This commit addresses a few miscellaneous issues with upgrader:

- The server health check at the end was being done starting with connection handlers disabled which would fail to catch some problems.

- The registration of the log publishers for DirectoryServer.startServer was being done at the wrong time and so starting server in process never picked up log messages that may indicate a problem.

- The .zip file was being extracted a second time unnecessarily for the CLI version of the tool.