Fix Argument Precedence

[harryswift01]

Summary

In this PR, the argument merging logic is fixed to ensure the correct precedence: CLI > YAML > Defaults. Previously, YAML values were sometimes ignored due to argparse defaults being mistakenly treated as explicit CLI inputs. This PR ensures that CLI arguments take priority, YAML fills in missing values, and defaults are used only as a last resort.

Changes

Fix argument precedence handling:

• Compare CLI arguments against argparse’s default values parse_args([]) to correctly detect which values were explicitly set by the user.
• Apply YAML values only if the CLI has not explicitly overridden them.
• Ensure default values are only used when both CLI and YAML are absent.

Improve merging logic in merge_configs():

• Prevent YAML values from being ignored when CLI inputs are not explicitly provided.
• Maintain correct priority order: CLI > YAML > Defaults.

Enhance logging for debugging:

• Log when values are being overridden by CLI or YAML.
• Improve debugging output to track final argument values after merging.

Impact

• Ensures CLI arguments always take priority over YAML and default values.
• Fixes cases where YAML inputs were incorrectly ignored.
• Improves reliability of configuration handling.
• Provides better logging for debugging configuration issues.

[jimboid]

From the code this looks like it now has the correct flow. Argparse is initialised in a custom way so as to not treat defaults on the CLI as if they have been set. This then flows that any yaml files are set to args first, then any defaults pulled in to complete the args setup. This then has a hard override for params explicitly set on the CLI. It should be fairly trivial to create tests to ensure this remains the case, but the code looks correct. I the bug was reproduced and then shown by execution to be fixed then happy to merge PR.