fix(management): serialize marketplace registry reconciliation

- keep bare and non-bare marketplace normalization inside the plugin-layout lock
- warn when malformed registry sources are skipped during reconciliation
- add regression coverage for cross-instance refresh metadata and legacy layout upgrade

src/management/instance-manager.ts

@@ -59,14 +59,15 @@ class InstanceManager {
       await this.sharedManager.syncProjectContext(instancePath, contextPolicy);
       await this.sharedManager.syncAdvancedContinuityArtifacts(instancePath, contextPolicy);
 
-      if (!options.bare) {
-        await this.pluginLayoutLock.withNamedLock('__plugin-layout__', async () => {
+      await this.pluginLayoutLock.withNamedLock('__plugin-layout__', async () => {
+        if (!options.bare) {
           this.sharedManager.linkSharedDirectories(instancePath);
-        });
-      }
-    });
+          return;
+        }
 
-    this.sharedManager.normalizeSharedPluginMetadataPaths(options.bare ? undefined : instancePath);
+        this.sharedManager.normalizeSharedPluginMetadataPaths();
+      });
+    });
 
     // Sync MCP servers from global ~/.claude.json (unless bare)
     if (!options.bare) {

src/management/shared-manager.ts

@@ -899,8 +899,10 @@ class SharedManager {
         for (const [name, value] of Object.entries(parsed as Record<string, unknown>)) {
           merged[name] = normalizePluginMetadataValue(value, targetConfigDir).normalized;
         }
-      } catch (_err) {
-        // Best-effort merge: malformed sources should not block self-heal.
+      } catch (err) {
+        console.log(
+          warn(`Skipping malformed marketplace registry ${registryPath}: ${(err as Error).message}`)
+        );
       }
     }
 

tests/unit/instance-manager-mcp-sync.test.ts

@@ -34,6 +34,28 @@ describe('InstanceManager MCP sync', () => {
     );
   }
 
+  function writeMarketplaceRegistryWithMetadata(
+    registryPath: string,
+    installLocation: string,
+    metadata: Record<string, unknown>
+  ): void {
+    fs.mkdirSync(path.dirname(registryPath), { recursive: true });
+    fs.writeFileSync(
+      registryPath,
+      JSON.stringify(
+        {
+          'claude-code-plugins': {
+            installLocation,
+            ...metadata,
+          },
+        },
+        null,
+        2
+      ),
+      'utf8'
+    );
+  }
+
   function expectMarketplaceLocation(registryPath: string, expectedLocation: string): void {
     const parsed = readJson(registryPath) as Record<string, { installLocation?: string }>;
     expect(parsed['claude-code-plugins']?.installLocation).toBe(expectedLocation);
@@ -226,43 +248,100 @@ describe('InstanceManager MCP sync', () => {
     expect(syncMcpSpy).toHaveBeenCalledWith(instancePath);
   });
 
-  it('keeps alternating instances independently valid for Claude Code validation', async () => {
+  it('reconciles marketplace metadata across isolated instances without losing refresh fields', async () => {
     spyOn(SharedManager.prototype, 'syncProjectContext').mockResolvedValue(undefined);
     spyOn(SharedManager.prototype, 'syncAdvancedContinuityArtifacts').mockResolvedValue(undefined);
-    spyOn(InstanceManager.prototype, 'syncMcpServers').mockImplementation(() => false);
-
-    const globalRegistryPath = path.join(claudeDir(), 'plugins', 'known_marketplaces.json');
-    writeMarketplaceRegistry(
-      globalRegistryPath,
-      path.join(tempRoot, '.claude', 'plugins', 'marketplaces', 'claude-code-plugins')
-    );
 
     const manager = new InstanceManager();
     const workPath = await manager.ensureInstance('work', { mode: 'isolated' });
+    const workRegistryPath = path.join(workPath, 'plugins', 'known_marketplaces.json');
+    writeMarketplaceRegistryWithMetadata(workRegistryPath, marketplacePath(workPath), {
+      label: 'Official marketplace',
+      refreshToken: 'refresh-token',
+      metadata: {
+        source: 'refresh-flow',
+        lastSyncedAt: '2026-03-18T00:00:00Z',
+      },
+    });
+
     const personalPath = await manager.ensureInstance('personal', { mode: 'isolated' });
-    await manager.ensureInstance('work', { mode: 'isolated' });
+    const workRegistry = readJson(workRegistryPath) as Record<
+      string,
+      {
+        installLocation?: string;
+        label?: string;
+        refreshToken?: string;
+        metadata?: Record<string, unknown>;
+      }
+    >;
+    const personalRegistry = readJson(path.join(personalPath, 'plugins', 'known_marketplaces.json')) as Record<
+      string,
+      {
+        installLocation?: string;
+        label?: string;
+        refreshToken?: string;
+        metadata?: Record<string, unknown>;
+      }
+    >;
 
-    const workInstallLocation = (
-      readJson(path.join(workPath, 'plugins', 'known_marketplaces.json')) as Record<
-        string,
-        { installLocation?: string }
-      >
-    )['claude-code-plugins']?.installLocation;
-    const personalInstallLocation = (
-      readJson(path.join(personalPath, 'plugins', 'known_marketplaces.json')) as Record<
-        string,
-        { installLocation?: string }
-      >
-    )['claude-code-plugins']?.installLocation;
+    expect(workRegistry['claude-code-plugins']).toMatchObject({
+      installLocation: marketplacePath(workPath),
+      label: 'Official marketplace',
+      refreshToken: 'refresh-token',
+      metadata: {
+        source: 'refresh-flow',
+        lastSyncedAt: '2026-03-18T00:00:00Z',
+      },
+    });
+    expect(personalRegistry['claude-code-plugins']).toMatchObject({
+      installLocation: marketplacePath(personalPath),
+      label: 'Official marketplace',
+      refreshToken: 'refresh-token',
+      metadata: {
+        source: 'refresh-flow',
+        lastSyncedAt: '2026-03-18T00:00:00Z',
+      },
+    });
+  });
 
-    expect(workInstallLocation).toBe(marketplacePath(workPath));
-    expect(personalInstallLocation).toBe(marketplacePath(personalPath));
-    expect(path.resolve(workInstallLocation ?? '')).toStartWith(
-      path.resolve(path.join(workPath, 'plugins', 'marketplaces'))
+  it('upgrades a legacy shared plugins symlink to an instance-local layout', async () => {
+    spyOn(SharedManager.prototype, 'syncProjectContext').mockResolvedValue(undefined);
+    spyOn(SharedManager.prototype, 'syncAdvancedContinuityArtifacts').mockResolvedValue(undefined);
+
+    const manager = new InstanceManager();
+    const legacyPath = manager.getInstancePath('legacy');
+    const sharedPluginsPath = path.join(tempRoot, '.ccs', 'shared', 'plugins');
+    fs.mkdirSync(sharedPluginsPath, { recursive: true });
+    fs.mkdirSync(legacyPath, { recursive: true });
+    fs.symlinkSync(sharedPluginsPath, path.join(legacyPath, 'plugins'), 'dir');
+
+    writeMarketplaceRegistryWithMetadata(
+      path.join(claudeDir(), 'plugins', 'known_marketplaces.json'),
+      path.join(tempRoot, '.ccs', 'shared', 'plugins', 'marketplaces', 'claude-code-plugins'),
+      {
+        label: 'Legacy marketplace',
+        refreshToken: 'legacy-refresh-token',
+      }
     );
-    expect(path.resolve(personalInstallLocation ?? '')).toStartWith(
-      path.resolve(path.join(personalPath, 'plugins', 'marketplaces'))
+
+    await manager.ensureInstance('legacy', { mode: 'isolated' });
+
+    expect(fs.lstatSync(path.join(legacyPath, 'plugins')).isSymbolicLink()).toBe(false);
+    expectMarketplaceLocation(
+      path.join(legacyPath, 'plugins', 'known_marketplaces.json'),
+      marketplacePath(legacyPath)
     );
-    expectMarketplaceLocation(globalRegistryPath, marketplacePath(claudeDir()));
+
+    const legacyRegistry = readJson(
+      path.join(legacyPath, 'plugins', 'known_marketplaces.json')
+    ) as Record<
+      string,
+      { installLocation?: string; label?: string; refreshToken?: string }
+    >;
+    expect(legacyRegistry['claude-code-plugins']).toMatchObject({
+      installLocation: marketplacePath(legacyPath),
+      label: 'Legacy marketplace',
+      refreshToken: 'legacy-refresh-token',
+    });
   });
 });

tests/unit/shared-manager.test.ts

@@ -204,6 +204,44 @@ describe('SharedManager', () => {
       });
     });
 
+    it('warns and skips malformed marketplace registries while keeping valid sources', () => {
+      const manager = new SharedManager();
+      const instancePath = instanceDir('work');
+      fs.mkdirSync(instancePath, { recursive: true });
+      manager.linkSharedDirectories(instancePath);
+
+      const globalRegistryPath = path.join(claudeDir(), 'plugins', 'known_marketplaces.json');
+      writeJson(globalRegistryPath, {
+        'claude-code-plugins': {
+          installLocation: path.join(
+            tempRoot,
+            '.ccs',
+            'instances',
+            'work',
+            'plugins',
+            'marketplaces',
+            'claude-code-plugins'
+          ),
+          label: 'Official marketplace',
+        },
+      });
+
+      const malformedRegistryPath = path.join(instancePath, 'plugins', 'known_marketplaces.json');
+      fs.writeFileSync(malformedRegistryPath, '{invalid-json', 'utf8');
+      const logSpy = spyOn(console, 'log').mockImplementation(() => {});
+
+      manager.normalizeMarketplaceRegistryPaths(instancePath);
+
+      expect(readMarketplaceLocation(malformedRegistryPath)).toBe(marketplacePath(instancePath));
+      expect(
+        logSpy.mock.calls.some(
+          ([message]) =>
+            String(message).includes('Skipping malformed marketplace registry') &&
+            String(message).includes(malformedRegistryPath)
+        )
+      ).toBe(true);
+    });
+
     it('keeps the instance-local registry valid under Windows copy fallback', () => {
       Object.defineProperty(process, 'platform', { value: 'win32' });
       spyOn(fs, 'symlinkSync').mockImplementation(() => {