Outdated CLI `run` command flags

A couple of new flags have been added to the CLI's `run` command which are not documented in https://github.com/DiamondLightSource/httomo/blob/01a5f3073a85145193145d03b93c531f1f3d7834/docs/source/howto/run_httomo.rst#the-run-command, namely:
- `--gpu-id`
- `--intermediate-format`
- `--compress-intermediate`
- `--syslog-host`
- `--syslog-port`
- `--frames-per-chunk`

Note that `--create-folder` has been renamed to `--output-folder-name` in #460, and the docs will be updated in that PR to reflect the change of name, in addition to adding a description for the flag.