I have received a critical error in Magento inbox to download and Install 2 patch files in .sh format. I downloaded and as per instructions copied them to my root directory of Magento. Now, I have no idea how to apply them. There are few ways on web, to use CMD for applying patch files, but I do no understand how. My Magento directory is not on my localhost, but on server. I can install or delete files from server, but how am I supposed to use them/apply them using CMD which is on my local machine.
Please, guide me how to apply patch files for Magento, when Magento is installed on a server and I have access to its directory using FileZilla.
Thank you very much.
If you don't have SSH access or the ability to run /bin/ssh PATCH-xxx.sh on the server, then you'll have to run the patch on your local copy and then FTP the files across to the server. For the recent SUPEE patch which you're probably referring to, only 5 files are changed so this is the simplest solution, even if it isn't as ideal as running the command via SSH (which would give you the ability to revert the patch, etc).
You can apply these patches without SSH by uploading patched files as described here: http://magentary.com/kb/apply-supee-5344-and-supee-1533-without-ssh/
If you want to patch your Magento with the latest 5344 security patch but don't have SSH access then we have made a git repo with the updated files. Just download a copy and upload the new files to your Magento store.