docs: restructure docs, fix install story, add complete usage guide

[CodeWithJuber]

What & why

Redesigns the documentation and install story around the cognitive-substrate paper, applying a ponytail discipline (YAGNI / reuse-first / shortest-diff) — docs and config only, no source rewrites, no speculatively-built "gaps." The working, tested runtime is untouched.

The main ask: stop leading with bash install.sh.

• Recommended install paths are now the plugin (Claude Code / Codex) and a token-free CLI install, npm install -g github:CodeWithJuber/forgekit — verified to install in seconds with no clone and no GitHub Packages token.
• bash install.sh is demoted to the symlink/dev path; the GitHub Packages route is marked CI-only. Applied consistently across README, ONBOARDING, docs/cognitive-substrate/README.md, and the landing page (install snippet + stale version 0.2.0 → 0.3.1).

Documentation, professionalized:

• README rewritten to a professional standard — value prop, an install matrix, quickstart, a three-layer "how it works" table, an auto-use section, the full command list, honest limits, and a docs index. Dropped the broken public-npm version badge.
• New docs/GUIDE.md — the complete guide the issue asked for: every command with a worked example and its real output (captured from a live run), the everyday workflow, auto-use inside an agent (Claude hooks + MCP + emitted rule), recipes, and how to extend each layer (rules, tools, guards, crew, routing signals, emitters, rebrand).
• CHANGELOG.md updated under ## [Unreleased].

Auto-use verified, not asserted: the substrate genuinely runs itself end to end — Claude Code hooks (hooks/hooks.json) plus the forge-cortex MCP server exposing substrate_check / predict_impact / assumption_gate / route_task / scope_files, plus the "run substrate before risky work" rule that forge init emits into every tool. Docs match the code.

Checklist

• npm test passes (147/147, Node 22 locally; matrix runs 18/20/22 in CI)
• npm run check passes (Biome scopes to src/** + test/**; this PR touches neither)
• New public functions have a test — n/a (docs/config only, no code change)
• Conventional commit message (docs:)
• CHANGELOG.md updated under ## [Unreleased]
• No new runtime dependency
• Substrate/docs updated (this PR is the docs update; no forge substrate / MCP behavior changed)

Risk & rollback

• Risk level: low — Markdown/HTML/JSON-free docs only; no runtime code, no dependencies, no config schema changes.
• Rollback plan: revert this commit; nothing else depends on it.

Extra checks (tick if applicable)

• npm run typecheck — unaffected (no JS/TS changed)
• Logs contain no secrets/PII

🤖 Generated with Claude Code

https://claude.ai/code/session_01Eh3SNx15EeVbTmU4nH36XC

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Generated by Claude Code