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.

Validation

• docs-only change
• verified the updated guidance appears in the Quick Start and Auto-Rewrite Hook sections of README.md

[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

[pszymkowiak]

Thanks for the clarification — the content about Bash-only hook scope is useful.

However this PR has conflicts and the version bumps are outdated (we're on 0.28.1 now). Please:

1. Rebase on master:

   git fetch upstream master
   git rebase upstream/master

2. Drop the version bump changes — only keep the Bash-only scope clarifications in README.md. Don't modify CLAUDE.md or ARCHITECTURE.md (version numbers are managed by release-please).

3. Add DCO sign-off:

   git commit --amend -s --no-edit
   git push --force-with-lease

[tsubasakong]

Retargeted to develop, dropped the unrelated version bump edits, and reduced this back to the README-only clarification requested in review. The branch was also rebuilt as a fresh signed-off commit on top of current develop.