How to copy a directory from local machine to remote machine

Short answer:

$ ssh-keygen -p

This will then prompt you to enter the keyfile location, the old passphrase, and the new passphrase (which can be left blank to have no passphrase).

If you would like to do it all on one line without prompts do:

$ ssh-keygen -p [-P old_passphrase] [-N new_passphrase] [-f keyfile]

Important: Beware that when executing commands they will typically be logged in your ~/.bash_history file (or similar) in plain text including all arguments provided (i.e. the passphrases in this case). It is, therefore, is recommended that you use the first option unless you have a specific reason to do otherwise.

Notice though that you can still use -f keyfile without having to specify -P nor -N, and that the keyfile defaults to ~/.ssh/id_rsa, so in many cases, it's not even needed.

You might want to consider using ssh-agent, which can cache the passphrase for a time. The latest versions of gpg-agent also support the protocol that is used by ssh-agent.

If Machine A is a Windows box, you can use Plink (part of PuTTY) with the -m parameter, and it will execute the local script on the remote server.

plink root@MachineB -m local_script.sh

If Machine A is a Unix-based system, you can use:

ssh root@MachineB 'bash -s' < local_script.sh

You shouldn't have to copy the script to the remote server to run it.