Generalize atmos_init to dry and no radiation cases

[LenkaNovak]

Currently, we are assuming that we are always running with a radiation and moisture models. As part of #392 we need to be able to relax these assumptions.

Components

• add hasradiation and hasmoisture functions and update the relevant get_field functions
• add buildkite driver with conservation checks (but asserts set to softfail due to division by zero for water conservation)
• move time_to_seconds to user_io/io_helpers.jl, as it is not dependent on cli_options.
• renmed get_atmos_config to get_atmos_config_dict to differentiate between the config Dict and AtmosConfig objects
• generalize flux calculation
• generalize dir_paths so they can be easily manipulated for different experiments
• update driver

QA

• ensure energy conservation build