Fix UI/CLI

[tdpham2]

Config values used only by Streamlit UI, not by CLI:

general.thread -- Streamlit uses it as thread_id; CLI hardcodes 1
chemistry.optimization.method -- Streamlit sidebar display only
chemistry.optimization.fmax -- Streamlit sidebar display only
chemistry.optimization.steps -- Streamlit sidebar display only
chemistry.calculators.default -- Streamlit sidebar display only
chemistry.calculators.fallback -- Streamlit sidebar display only

Proposed solution:

• Completely refactor UI/CLI. Remove dead parameters.
• Try to integrate some parameters (e.g default fmax, steps) into UI via either updating tool call default parameters/prompt injection.

[tdpham2]

Fixed some of this on #118. Still need further fix.