docs: correct runtime and scan guidance

[mldangelo-oai]

Summary

Keep the TypeScript README aligned with the current CLI and SDK.

• Explain which commands require Python and how --python, pythonPath, and PYTHON select the interpreter.
• Correct credential-store and deep-scan defaults, including user configuration and command-line overrides.
• Document nested Git repositories, clean submodules, bulk-scan concurrency and retries, and workbench database locations.
• Check documented defaults against the runtime configuration.

Preserves @GautamSharma99's original contribution from #124.

Verification

• pnpm run format
• pnpm run types
• pnpm run build
• pnpm run test: 1,037 passed; 11 expected platform and integration skips.

[mldangelo-oai]

@codex review

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Security review completed. No security issues were found in this pull request.

Reviewed commit: 23cf480161

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[mldangelo-oai]

@codex review

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Security review completed. No security issues were found in this pull request.

Reviewed commit: f4454b63f3

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ℹ️ About Codex security reviews in GitHub

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Codex Review: Didn't find any major issues. You're on a roll.

Reviewed commit: f4454b63f3

ℹ️ About Codex in GitHub

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• Comment "@codex review".

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