When I Updating zf-commons/zfc-admin using composer, it gives an RuntimeException error saying that
[RuntimeException]
The .git directory is missing from /var/www/site2.com/vendor/zf-commons/zfc
-admin, see http://getcomposer.org/commit-deps for more information
Since this error i cannot update any other modules in framework.
When ever I have "issues" with composer the first thing I do is delete the vendor folder and do a "composer update"
You could also try to delete just that one component "vendor/zf-commons"
The easiest way is to remove the install folder of that component before making the composer update
rm -rf /var/www/site2.com/vendor/zf-commons/zfc
composer update
delete zf-commons/zfc-admin then execute composer update.
usually you are not adviced to commit zf-commons/zfc-admin to your repository