Update documentation structure and enhance .gitignore

- Added generated index files and report directories to .gitignore to prevent unnecessary tracking of transient files.
- Updated README links to reflect new documentation paths for better navigation.
- Improved documentation organization by ensuring all links point to the correct locations, enhancing user experience and accessibility.

README.md

@@ -109,7 +109,7 @@ SENTRY_AUTH_TOKEN=
 NEXT_PUBLIC_ANALYTICS_ID=
 ```
 
-See [ENV_EXAMPLES.md](./ENV_EXAMPLES.md) for complete environment variable documentation.
+See [ENV_EXAMPLES.md](./docs/ENV_EXAMPLES.md) for complete environment variable documentation.
 
 ## Project Structure
 
@@ -166,7 +166,7 @@ Sankofa Phoenix is built on the principle of **Remember → Retrieve → Restore
 
 ### Quick Links
 - **[Project Status](./PROJECT_STATUS.md)** - Current project status and recent changes
-- **[Configuration Guide](./CONFIGURATION_GUIDE.md)** - Setup and configuration instructions
+- **[Configuration Guide](./docs/CONFIGURATION_GUIDE.md)** - Setup and configuration instructions
 - **[Environment Variables](./ENV_EXAMPLES.md)** - Environment variable examples
 - **[Infrastructure Management](./infrastructure/README.md)** - Proxmox, Omada, and infrastructure management
 - **[Tenant Management](./docs/tenants/TENANT_MANAGEMENT.md)** - Multi-tenant operations guide