[REFACTOR] Stage 1 improvements & tests

[eleanorfrajka]

Refactor Stage 1 using Claude.

Description:

Now uses classes in stage1.py to more cleanly import and process to netCDF the data files.

Note that there are some choices articulated in there like:

    VARS_TO_REMOVE = {
        'sbe-cnv': ['potential_temperature', 'julian_days_offset', 'density'],
        'sbe-asc': ['potential_temperature', 'julian_days_offset', 'density'],
    }
    COORDS_TO_REMOVE = {
        'sbe-cnv': ['depth', 'latitude', 'longitude'],
        'sbe-asc': ['depth', 'latitude', 'longitude'],
    }

which may later need to be updated if ctd_tools changes.

Also enriches with metadata as:

    def _add_global_attributes(self, dataset, yaml_data: Dict[str, Any]):
        """Add global attributes from YAML configuration."""
        global_attrs = {
            'mooring_name': yaml_data['name'],
            'waterdepth': yaml_data['waterdepth'],
            'longitude': yaml_data.get('longitude', 0.0),
            'latitude': yaml_data.get('latitude', 0.0),
            'deployment_latitude': yaml_data.get('deployment_latitude', '00 00.000 N'),
            'deployment_longitude': yaml_data.get('deployment_longitude', '000 00.000 W'),
            'deployment_time': yaml_data.get('deployment_time', 'YYYY-mm-ddTHH:MM:ss'),
            'seabed_latitude': yaml_data.get('seabed_latitude', '00 00.000 N'),
            'seabed_longitude': yaml_data.get('seabed_longitude', '000 00.000 W'),
            'recovery_time': yaml_data.get('recovery_time', 'YYYY-mm-ddTHH:MM:ss'),
        }

Checklist:

• I have followed the coding conventions.
• I have updated or added tests to cover my changes.
• I have updated the documentation if needed.
• I have run pytest to check that all tests pass.
• I have run pre-commit run --all-files to lint and format the code.