Fix quick-setup handling for deprecated secret flags

> [!CAUTION]
> Protected files were modified in this change.
> This pull request is in `request_review` mode and requires explicit human scrutiny before merge.
>
> Protected files: `README.md`

## Summary
- accept `--set-secret` and `--skip-secret` in `scripts/quick-setup.sh` as deprecated no-op flags for backwards compatibility
- update script help/usage text to document both deprecated flags
- align quick-setup docs in `README.md` and `gh-agent-workflows/README.md` with current behavior

## Why
The docs described deprecated secret-related flags, but the script rejected them with `Unknown flag`, causing quick-setup to fail immediately for users copying documented commands.

Closes \#1716

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[What is this?](https://ela.st/github-ai-tools) | [From workflow: Trigger Bug Hunter](https://github.com/elastic/ai-github-actions/actions/runs/30539483875)

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---

> [!NOTE]
> This was originally intended as a pull request, but the git push operation failed.
>
> **Original error:** pushSignedCommits: refusing unsigned push for branch 'fix-issue-1716-quick-setup-deprecated-flags-708d6fe34aaaf1d9': Signed-commit payload violates file-protection policy (request_review): README.md, gh-agent-workflows/README.md
>
> **Workflow Run:** [View run details and download bundle artifact](https://github.com/elastic/ai-github-actions/actions/runs/30539483875)
>
> The bundle file is available in the `agent` artifact in the workflow run linked above.

To create a pull request with the changes:

```sh
# Download the artifact from the workflow run
gh run download 30539483875 -n agent -D /tmp/agent-30539483875

# Fetch the bundle into a temporary ref, then update the local branch
git fetch /tmp/agent-30539483875/aw-fix-issue-1716-quick-setup-deprecated-flags.bundle refs/heads/fix-issue-1716-quick-setup-deprecated-flags:refs/bundles/create-pr-fix-issue-1716-quick-setup-deprecated-flags-708d6fe34aaaf1d9-c9fed417
git update-ref refs/heads/fix-issue-1716-quick-setup-deprecated-flags-708d6fe34aaaf1d9 refs/bundles/create-pr-fix-issue-1716-quick-setup-deprecated-flags-708d6fe34aaaf1d9-c9fed417
git checkout fix-issue-1716-quick-setup-deprecated-flags-708d6fe34aaaf1d9
# Ensure the working tree matches the updated branch
git reset --hard
# Remove the temporary bundle ref
git update-ref -d refs/bundles/create-pr-fix-issue-1716-quick-setup-deprecated-flags-708d6fe34aaaf1d9-c9fed417

# Push the branch to origin
git push origin fix-issue-1716-quick-setup-deprecated-flags-708d6fe34aaaf1d9

# Create the pull request
gh pr create --title 'Fix quick-setup handling for deprecated secret flags' --base main --head fix-issue-1716-quick-setup-deprecated-flags-708d6fe34aaaf1d9 --repo elastic/ai-github-actions
```

Start with scripts/quick-setup.sh and inspect its flag parsing and help text for the deprecated secret flags. Compare the quick-setup documentation in README.md and gh-agent-workflows/README.md, then verify documented commands no longer fail with Unknown flag.

Written by the indexing model from the issue text.