Fix several reference warnings during the docs build. They where actually not critical but due to the amount of them, actually relevant warnings could easily be missed.
Fix some syntax issues in the list of configuration values.
Add initialize_job and finalize_job to the API docs (seems they got accidentally removed when reverting a commit in a previous PR).
There were still some references to read_params_from_cmdline/save_metrics_params. Change them to use the new names.
initialize_jobandfinalize_jobto the API docs (seems they got accidentally removed when reverting a commit in a previous PR).read_params_from_cmdline/save_metrics_params. Change them to use the new names.