Improve Configuration User Experience and Defaults

[Aurelian-Shuttleworth]

What was done

• Enhanced TOML loader to support [default] section.
• Updated argparser to respect config defaults.
• Added documentation in docs/configuration.md.

Why

• DX: Simplifies CLI usage and reduces need for aliases.
• Consistency: Centralized configuration source of truth.

Verification Steps

Automated Tests

Verified default value propagation:

$ nix develop --command pytest tests/test_config_defaults.py
tests/test_config_defaults.py ..                                       [100%]
========================= 2 passed, 1 warning in 0.03s =========================

[kody-ai]

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