docs: improve README readability and structure

[wangleiofficial]

Motivation

• Improve README clarity and navigation so users can quickly find installation, model details and usage examples.
• Make installation prerequisites and options explicit to reduce setup errors for new users.
• Increase readability of code examples and model metadata so they are easier to copy and understand.

Description

• Replace the original heading and one-line intro with a concise project title and short description, and split badges onto separate lines for reduced clutter.
• Add a Table of contents section for quick navigation to Installation, Model details, Usage, License, and Citation sections.
• Rework the Installation section to call out the PyTorch prerequisite and present two install options with clear pip commands (git+https for latest and ProtFlash from PyPI for stable).
• Reformat the Model details table for clearer columns and tidy the Usage examples by adding python-marked code blocks and restructuring the FLASHTransformer constructor across multiple lines for readability.

Testing

• Ran git diff -- README.md | sed -n '1,260p' to review the patch and it completed successfully.
• Ran nl -ba README.md | sed -n '1,220p' to inspect the updated file contents and it completed successfully.
• Ran git status --short to verify the working tree state before finalizing edits and it completed successfully.

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Codex Task