refactor parameter system to use structured TOML config

[jf---]

Problem

The current parameter passing system is confusing and inconsistent. Parameters are passed around in ways that don't make sense.

Proposed Solution

• Default parameters should be read from a structured TOML file
• Single source of truth for configuration
• Clear hierarchy: defaults → user config → runtime overrides

Notes

This may have been partially addressed in previous refactoring but needs to be completed/reviewed.