I followed instructions here carefully however I haven't get this working right. Here is what I did:

  1. Run WinSCP enter Hostname (Elastic IP of my Instance)
  2. enter username "ec2-user"
  3. enter public key file
  4. chose SCP for the protocol
  5. Under SCP/Shell settings I chose "sudo su -"
  6. Hit Login
  7. WinSCP asks me for passphrase key, Hit OK
  8. Shows up this error

Error skipping startup message. Your shell is probably incompatible with the application (BASH is recommended).

NOTE: This works on Putty

amazon-ec2 sudo putty scp winscp
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