fix: use defaults from user config

[Máté Balajti]

Describe the bug
Without specificing the parameters for --cores and --dependency-embedding for the run, ZARP runs with the default parameters instead of the arguments set up at the initialization.

To Reproduce
Steps to reproduce the behavior:

1. Initialize ZARP with zarp --init and cores set to some int other than 1.
2. Run ZARP without specifying --cores.
3. Check the run configs; the --cores argument is set to the default of 1.
4. The same applies to --dependency-embedding: when initializing it with SINGULARITY, it defaults back to CONDA.

Additional context
Add any other context about the problem here.

[Alex Kanitz]

The same is likely also true for --execution-mode