Config.json values are always overwritten by default cli arguments

Users can configure daphne either via cli arguments or providing a .json configuration file:
`./bin/daphne --config=UserConfig.json ...`

In [daphne.cpp](https://github.com/daphne-eu/daphne/blob/main/src/api/internal/daphne_internal.cpp) we setup the configuration object with values from the `config.json` file (if provided) and then we replace them in case the user provides command line arguments. However for a lot of cases we overwrite the values from the `.json` file with the default cli values, that have not been actually provided as CLI arguments by the user.
E.g.:

```C++
// Initialize user_config object with values from the .json file.
...
...
static opt queueSetupScheme("queue_layout",
cat(schedulingOptions), desc("Choose queue setup scheme:"),
values(
clEnumVal(CENTRALIZED, "One queue (default)"),
clEnumVal(PERGROUP, "One queue per CPU group"),
clEnumVal(PERCPU, "One queue per CPU core")
),
init(CENTRALIZED)
);
... // Default queueSetupScheme is CENTRALIZED
...
user_config.queueSetupScheme = queueSetupScheme;
```
We always replace the existing queueSetupScheme which at this point could be a parsed value from the configuration file.

Read src/api/internal/daphne_internal.cpp, starting where the configuration object is initialized from the JSON file and where queueSetupScheme is assigned from the CLI option. Run Daphne with a config file that sets queue_layout and no corresponding CLI argument. Done means omitted CLI options preserve JSON values while explicitly provided arguments still override them.

Written by the indexing model from the issue text.