GC-15: Prevent server command from overwriting artifacts and clean-up incorrect CLI tests:

- Added functional test for scenario where a server certificate has
already been issued.
- Updated server certificate issuance command not to overwrite the
artifacts.
- Fixed a couple of both server and init tests related to CLI parsing
to not create artifacts unless necessary, and if necessary to create
artifacts in temporary (test) directory. Otherwise intermittent
failures will happen.