Document the task-oriented HypAware CLI

[philcunliffe]

Summary

• Add a task-oriented CLI guide for installation, configuration, upgrades, recovery, privacy, and troubleshooting.
• Add a complete command reference covering all 90 visible core and config-active plugin registrations.
• Explain conditional plugin command availability, Claude OTEL capture, destructive and remote operations, compatibility aliases, and unavailable future commands.
• Link both pages from the README documentation index.

Documentation coverage

The guide covers first installation, ordinary reconfiguration, compatible upgrades, breaking-version upgrades, and reinstallation or recovery. The reference documents every shipped visible group and leaf with syntax, availability, effects, important options, stable output or exit behavior, and an example.

Hidden credential and hook machine contracts remain excluded. Hidden Gas City routes remain unavailable. The future setup update, setup repair, and setup rollback flows are clearly labeled as planned rather than shipped.

Verification

• node --test test/core/cli-consistency-gate.test.js test/core/group-and-verb-help.test.js
• npm run typecheck
• npm test (local: 4,505 passed, 2 skipped, 0 failed)
• Visible command coverage audit: 68 core plus 22 plugin-manifest registrations, 0 missing
• Markdown render, local-link, heading-hierarchy, canonical-command, hidden-contract, future-command, U+2014, and git diff --check audits

GitHub test jobs currently inherit the existing #857 failure in test/core/command-dispatch.test.js: the clean CI configuration omits inactive graph from top-level help, while that assertion expects it. The same Node 22 and Node 24 jobs fail on #857; type checking passes. This documentation-only layer does not change code or tests.

Stack dependency

This documentation PR depends directly on #857 and intentionally uses codex/cli-reorg as its base. Reviewers therefore see only the documentation layer. Do not merge this PR before #857.