docs: add AGENTS.md and reorganize project documentation

[SeriousCoding789]

What does this PR do?

• Adds AGENTS.md — a build/test/architecture guide for AI coding assistants and new contributors, covering the pre-commit checklist that mirrors the CI gates, the module dependency rules, and the invariants that must not be broken.
• Adds a Documentation index to the README linking every guide.
• Moves the protobuf protocol document and the metrics changelog into docs/ with consistent kebab-case names; marks two 2022-era protocol copies as superseded.
• Adds Super-Representative private-key security notes to the configuration guide.
• Removes obsolete deployment scripts (start.sh, start.sh.simple, shell.md) — they are no longer maintained; node deployment is covered by the Docker image and is handed over to tron-deployment.
• Removes unused CI configuration (.codeclimate.yml, sonar-project.properties, stale Sonar entries in the dependency verification metadata) and the .dockerignore file.

Why are these changes required?

• No single entry point told contributors — or AI assistants — how to build and test the project, how the modules relate, or which constraints CI enforces. Several CI gates (the java.lang.Math prohibition, the reference.conf schema and comment checks, dependency verification) were undocumented, so a contributor could only discover them by failing a build.
• Several guides existed but were unlinked from the README; the protocol document and metrics changelog cluttered the repository root and the proto tree.
• Two 2022-era protocol copies gave no indication that they were stale.
• The configuration guide never warned that a plaintext block-producing key can leak through file permissions or be committed to Git.
• The deployment scripts had drifted out of maintenance: they referenced release artefacts that are no longer published and configuration URLs that have moved.
• .codeclimate.yml and sonar-project.properties are no longer used by CI.

This PR has been tested by:

• Unit Tests — N/A (documentation and configuration-file removal only; no code paths touched)
• Manual Testing — verified every claim in AGENTS.md against the build configuration and sources, including running each command in the pre-commit checklist; confirmed all moved paths and cross-document links resolve

Follow up

None.

Extra details

[abn2357]

Two issues and one optional naming nit as below, please consider whether modifications are required.:

• Reconcile the remaining Sonar references

  This PR removes .codeclimate.yml and sonar-project.properties because they are no longer used by CI, but Sonar-related references remain:

  • framework/build.gradle:3 still applies org.sonarqube.
  • CONTRIBUTING.md:150 says that the Sonar scanner is automatically triggered for pull requests.
  • CONTRIBUTING.md:161 requires contributions to pass the Sonar scanner test.

  Please update CONTRIBUTING.md to reflect the current CI process.

• Fix the relative source link after moving the metrics changelog

  After moving METRICS_CHANGELOG.md into docs/, the link to common/src/main/java/org/tron/common/prometheus/ on line 22 now resolves to the non-existent path:

  docs/common/src/main/java/org/tron/common/prometheus/

  Please change the link target from:

  common/src/main/java/org/tron/common/prometheus/

  to:

  ../common/src/main/java/org/tron/common/prometheus/

• [Nit] Consider using kebab-case consistently

  Most files under docs/ use kebab-case, while metrics_changelog.md uses snake_case. Consider renaming it to metrics-changelog.md for consistency with names such as protobuf-protocol-document.md.

[SeriousCoding789]

Two issues and one optional naming nit as below, please consider whether modifications are required.:

• Reconcile the remaining Sonar references
  This PR removes .codeclimate.yml and sonar-project.properties because they are no longer used by CI, but Sonar-related references remain:

  • framework/build.gradle:3 still applies org.sonarqube.
  • CONTRIBUTING.md:150 says that the Sonar scanner is automatically triggered for pull requests.
  • CONTRIBUTING.md:161 requires contributions to pass the Sonar scanner test.

  Please update CONTRIBUTING.md to reflect the current CI process.

• Fix the relative source link after moving the metrics changelog
  After moving METRICS_CHANGELOG.md into docs/, the link to common/src/main/java/org/tron/common/prometheus/ on line 22 now resolves to the non-existent path:
  docs/common/src/main/java/org/tron/common/prometheus/
  Please change the link target from:
  common/src/main/java/org/tron/common/prometheus/
  to:
  ../common/src/main/java/org/tron/common/prometheus/

• [Nit] Consider using kebab-case consistently
  Most files under docs/ use kebab-case, while metrics_changelog.md uses snake_case. Consider renaming it to metrics-changelog.md for consistency with names such as protobuf-protocol-document.md.

very good suggestion, will fix all.