enh: Support duct config files

[asmacdo]

@yarikoptic this is a WIP, but non-draft since this could use design review before continuing into the weeds

• Fixes Add ability to read from duct config #279

TODO (adjust) At the high level:

• startup using DEFAULT_CONFIG defined in __main__
• retrieve -C --config first if passed
• load in DEFAULT_CONFIG and then override from each file in order (colon separated)
• use environment variables if they are present (this is also reflected in the config object
• the config is then used by the CLI to set default values, which the user can override

NOTE! If you use config files, duct --help will show options' default values to be the ones specified in the config, which I think makes sense but a little unusual.

TODO:

• fix tests
• add tests
• add to con-duct CLI
• make sure -C --config shows up in helptext (currently not)
• reconsider behavior "fail if user-provided paths DNE, but pass if default paths DNE" maybe just try and proceed with DEBUG
• hand-test thoroughly
• optional: use config everywhere instead of args. IMO nicer usage, but uglier code and a substantially large patch so not worth it
• optional: add con-duct init-conf to scaffold a config.json file with all default values.

[mergify]

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Pull Request Overview

This PR adds comprehensive configuration file support to the con-duct tool, allowing users to configure options through JSON files, environment variables, or command line arguments with proper precedence handling.

• Implements a configuration system with precedence: defaults < config files < environment variables < CLI arguments
• Refactors argument parsing to use a custom ConfigurableArgumentParser that integrates with the new config system
• Updates the help text to reflect configuration capabilities and show current default values

Reviewed Changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 2 comments.

File	Description
src/con_duct/main.py	Core implementation of config system including Config class, ConfigurableArgumentParser, and integration with argument parsing
src/con_duct/suite/main.py	Added TODO comments for future config integration in the suite subcommands

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[asmacdo]

@yarikoptic also mergify says green but tests failed... now that I think about it, I'm not sure if I've seen mergify comments that were helpful, have you?

[yarikoptic]

Suggested change

	file < environment variables < command line arguments.
	file(s) < environment variables < command line arguments.

per directory, per user, system?

[yarikoptic]

I think we decided to go with jsonargparse and thus this PR could be closed