docs: clarify Bash-only auto-rewrite scope

[tsubasakong]

Summary

• clarify that the auto-rewrite hook only runs on Bash tool calls
• note that Claude Code built-in Read, Grep, and Glob tools are not auto-rewritten
• point readers to shell commands or explicit rtk read / rtk grep / rtk find when they want RTK filtering

Fixes #387.

[aeppling]

Hello, this should target develop branch, please read CONTRIBUTING.md

[aeppling]

You're still targeting master branch, please recreate this PR to develop branch so we validate