Fix microsoft#167285 (microsoft#167378)

Author: sandy081

src/vs/platform/extensionManagement/node/extensionManagementService.ts

@@ -613,7 +613,7 @@ export class ExtensionsScanner extends Disposable {
 				await this.beforeRemovingExtension(await this.toLocalExtension(latest));
 			}
 		}));
-		const toRemove = extensions.filter(e => uninstalled[ExtensionKey.create(e).toString()]);
+		const toRemove = extensions.filter(e => e.metadata /* Installed by VS Code */ && uninstalled[ExtensionKey.create(e).toString()]);
 		await Promises.settled(toRemove.map(e => this.removeUninstalledExtension(e)));
 	}
 

src/vs/platform/extensionManagement/node/extensionsWatcher.ts

@@ -180,7 +180,7 @@ export class ExtensionsWatcher extends Disposable {
 
 	private async uninstallExtensionsNotInProfiles(): Promise<void> {
 		const installed = await this.extensionManagementService.getAllUserInstalled();
-		const toUninstall = installed.filter(installedExtension => !this.allExtensions.has(this.getKey(installedExtension.identifier, installedExtension.manifest.version)));
+		const toUninstall = installed.filter(installedExtension => installedExtension.installedTimestamp /* Installed by VS Code */ && !this.allExtensions.has(this.getKey(installedExtension.identifier, installedExtension.manifest.version)));
 		if (toUninstall.length) {
 			await this.extensionManagementService.markAsUninstalled(...toUninstall);
 		}