Make CLI config arguments selectively override manifest metadata configuration

[bestdevever123]

Currently, when any configuration argument is passed via the CLI, the entire config of the manifest's metadata is ignored. This behavior is limiting and could be improved to allow CLI arguments to override only the specific equivalent configurations in the manifest while keeping the rest intact.

Proposed Solution

Change the behavior so that CLI configuration arguments only override their corresponding configurations in the manifest's metadata. The rest of the configurations from the manifest should remain in effect unless explicitly overridden by CLI arguments.

Rationale

Selective Overrides: This approach allows users to benefit from default configurations in the manifest without needing to duplicate them in CLI arguments.

Practical Example:

Consider a scenario where the manifest contains a very long exclude-crate-paths configuration.
If I want to override only the platform configuration via the CLI, I am forced to re-specify the entire exclude-crate-paths value as a CLI argument, which is sub optimal.

With the proposed change, I could override the platform while leaving exclude-crate-paths and other configurations untouched.

Thx for your work!

[cgwalters]

Change the behavior so that CLI configuration arguments only override their corresponding configurations in the manifest's metadata. The rest of the configurations from the manifest should remain in effect unless explicitly overridden by CLI arguments.

I'm OK with this, I think it's a relatively safe change to make by default. I wonder if we should add a --no-inherit-manifest or something to opt in to the previous behavior in case? Dunno if it's needed.