docs: rename INDEX files to meaningful names and fix navigation

- Renamed subdirectory INDEX.md files to section-specific names:
  - user/INDEX.md → user/user-guide.md
  - developer/INDEX.md → developer/development.md
  - operations/INDEX.md → operations/operations.md
  - contributing/INDEX.md → contributing/contributing.md
  - developer/api/INDEX.md → developer/api/api-reference.md
  - developer/api/collections/INDEX.md → developer/api/collections/collections-api.md

- Updated all internal links to use new filenames
- Updated navigation.go to skip subdirectory INDEX files from sidebar
- Added Dockerfile to include docs directory in container build

This fixes the issue where multiple 'INDEX' links appeared in the sidebar,
making navigation confusing. Now each section has a descriptive name.

docs/INDEX.md

@@ -8,7 +8,7 @@ Complete guide to Bookhoard documentation. Find what you need quickly.
 
 ### 👤 For End Users
 
-**[User Documentation Portal](user/INDEX.md)** - Guides for using Bookhoard features
+**[User Documentation Portal](user/user-guide.md)** - Guides for using Bookhoard features
 
 - **Device Setup**
   - [Kobo Setup Guide](user/devices/kobo-setup.md) - Complete Kobo e-reader configuration
@@ -25,11 +25,11 @@ Complete guide to Bookhoard documentation. Find what you need quickly.
 
 ### 👨‍💻 For Developers
 
-**[Developer Documentation Portal](developer/INDEX.md)** - Technical documentation & API reference
+**[Developer Documentation Portal](developer/development.md)** - Technical documentation & API reference
 
 - **API Documentation**
   - [Complete API Reference](developer/api-reference.md) - Monolithic REST API reference (1,300+ lines)
-  - [Split Endpoint Docs](developer/api/INDEX.md) - Individual endpoints with interactive API Explorer
+   - [Split Endpoint Docs](developer/api/api-reference.md) - Individual endpoints with interactive API Explorer
   - [Collections API](developer/collections-api.md) - Collections management API
 
 - **Protocol Specifications**
@@ -39,7 +39,7 @@ Complete guide to Bookhoard documentation. Find what you need quickly.
 
 ### 🔧 For Operations
 
-**[Operations Documentation Portal](operations/INDEX.md)** - Deployment & maintenance
+**[Operations Documentation Portal](operations/operations.md)** - Deployment & maintenance
 
 - **Deployment**
   - [Troubleshooting Guide](operations/troubleshooting.md) - Common deployment issues and solutions
@@ -51,7 +51,7 @@ Complete guide to Bookhoard documentation. Find what you need quickly.
 
 ### 🤝 For Contributors
 
-**[Contributing Portal](contributing/INDEX.md)** - Development workflow
+**[Contributing Portal](contributing/contributing.md)** - Development workflow
 
 - [Development Guide](contributing/DEVELOPMENT.md) - Architecture, setup, testing
 - [PROJECT_GUIDELINES.md](PROJECT_GUIDELINES.md) - Development rules and standards
@@ -63,8 +63,8 @@ Complete guide to Bookhoard documentation. Find what you need quickly.
 | Want to... | Go to |
 |------------|-------|
 | **Get started** | [README.md](../README.md) - Project overview and quick start |
-| **Set up a device** | [User Portal → Device Setup](user/INDEX.md) |
-| **Use the API** | [Developer Portal → API Docs](developer/INDEX.md) |
+| **Set up a device** | [User Portal → Device Setup](user/user-guide.md) |
+| **Use the API** | [Developer Portal → API Docs](developer/development.md) |
 | **Deploy Bookhoard** | [Operations Portal → Troubleshooting](operations/troubleshooting.md) |
 | **Contribute code** | [Contributing Portal → Development Guide](contributing/DEVELOPMENT.md) |
 | **Understand sync** | [User Portal → Sync Guide](user/sync-guide.md) |
@@ -127,7 +127,7 @@ When adding new features:
 1. **User-facing features** → Update relevant User docs
 2. **API endpoints** → Update [API Reference](developer/api-reference.md) & split docs
 3. **Backend changes** → Update [Development Guide](contributing/DEVELOPMENT.md)
-4. **Deployment changes** → Update [Operations Portal](operations/INDEX.md)
+4. **Deployment changes** → Update [Operations Portal](operations/operations.md)
 
 Keep [PROJECT_GUIDELINES.md](PROJECT_GUIDELINES.md) in mind for documentation standards.