docs: enhance multiple APIs documentation with diagram and flattened example

[devin-ai-integration]

Summary

Enhances the "Include more than one API Reference" section in the API Reference documentation with:

• A visual <Files> component diagram showing the recommended apis/ folder structure with plant-store-api and seed-api subfolders (replacing the ASCII tree)
• A new "Flattened API References" subsection explaining how to use flattened: true to display endpoints without extra nesting
• Clearer organization with subheadings: Folder structure, Basic configuration, Flattened API References, Using tabs
• Updated examples to use plant-themed naming consistent with Fern documentation conventions

Review & Testing Checklist for Human

• Verify the <Files> component diagram renders correctly in the preview
• Confirm the flattened: true explanation is accurate and consistent with the existing documentation in customize-api-ref.mdx
• Check that the YAML code examples are syntactically correct and follow docs.yml conventions

Test plan: Open the preview link and navigate to the "Generate API Reference" page, scroll to "Include more than one API Reference" section, and verify the folder diagram displays properly and all code examples are readable.

Notes

• fern check passed with no errors
• Requested by kenny@buildwithfern.com via Slack
• Devin session: https://app.devin.ai/sessions/0d5b816fdff34a03a0395e7f0ed4651e

[devin-ai-integration]

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[github-actions]

📝 [vale] _{reported by reviewdog 🐶}
[FernStyles.Headings] 'Flattened API References' should use sentence-style capitalization.