docs: concepts and building_applications migration (#3534)

# What does this PR do?

- Migrates the remaining documentation sections to the new documentation format

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## Test Plan

- Partial migration

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docs/docs/distributions/customizing_run_yaml.mdx

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+---
+title: Customizing run.yaml
+description: Customizing run.yaml files for Llama Stack templates
+sidebar_label: Customizing run.yaml
+sidebar_position: 4
+---
+# Customizing run.yaml Files
+
+The `run.yaml` files generated by Llama Stack templates are **starting points** designed to be customized for your specific needs. They are not meant to be used as-is in production environments.
+
+## Key Points
+
+- **Templates are starting points**: Generated `run.yaml` files contain defaults for development/testing
+- **Customization expected**: Update URLs, credentials, models, and settings for your environment
+- **Version control separately**: Keep customized configs in your own repository
+- **Environment-specific**: Create different configurations for dev, staging, production
+
+## What You Can Customize
+
+You can customize:
+- **Provider endpoints**: Change `http://localhost:8000` to your actual servers
+- **Swap providers**: Replace default providers (e.g., swap Tavily with Brave for search)
+- **Storage paths**: Move from `/tmp/` to production directories
+- **Authentication**: Add API keys, SSL, timeouts
+- **Models**: Different model sizes for dev vs prod
+- **Database settings**: Switch from SQLite to PostgreSQL
+- **Tool configurations**: Add custom tools and integrations
+
+## Best Practices
+
+- Use environment variables for secrets and environment-specific values
+- Create separate `run.yaml` files for different environments (dev, staging, prod)
+- Document your changes with comments
+- Test configurations before deployment
+- Keep your customized configs in version control
+
+Example structure:
+```
+your-project/
+├── configs/
+│   ├── dev-run.yaml
+│   ├── prod-run.yaml
+└── README.md
+```
+
+The goal is to take the generated template and adapt it to your specific infrastructure and operational needs.