docs(agent): fix stale command contract docs

[morehardy]

Summary

• Update agent-facing project docs to describe the current doctor/config-focused core instead of removed read/search routing.
• Replace stale channel contract wording with the current Channel can_handle / check / active_backend contract.
• Correct llms.txt command, platform, and backend guidance so agents use install/doctor plus SKILL.md instead of removed wrapper commands.

Why

Agent-facing docs still described wrapper-era commands and channel APIs, which can cause agents to run obsolete agent-reach read/search-* commands even when doctor reports the current backend state correctly.

Test Plan

• . /tmp/agent-reach-stopgap-venv/bin/activate && pytest tests/ -v
• git diff --cached --check before commit
• Checked changed docs for stale wrapper-era command and channel-contract patterns

[Panniantong]

感谢修正 Agent 命令契约。merged #575 与 #577 已删除 phantom commands，并用真实安装、Doctor 和上游命令模板建立回归门禁，因此关闭。