Inconsistency between parsing from command line and from configuration file

[GernotMaier]

Running simtools with configurations from the command line and from config file should be identical.

However:

usage: simulate_flasher [-h] --run_mode {direct_injection,full_simulation} --light_source LIGHT_SOURCE [--number_of_events NUMBER_OF_EVENTS] [--output_prefix OUTPUT_PREFIX] [--model_version MODEL_VERSION [MODEL_VERSION ...]]
                        [--site SITE] [--telescope TELESCOPE] [--telescope_model_file TELESCOPE_MODEL_FILE]
                        (--array_layout_name ARRAY_LAYOUT_NAME [ARRAY_LAYOUT_NAME ...] | --array_element_list ARRAY_ELEMENT_LIST [ARRAY_ELEMENT_LIST ...]) --run_number RUN_NUMBER --azimuth_angle AZIMUTH_ANGLE --zenith_angle
                        ZENITH_ANGLE [--sim_telarray_instrument_seeds SIM_TELARRAY_INSTRUMENT_SEEDS] [--sim_telarray_random_instrument_instances SIM_TELARRAY_RANDOM_INSTRUMENT_INSTANCES] [--db_api_user DB_API_USER]
                        [--db_api_pw DB_API_PW] [--db_api_port DB_API_PORT] [--db_server DB_SERVER] [--db_api_authentication_database DB_API_AUTHENTICATION_DATABASE] [--db_simulation_model DB_SIMULATION_MODEL]
                        [--db_simulation_model_version DB_SIMULATION_MODEL_VERSION] [--data_path DATA_PATH] [--output_path OUTPUT_PATH] [--use_plain_output_path] [--model_path MODEL_PATH] [--simtel_path SIMTEL_PATH] [--config CONFIG]
                        [--env_file ENV_FILE] [--test] [--label LABEL] [--log_level LOG_LEVEL] [--version] [--user_name USER_NAME] [--user_organization USER_ORGANIZATION] [--user_email USER_EMAIL] [--user_orcid USER_ORCID]
simulate_flasher: error: the following arguments are required: --run_number, --azimuth_angle, --zenith_angle

but running

python src/simtools/applications/simulate_flasher.py --config tests/integration_tests/config/simulate_flasher_full_simulation.yml

with tests/integration_tests/config/simulate_flasher_full_simulation.yml :

---
applications:
- application: simtools-simulate-flasher
  configuration:
    run_mode: full_simulation
    light_source: MSFx-FlashCam
    model_version: 6.0.0
    output_path: simtools-output
    site: South
    telescope: MSTS-04
    test: true
    log_level: DEBUG
  integration_tests:
  - output_file: logfile.log
  - output_file: ff-1m.simtel.zst
  model_version_use_current: true
  test_name: full-simulation
schema_name: application_workflow.metaschema
schema_version: 0.4.0

works without issues.

As outlined in #1055, the tool configuration code needs a full review.