
+        sharedSkillCount: claim?.skillCount || 0,
+      });
+
+      if (target && !claim) {
+        const writtenCount = result.handlerResult?.results?.skillDirectories || result.handlerResult?.results?.skills || 0;
+        // Only claim the target when the install actually succeeded and wrote skills.
+        // If the first platform fails (ancestor conflict, exception, etc.), leave the
+        // dir unclaimed so the next peer becomes the new first writer instead of
+        // silently skipping into a broken/empty target_dir.
+        if (result.success && writtenCount > 0) {
+          claimedTargets.set(target, { firstIde: ideName, skillCount: writtenCount });
+        }
+      }
+      results.push(result);
+    }
+
+    return results;
+  }
+
   /**
    * Cleanup IDE configurations
    * @param {string} projectDir - Project directory
@@ -198,6 +259,8 @@ class IdeManager {
    * @param {string} projectDir - Project directory
    * @param {Array<string>} ideList - List of IDE names to clean up
    * @param {Object} [options] - Cleanup options passed through to handlers
+   *   options.remainingIdes - IDE names still installed after this cleanup; used
+   *     to skip target_dir wipe when a co-installed platform shares the dir.
    * @returns {Array} Results array
    */
   async cleanupByList(projectDir, ideList, options = {}) {
@@ -211,13 +274,27 @@ class IdeManager {
     // Build lowercase lookup for case-insensitive matching
     const lowercaseHandlers = new Map([...this.handlers.entries()].map(([k, v]) => [k.toLowerCase(), v]));
 
+    // Resolve target_dirs for IDEs that will remain installed after this cleanup
+    const remainingTargets = new Set();
+    if (Array.isArray(options.remainingIdes)) {
+      for (const remaining of options.remainingIdes) {
+        const h = lowercaseHandlers.get(String(remaining).toLowerCase());
+        const t = h?.installerConfig?.target_dir;
+        if (t) remainingTargets.add(t);
+      }
+    }
+
     for (const ideName of ideList) {
       const handler = lowercaseHandlers.get(ideName.toLowerCase());
       if (!handler) continue;
 
+      const target = handler.installerConfig?.target_dir || null;
+      const skipTarget = target && remainingTargets.has(target);
+      const cleanupOptions = skipTarget ? { ...options, skipTarget: true } : options;
+
       try {
-        await handler.cleanup(projectDir, options);
-        results.push({ ide: ideName, success: true });
+        await handler.cleanup(projectDir, cleanupOptions);
+        results.push({ ide: ideName, success: true, skippedTarget: !!skipTarget });
       } catch (error) {
         results.push({ ide: ideName, success: false, error: error.message });
       }
diff --git a/tools/installer/ide/platform-codes.yaml b/tools/installer/ide/platform-codes.yaml
index 1899473c0..0f49a7fbe 100644
--- a/tools/installer/ide/platform-codes.yaml
+++ b/tools/installer/ide/platform-codes.yaml
@@ -5,128 +5,203 @@
 #   preferred: Whether shown as a recommended option on install
 #   suspended: (optional) Message explaining why install is blocked
 #   installer:
-#     target_dir: Directory where skill directories are installed
-#     legacy_targets: (optional) Old target dirs to clean up on reinstall
+#     target_dir: Directory where skill directories are installed (project/workspace)
+#     global_target_dir: (optional) User-home directory for global install
 #     ancestor_conflict_check: (optional) Refuse install when ancestor dir has BMAD files
+#
+# Multiple platforms may share the same target_dir or global_target_dir — many tools
+# read from the shared `.agents/skills/` and `~/.agents/skills/` cross-tool standard.
+# Paths verified against each tool's primary docs as of 2026-04-25.
 
 platforms:
+  adal:
+    name: "AdaL"
+    preferred: false
+    installer:
+      target_dir: .adal/skills
+      global_target_dir: ~/.adal/skills
+
+  amp:
+    name: "Sourcegraph Amp"
+    preferred: false
+    installer:
+      target_dir: .agents/skills
+      global_target_dir: ~/.config/agents/skills
+
   antigravity:
     name: "Google Antigravity"
     preferred: false
     installer:
-      legacy_targets:
-        - .agent/workflows
       target_dir: .agent/skills
+      global_target_dir: ~/.gemini/antigravity/skills
 
   auggie:
     name: "Auggie"
     preferred: false
     installer:
-      legacy_targets:
-        - .augment/commands
-      target_dir: .augment/skills
+      target_dir: .agents/skills
+      global_target_dir: ~/.agents/skills
+
+  bob:
+    name: "IBM Bob"
+    preferred: false
+    installer:
+      target_dir: .bob/skills
+      global_target_dir: ~/.bob/skills
 
   claude-code:
     name: "Claude Code"
     preferred: true
     installer:
-      legacy_targets:
-        - .claude/commands
       target_dir: .claude/skills
+      global_target_dir: ~/.claude/skills
 
   cline:
     name: "Cline"
     preferred: false
     installer:
-      legacy_targets:
-        - .clinerules/workflows
       target_dir: .cline/skills
+      global_target_dir: ~/.cline/skills
 
   codex:
     name: "Codex"
-    preferred: false
+    preferred: true
     installer:
-      legacy_targets:
-        - .codex/prompts
-        - ~/.codex/prompts
       target_dir: .agents/skills
+      global_target_dir: ~/.codex/skills
 
   codebuddy:
     name: "CodeBuddy"
     preferred: false
     installer:
-      legacy_targets:
-        - .codebuddy/commands
       target_dir: .codebuddy/skills
+      global_target_dir: ~/.codebuddy/skills
+
+  command-code:
+    name: "Command Code"
+    preferred: false
+    installer:
+      target_dir: .agents/skills
+      global_target_dir: ~/.agents/skills
+
+  cortex:
+    name: "Snowflake Cortex Code"
+    preferred: false
+    installer:
+      target_dir: .cortex/skills
+      global_target_dir: ~/.snowflake/cortex/skills
 
   crush:
     name: "Crush"
     preferred: false
     installer:
-      legacy_targets:
-        - .crush/commands
-      target_dir: .crush/skills
+      target_dir: .agents/skills
+      global_target_dir: ~/.config/agents/skills
 
   cursor:
     name: "Cursor"
     preferred: true
     installer:
-      legacy_targets:
-        - .cursor/commands
-      target_dir: .cursor/skills
+      target_dir: .agents/skills
+      global_target_dir: ~/.agents/skills
+
+  droid:
+    name: "Factory Droid"
+    preferred: false
+    installer:
+      target_dir: .factory/skills
+      global_target_dir: ~/.factory/skills
+
+  firebender:
+    name: "Firebender"
+    preferred: false
+    installer:
+      target_dir: .firebender/skills
+      global_target_dir: ~/.agents/skills
 
   gemini:
     name: "Gemini CLI"
     preferred: false
     installer:
-      legacy_targets:
-        - .gemini/commands
-      target_dir: .gemini/skills
+      target_dir: .agents/skills
+      global_target_dir: ~/.agents/skills
 
   github-copilot:
     name: "GitHub Copilot"
+    preferred: true
+    installer:
+      target_dir: .agents/skills
+      global_target_dir: ~/.agents/skills
+
+  goose:
+    name: "Block Goose"
     preferred: false
     installer:
-      legacy_targets:
-        - .github/agents
-        - .github/prompts
-      target_dir: .github/skills
+      target_dir: .agents/skills
+      global_target_dir: ~/.config/agents/skills
 
   iflow:
     name: "iFlow"
     preferred: false
     installer:
-      legacy_targets:
-        - .iflow/commands
       target_dir: .iflow/skills
+      global_target_dir: ~/.iflow/skills
 
   junie:
     name: "Junie"
     preferred: false
     installer:
-      target_dir: .agents/skills
+      target_dir: .junie/skills
+      global_target_dir: ~/.junie/skills
 
   kilo:
     name: "KiloCoder"
     preferred: false
     installer:
-      legacy_targets:
-        - .kilocode/workflows
-      target_dir: .kilocode/skills
+      target_dir: .agents/skills
+      global_target_dir: ~/.kilocode/skills
 
   kimi-code:
     name: "Kimi Code"
     preferred: false
     installer:
-      target_dir: .kimi/skills
+      target_dir: .agents/skills
+      global_target_dir: ~/.agents/skills
 
   kiro:
     name: "Kiro"
     preferred: false
     installer:
-      legacy_targets:
-        - .kiro/steering
       target_dir: .kiro/skills
+      global_target_dir: ~/.kiro/skills
+
+  kode:
+    name: "Kode"
+    preferred: false
+    installer:
+      target_dir: .kode/skills
+      global_target_dir: ~/.kode/skills
+
+  mistral-vibe:
+    name: "Mistral Vibe"
+    preferred: false
+    installer:
+      target_dir: .agents/skills
+      global_target_dir: ~/.vibe/skills
+
+  mux:
+    name: "Mux"
+    preferred: false
+    installer:
+      target_dir: .agents/skills
+      global_target_dir: ~/.agents/skills
+
+  neovate:
+    name: "Neovate"
+    preferred: false
+    installer:
+      target_dir: .neovate/skills
+      global_target_dir: ~/.neovate/skills
 
   ona:
     name: "Ona"
@@ -134,65 +209,98 @@ platforms:
     installer:
       target_dir: .ona/skills
 
+  openclaw:
+    name: "OpenClaw"
+    preferred: false
+    installer:
+      target_dir: .agents/skills
+      global_target_dir: ~/.agents/skills
+
   opencode:
     name: "OpenCode"
     preferred: false
     installer:
-      legacy_targets:
-        - .opencode/agents
-        - .opencode/commands
-        - .opencode/agent
-        - .opencode/command
-      target_dir: .opencode/skills
+      target_dir: .agents/skills
+      global_target_dir: ~/.agents/skills
+
+  openhands:
+    name: "OpenHands"
+    preferred: false
+    installer:
+      target_dir: .agents/skills
+      global_target_dir: ~/.agents/skills
 
   pi:
     name: "Pi"
     preferred: false
     installer:
-      target_dir: .pi/skills
+      target_dir: .agents/skills
+      global_target_dir: ~/.agents/skills
+
+  pochi:
+    name: "Pochi"
+    preferred: false
+    installer:
+      target_dir: .agents/skills
+      global_target_dir: ~/.agents/skills
 
   qoder:
     name: "Qoder"
     preferred: false
     installer:
       target_dir: .qoder/skills
+      global_target_dir: ~/.qoder/skills
 
   qwen:
     name: "QwenCoder"
     preferred: false
     installer:
-      legacy_targets:
-        - .qwen/commands
       target_dir: .qwen/skills
+      global_target_dir: ~/.qwen/skills
+
+  replit:
+    name: "Replit Agent"
+    preferred: false
+    installer:
+      target_dir: .agents/skills
 
   roo:
     name: "Roo Code"
     preferred: false
     installer:
-      legacy_targets:
-        - .roo/commands
-      target_dir: .roo/skills
+      target_dir: .agents/skills
+      global_target_dir: ~/.agents/skills
 
   rovo-dev:
     name: "Rovo Dev"
     preferred: false
     installer:
-      legacy_targets:
-        - .rovodev/workflows
-      target_dir: .rovodev/skills
+      target_dir: .agents/skills
+      global_target_dir: ~/.agents/skills
 
   trae:
     name: "Trae"
     preferred: false
     installer:
-      legacy_targets:
-        - .trae/rules
       target_dir: .trae/skills
 
+  warp:
+    name: "Warp"
+    preferred: false
+    installer:
+      target_dir: .agents/skills
+      global_target_dir: ~/.agents/skills
+
   windsurf:
     name: "Windsurf"
     preferred: false
     installer:
-      legacy_targets:
-        - .windsurf/workflows
-      target_dir: .windsurf/skills
+      target_dir: .agents/skills
+      global_target_dir: ~/.agents/skills
+
+  zencoder:
+    name: "Zencoder"
+    preferred: false
+    installer:
+      target_dir: .zencoder/skills
+      global_target_dir: ~/.zencoder/skills
diff --git a/tools/installer/ide/shared/installed-skills.js b/tools/installer/ide/shared/installed-skills.js
new file mode 100644
index 000000000..7c68f990f
--- /dev/null
+++ b/tools/installer/ide/shared/installed-skills.js
@@ -0,0 +1,50 @@
+const path = require('node:path');
+const fs = require('../../fs-native');
+const csv = require('csv-parse/sync');
+
+/**
+ * Read the global skill-manifest.csv and return the set of canonicalIds.
+ * These define which directory entries in a target_dir are BMAD-owned, regardless
+ * of whether they happen to start with "bmad-" (custom modules can ship skills
+ * with any prefix, e.g. "fred-cool-skill").
+ *
+ * @param {string} bmadDir - Path to the _bmad install directory
+ * @returns {Promise<Set<string>>} Set of canonicalIds, or empty set if manifest missing
+ */
+async function getInstalledCanonicalIds(bmadDir) {
+  const ids = new Set();
+  if (!bmadDir) return ids;
+
+  const csvPath = path.join(bmadDir, '_config', 'skill-manifest.csv');
+  if (!(await fs.pathExists(csvPath))) return ids;
+
+  try {
+    const content = await fs.readFile(csvPath, 'utf8');
+    const records = csv.parse(content, { columns: true, skip_empty_lines: true });
+    for (const record of records) {
+      if (record.canonicalId) ids.add(record.canonicalId);
+    }
+  } catch {
+    // Unreadable/invalid manifest — treat as no info
+  }
+
+  return ids;
+}
+
+/**
+ * Test whether a directory entry is BMAD-owned.
+ * Prefers the manifest's canonicalIds; falls back to the legacy "bmad" prefix
+ * when no manifest is available (early install, ancestor lookup with no bmad dir).
+ *
+ * @param {string} entry - Directory entry name
+ * @param {Set<string>|null} canonicalIds - From getInstalledCanonicalIds, or null
+ * @returns {boolean}
+ */
+function isBmadOwnedEntry(entry, canonicalIds) {
+  if (!entry || typeof entry !== 'string') return false;
+  if (entry.toLowerCase().startsWith('bmad-os-')) return false;
+  if (canonicalIds && canonicalIds.size > 0) return canonicalIds.has(entry);
+  return entry.toLowerCase().startsWith('bmad');
+}
+
+module.exports = { getInstalledCanonicalIds, isBmadOwnedEntry };
diff --git a/tools/platform-codes.yaml b/tools/platform-codes.yaml
deleted file mode 100644
index f57e9ef5c..000000000
--- a/tools/platform-codes.yaml
+++ /dev/null
@@ -1,175 +0,0 @@
-# BMAD Platform Codes Configuration
-# Central configuration for all platform/IDE codes used in the BMAD system
-#
-# This file defines the standardized platform codes that are used throughout
-# the installation system to identify different platforms (IDEs, tools, etc.)
-#
-# Format:
-#   code: Platform identifier used internally
-#   name: Display name shown to users
-#   preferred: Whether this platform is shown as a recommended option on install
-#   category: Type of platform (ide, tool, service, etc.)
-
-platforms:
-  # Recommended Platforms
-  claude-code:
-    name: "Claude Code"
-    preferred: true
-    category: cli
-    description: "Anthropic's official CLI for Claude"
-
-  cursor:
-    name: "Cursor"
-    preferred: true
-    category: ide
-    description: "AI-first code editor"
-
-  # Other IDEs and Tools
-  cline:
-    name: "Cline"
-    preferred: false
-    category: ide
-    description: "AI coding assistant"
-
-  opencode:
-    name: "OpenCode"
-    preferred: false
-    category: ide
-    description: "OpenCode terminal coding assistant"
-
-  codebuddy:
-    name: "CodeBuddy"
-    preferred: false
-    category: ide
-    description: "Tencent Cloud Code Assistant - AI-powered coding companion"
-
-  auggie:
-    name: "Auggie"
-    preferred: false
-    category: cli
-    description: "AI development tool"
-
-  roo:
-    name: "Roo Code"
-    preferred: false
-    category: ide
-    description: "Enhanced Cline fork"
-
-  rovo-dev:
-    name: "Rovo Dev"
-    preferred: false
-    category: ide
-    description: "Atlassian's Rovo development environment"
-
-  kiro:
-    name: "Kiro"
-    preferred: false
-    category: ide
-    description: "Amazon's AI-powered IDE"
-
-  github-copilot:
-    name: "GitHub Copilot"
-    preferred: false
-    category: ide
-    description: "GitHub's AI pair programmer"
-
-  codex:
-    name: "Codex"
-    preferred: false
-    category: cli
-    description: "OpenAI Codex integration"
-
-  qwen:
-    name: "QwenCoder"
-    preferred: false
-    category: ide
-    description: "Qwen AI coding assistant"
-
-  gemini:
-    name: "Gemini CLI"
-    preferred: false
-    category: cli
-    description: "Google's CLI for Gemini"
-
-  iflow:
-    name: "iFlow"
-    preferred: false
-    category: ide
-    description: "AI workflow automation"
-
-  kilo:
-    name: "KiloCoder"
-    preferred: false
-    category: ide
-    description: "AI coding platform"
-
-  kimi-code:
-    name: "Kimi Code"
-    preferred: false
-    category: cli
-    description: "Moonshot AI's Kimi Code CLI"
-
-  crush:
-    name: "Crush"
-    preferred: false
-    category: ide
-    description: "AI development assistant"
-
-  antigravity:
-    name: "Google Antigravity"
-    preferred: false
-    category: ide
-    description: "Google's AI development environment"
-
-  trae:
-    name: "Trae"
-    preferred: false
-    category: ide
-    description: "AI coding tool"
-
-  windsurf:
-    name: "Windsurf"
-    preferred: false
-    category: ide
-    description: "AI-powered IDE with cascade flows"
-
-  junie:
-    name: "Junie"
-    preferred: false
-    category: cli
-    description: "AI coding agent by JetBrains"
-
-  ona:
-    name: "Ona"
-    preferred: false
-    category: ide
-    description: "Ona AI development environment"
-
-# Platform categories
-categories:
-  ide:
-    name: "Integrated Development Environment"
-    description: "Full-featured code editors with AI assistance"
-
-  cli:
-    name: "Command Line Interface"
-    description: "Terminal-based tools"
-
-  tool:
-    name: "Development Tool"
-    description: "Standalone development utilities"
-
-  service:
-    name: "Cloud Service"
-    description: "Cloud-based development platforms"
-
-  extension:
-    name: "Editor Extension"
-    description: "Plugins for existing editors"
-
-# Naming conventions and rules
-conventions:
-  code_format: "lowercase-kebab-case"
-  name_format: "Title Case"
-  max_code_length: 20
-  allowed_characters: "a-z0-9-"