diff --git a/Dockerfile b/Dockerfile
index 163d8dd..c588c97 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -61,6 +61,9 @@ COPY --from=builder /app/templates ./templates
 # Copy web assets (HTML, CSS, JS, etc.)
 COPY --from=builder /app/web ./web
 
+# Copy documentation
+COPY --from=builder /app/docs ./docs
+
 # Expose port
 EXPOSE 8765
 
diff --git a/docs/INDEX.md b/docs/INDEX.md
index 6ca5b8f..7d10383 100644
--- a/docs/INDEX.md
+++ b/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.
 
diff --git a/docs/contributing/INDEX.md b/docs/contributing/contributing.md
similarity index 100%
rename from docs/contributing/INDEX.md
rename to docs/contributing/contributing.md
diff --git a/docs/developer/api/INDEX.md b/docs/developer/api/api-reference.md
similarity index 100%
rename from docs/developer/api/INDEX.md
rename to docs/developer/api/api-reference.md
diff --git a/docs/developer/api/collections/INDEX.md b/docs/developer/api/collections/collections-api.md
similarity index 100%
rename from docs/developer/api/collections/INDEX.md
rename to docs/developer/api/collections/collections-api.md
diff --git a/docs/developer/INDEX.md b/docs/developer/development.md
similarity index 100%
rename from docs/developer/INDEX.md
rename to docs/developer/development.md
diff --git a/docs/operations/INDEX.md b/docs/operations/operations.md
similarity index 100%
rename from docs/operations/INDEX.md
rename to docs/operations/operations.md
diff --git a/docs/user/INDEX.md b/docs/user/user-guide.md
similarity index 100%
rename from docs/user/INDEX.md
rename to docs/user/user-guide.md
diff --git a/internal/docs/navigation.go b/internal/docs/navigation.go
index b180245..3de5f3b 100644
--- a/internal/docs/navigation.go
+++ b/internal/docs/navigation.go
@@ -28,6 +28,12 @@ func (h *DocsHandler) BuildNavigation() *templates.Navigation {
 	categories := make(map[string][]templates.NavItem)
 
 	for _, doc := range docs {
+		// Skip INDEX.md files in subdirectories (they're section landing pages, not nav items)
+		// Only show root INDEX.md, skip all others like user/INDEX.md, api/INDEX.md, etc.
+		if strings.HasSuffix(doc, "INDEX.md") && doc != "INDEX.md" {
+			continue
+		}
+
 		item := h.createNavItem(doc)
 		category := h.getCategoryForNav(doc)
 		categories[category] = append(categories[category], item)
@@ -100,9 +106,19 @@ func (h *DocsHandler) getDocTitle(docPath string) string {
 	switch filename {
 	case "INDEX.md":
 		return "Documentation Index"
+	case "user/user-guide.md":
+		return "User Guide"
+	case "developer/development.md":
+		return "Developer Portal"
+	case "operations/operations.md":
+		return "Operations Guide"
+	case "contributing/contributing.md":
+		return "Contributing"
 	case "developer/api-reference.md":
 		return "API Reference"
-	case "developer/collections-api.md":
+	case "developer/api/api-reference.md":
+		return "API Reference"
+	case "developer/api/collections-api.md":
 		return "Collections API"
 	case "developer/websocket-api.md":
 		return "WebSocket API"