looper cli is not taking priority if cli modifiers are used in looper config

[donaldcampbelljr]

trafficstars

if i use looper with a limit command looper run --limit 2

but then place this in my looper config:

pep_config: project/project_config.yaml
output_dir: "results"
pipeline_interfaces:
  - pipeline/pipeline_interface.yaml
cli:
  run:
    limit: 1

The config file takes priority but it should be the other way around. The CLI should always take priority.