Make primary Shipgate flows prominent

[pengfei-threemoonslab]

Summary

• Make shipgate check, shipgate verify, and shipgate audit --host the only prominent top-level flows across CLI help, first-look output, docs, generated instructions, prompts, skills, and .well-known metadata.
• Keep supporting commands callable while hiding or demoting them from primary guidance.
• Add primary_commands to the runtime/public/local contracts, bump runtime contract version to 8, bump local contract schema version to 2, and update tests/goldens around the new prominence model.

Verification

• PYTHONPATH=src python -m ruff check .
• Focused CLI/contract/instruction/prompt/boundary/diagnostics tests: 670 passed, 3 skipped
• PYTHONPATH=src python -m pytest: 3229 passed, 5 skipped
• git diff --check
• AGENTS_SHIPGATE_AGENT_MODE=1 PYTHONPATH=src python -m agents_shipgate check --agent codex --workspace . --format codex-boundary-json (decision=warn)
• AGENTS_SHIPGATE_AGENT_MODE=1 PYTHONPATH=src python -m agents_shipgate verify --workspace . --config shipgate.yaml --ci-mode advisory --format json (merge_verdict=human_review_required, release_decision=review_required, 19 review items, 0 blockers; expected for trust-root and agent-instruction edits)