Refresh documentation and developer commands

[MontrealAI]

Motivation

• Bring developer-facing docs and commands up to date with the current proof_gradient package and local API surface.
• Replace legacy SkillOS/skillos references and scattered validation instructions with a single, discoverable developer quick start and make targets.
• Make the public-safe validation and API reference easier to find and keep synchronized with repository maps and contributor guidance.

Description

• Updated README.md to add a Local developer quick start, point to docs/api_reference.md, and refresh the repository map to include proof_gradient/ and schemas/.
• Rewrote Makefile to use python -m proof_gradient entry points, add help/api/validate targets, switch tests to pytest, and improve clean rules.
• Added/rewrote docs/api_reference.md to document the real FastAPI endpoints (/healthz, /readyz, /metrics, /tenants, /demo/run, /artifacts, /runs, /proofs) and the make api flow.
• Updated docs/GOALOS_DOCUMENTATION_INDEX.md, CONTRIBUTING.md, and QA_VERIFICATION.md to reference the API docs, prefer make validate, and add guidance to keep docs, API reference, Makefile, and QA notes synchronized.

Testing

• Installed development extras with python -m pip install -e ".[dev]", which completed successfully.
• Ran the test suite with pytest (and make test), which passed: 85 tests passed with 2 FastAPI/Starlette deprecation warnings.
• Ran the repository validation suite with make validate, which executed python scripts/check_no_paid_artifacts.py, python scripts/validate_goalos_catalog.py, python scripts/validate_docs_tables_figures.py, and python scripts/validate_goalos_public_site.py, and all validators passed.
• No automated test failures were observed.

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Codex Task