Add README docs for --methods-summary-path and methods summary JSON

[MicheleBonus]

Motivation

• Document the --methods-summary-path CLI option and the SimulationProtocol.to_methods_dict() output so users can produce compact, publication-ready JSON methods summaries that omit nonessential arrays and energy series.

Description

• Add a new "Methods summaries (--methods-summary-path)" section to README.md explaining that the output is always JSON, matches the CLI help by omitting nonessential arrays/energy series, includes an example command ambermeta plan --methods-summary-path methods.json /path/to/amber_runs, and lists the top-level keys (stage_sequence and stages with software, md_engine, system, and trajectory_output).

Testing

• No automated tests were run because this is a documentation-only change.

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Codex Task