Add layered configuration files

[skullydazed]

Summary

• load an optional system config before the platformdirs user config
• keep platformdirs as the normal save target and preserve standalone --config-file behavior
• add config --output/-o for exporting configuration

Testing

• uv run pytest
• uv run ruff check milc/milc.py milc/milc_interface.py milc/subcommand/config.py tests/test_config_file_search.py

[Copilot]

Pull request overview

Adds support for layered configuration loading (optional system config + platformdirs user config) while preserving explicit --config-file behavior, and introduces config --output/-o to export configuration to an arbitrary path. This extends MILC’s config discovery/saving model and updates documentation/tests accordingly.

Changes:

• Load an optional “system” config file first, then overlay the platformdirs user config (user values win), while keeping --config-file as an explicit single-file mode.
• Allow saving configuration to an explicit path via save_config(path) and expose that via config --output/-o.
• Add tests and documentation describing layered config behavior and export support.

Reviewed changes

Copilot reviewed 10 out of 10 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
tests/test_config_file_search.py	Adds coverage for system+user layering, explicit --config-file bypass, and config --output export behavior.
milc/subcommand/config.py	Adds --output/-o option and writes config to an explicit path when requested.
milc/milc.py	Implements layered config reads, adds explicit-path support to saving, and updates internal save logic to use the target path’s directory.
milc/milc_interface.py	Plumbs config_file through milc_options() and adds optional-path support to save_config().
docs/subcommand_config.md	Documents config --output usage.
docs/metadata.md	Documents milc_options(config_file=...) layered system config behavior.
docs/configuration.md	Documents system config layering and explicit-path saving.
docs/api_subcommand_config.md	Updates API docs to include the new --output argument.
docs/api_milc.md	Updates API docs for new MILC.__init__ and save_config() signatures.
docs/api_milc_interface.md	Updates API docs for new milc_options() and save_config() signatures.

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