diff --git a/tools/installer/core/installer.js b/tools/installer/core/installer.js
index abd9ee9a3..a68193bc6 100644
--- a/tools/installer/core/installer.js
+++ b/tools/installer/core/installer.js
@@ -42,10 +42,15 @@ class Installer {
       const officialModules = await OfficialModules.build(config, paths);
       const existingInstall = await ExistingInstall.detect(paths.bmadDir);
 
-      await warnPreNativeSkillsLegacy({
-        projectRoot: paths.projectRoot,
-        existingVersion: existingInstall.installed ? existingInstall.version : null,
-      });
+      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);
@@ -192,9 +197,15 @@ class Installer {
     // 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).
-    await this.ideManager.cleanupByList(paths.projectRoot, toRemove, {
+    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'}`);
+      }
+    }
   }
 
   /**
diff --git a/tools/installer/core/legacy-warnings.js b/tools/installer/core/legacy-warnings.js
index d73bbd9a1..e3098b82b 100644
--- a/tools/installer/core/legacy-warnings.js
+++ b/tools/installer/core/legacy-warnings.js
@@ -92,7 +92,7 @@ async function findStaleLegacyDirs(projectRoot) {
       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 });
+        findings.push({ path: resolved, displayPath: legacyPath, count: bmadEntries.length, entries: bmadEntries });
       }
     } catch {
       // Unreadable dir — skip
@@ -127,7 +127,13 @@ async function warnPreNativeSkillsLegacy({ projectRoot, existingVersion } = {})
         `Your AI tool may load these alongside the new skills, causing duplicates. Remove them manually:`,
     );
     for (const finding of staleDirs) {
-      await prompts.log.message(`    rm -rf "${finding.path}"/bmad*    # ${finding.count} stale entr${finding.count === 1 ? 'y' : 'ies'}`);
+      // 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(