docs: explain setup hoisting and working directory

[ikenyal]

Issue #, if available

N/A.

Description of changes

Both setup scripts default to removing the sibling language and moving the selected package to the repository root. Their completion messages already tell users to run cd .., but the Getting started sections omit that choice and go straight to dependency installation from the original language subdirectory.

This change documents the repository-layout prompt, its default y answer, and removal of the sibling language. It explains when to run cd .. before installing dependencies and when to stay in the language subdirectory after answering n.

The guidance stays inside the setup section, so the existing setup scripts remove it from the generated README when hoisting. No setup-script behavior or dependency changes.

Testing

Verified locally on macOS arm64 with Python 3.12.12 and Node.js 22.22.2:

• Ran both setup scripts in disposable copies with all eight components selected, using the default hoisting answer and explicit n to retain the monorepo layout.
• In Bash, confirmed the documented conditional cd .. reaches the package directory, and staying in the language directory works when hoisting is declined. Also verified the default-hoisting path in Zsh for both languages.
• Confirmed hoisted READMEs remove the setup-only guidance, renumber dependency installation, and no longer reference the removed language directory in clone instructions. Non-hoisted READMEs retain the guidance.
• Generated Python projects in both layouts: all 12 tests pass; Ruff formatting/lint and mypy pass.
• Generated TypeScript projects in both layouts: npm install --ignore-scripts, npm run check (11 tests), and npm run build pass.
• git diff --check passes.

No model calls, AWS resources, or GPU were used. Linux and Windows were not executed locally.

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