There are different ways we can upload files to remote servers. Few command line tools are listed here"
1- Securely Copy files (scp):
scp -v -r -o IdentityFile=<cert.pem> <source folder> <user>@<remoteserverip>:/home/<user>/<destination folder>
Note: If a certificate is needed, then IdentityFile=<cert.pem> should be used.
2- rSync:
rsync -vcrz --delete-after <source folder> <user>@<remoteserverip>:/home/<user>/<destination folder>