bmad-code-org
diff --git a/‎docs/cs/how-to/non-interactive-installation.md‎
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diff --git a/‎test/test-installation-components.js‎
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diff --git a/‎tools/docs/native-skills-migration-checklist.md‎
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diff --git a/‎tools/installer/core/installer.js‎
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diff --git a/‎tools/installer/core/legacy-warnings.js‎
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@@ -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
 
 
@@ -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
 
@@ -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 {
 
@@ -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,
+};