docs(protocol): consolidate guides and update README index

[Sunny6889]

What does this PR do?
Gather the project's scattered docs under docs/, give them consistent lower-case names, and surface them from a new README Documentation index.

Why are these changes required?

• No entry point: several guides (protocol doc, metrics changelog, config reference) existed but were unlinked — readers had no path to them from the README.
• Root/tree clutter: METRICS_CHANGELOG.md and the protobuf protocol doc sat outside docs/, mixed in with build files and proto sources.
• Stale duplicates: two 2022-era protocol copies under protocol/src/main/protos/ had no indication they were outdated, risking readers trusting the wrong file.
• SR key safety: the config guide didn't warn that a plaintext block-producing key can be leaked via file perms or committed to Git.

This PR has been tested by:

• Manual Testing

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