diff --git a/src/management/shared-manager.ts b/src/management/shared-manager.ts
index e423d77d..a0b5ec77 100644
--- a/src/management/shared-manager.ts
+++ b/src/management/shared-manager.ts
@@ -947,23 +947,20 @@ class SharedManager {
 
     const discoveredEntries = this.discoverMarketplaceEntries(targetConfigDir);
 
-    for (const [name, value] of Object.entries(discoveredEntries)) {
-      const existing = merged[name];
-      if (existing && typeof existing === 'object' && !Array.isArray(existing)) {
-        merged[name] = {
-          ...(existing as Record<string, unknown>),
-          installLocation: value.installLocation,
-        };
-        continue;
-      }
-
-      merged[name] = value;
-    }
-
+    // Keep only registry entries that have a physical directory, and update their
+    // installLocation. Entries only on disk (no registry record) are excluded —
+    // they lack required schema fields that Claude Code enforces.
     for (const name of Object.keys(merged)) {
+      const entry = merged[name];
       if (!(name in discoveredEntries)) {
         delete merged[name];
+      } else if (entry && typeof entry === 'object' && !Array.isArray(entry)) {
+        merged[name] = {
+          ...(entry as Record<string, unknown>),
+          installLocation: discoveredEntries[name].installLocation,
+        };
       }
+      // else: entry is in discoveredEntries but has a malformed value — preserve as-is
     }
 
     return JSON.stringify(merged, null, 2);
@@ -984,6 +981,11 @@ class SharedManager {
         continue;
       }
 
+      // Skip hidden dirs and Claude Code's .staging rename-dance work trees.
+      if (entry.name.startsWith('.') || entry.name.endsWith('.staging')) {
+        continue;
+      }
+
       discovered[entry.name] = {
         installLocation: path.join(targetConfigDir, 'plugins', 'marketplaces', entry.name),
       };
diff --git a/tests/unit/shared-manager.test.ts b/tests/unit/shared-manager.test.ts
index 240769c6..46feb170 100644
--- a/tests/unit/shared-manager.test.ts
+++ b/tests/unit/shared-manager.test.ts
@@ -360,6 +360,67 @@ describe('SharedManager', () => {
       expect(reconciled.stale).toBeUndefined();
     });
 
+    it('does not register .staging directories left behind by interrupted marketplace auto-updates', () => {
+      // Regression: CCS used to write bare { installLocation } entries for marketplace
+      // directories with no registry record. Claude Code requires source + lastUpdated,
+      // so those entries corrupted known_marketplaces.json and broke /plugin.
+      const manager = new SharedManager();
+      const instancePath = instanceDir('work');
+      fs.mkdirSync(instancePath, { recursive: true });
+      manager.linkSharedDirectories(instancePath);
+
+      // Simulate Claude Code leaving a .staging dir behind in both the global claude dir
+      // and the instance dir (discoverMarketplaceEntries scans each independently).
+      fs.mkdirSync(marketplacePath(claudeDir(), 'claude-plugins-official.staging'), {
+        recursive: true,
+      });
+      fs.mkdirSync(marketplacePath(instancePath, 'claude-plugins-official.staging'), {
+        recursive: true,
+      });
+
+      manager.normalizeMarketplaceRegistryPaths(instancePath);
+
+      const globalRegistryPath = path.join(claudeDir(), 'plugins', 'known_marketplaces.json');
+      const global = readJson(globalRegistryPath) as Record<string, unknown>;
+      expect(global['claude-plugins-official.staging']).toBeUndefined();
+
+      const instanceRegistryPath = path.join(instancePath, 'plugins', 'known_marketplaces.json');
+      const instance = readJson(instanceRegistryPath) as Record<string, unknown>;
+      expect(instance['claude-plugins-official.staging']).toBeUndefined();
+    });
+
+    it('removes registry entries whose physical marketplace directory no longer exists', () => {
+      // Regression guard: buildMarketplaceRegistryContent merges JSON sources then
+      // cross-checks against discoveredEntries. Any name in the merged registry that
+      // has no matching directory on disk must be pruned so stale entries don't
+      // accumulate across marketplace uninstalls or renames.
+      const manager = new SharedManager();
+      const instancePath = instanceDir('work');
+      fs.mkdirSync(instancePath, { recursive: true });
+      manager.linkSharedDirectories(instancePath);
+
+      // Write a registry entry for a marketplace that has no physical directory.
+      const globalRegistryPath = path.join(claudeDir(), 'plugins', 'known_marketplaces.json');
+      writeJson(globalRegistryPath, {
+        'vanished-marketplace': {
+          source: { type: 'github', repo: 'example/vanished' },
+          lastUpdated: '2024-01-01T00:00:00.000Z',
+          installLocation: marketplacePath(claudeDir(), 'vanished-marketplace'),
+        },
+      });
+      // Intentionally do NOT create the physical directory — simulate an uninstalled
+      // marketplace whose registry entry was not cleaned up.
+
+      manager.normalizeMarketplaceRegistryPaths(instancePath);
+
+      const global = readJson(globalRegistryPath) as Record<string, unknown>;
+      expect(global['vanished-marketplace']).toBeUndefined();
+
+      const instanceRegistryPath = path.join(instancePath, 'plugins', 'known_marketplaces.json');
+      const instance = readJson(instanceRegistryPath) as Record<string, unknown>;
+      expect(instance['vanished-marketplace']).toBeUndefined();
+    });
+
     it('warns and skips malformed marketplace registries while keeping valid sources', () => {
       const manager = new SharedManager();
       const instancePath = instanceDir('work');