docs: [#28] fix repository structure tree view in copilot instructions

- Update Repository Structure section to match actual filesystem
- Add missing root files (.editorconfig, .taplo.toml, .vscode/, etc.)
- Remove non-existent files and directories
- Correct application/storage structure (remove certbot/, dhparam/)
- Add missing scripts (manage-hetzner-dns.sh, shell-utils.sh)
- Fix infrastructure docs organization
- Update to reflect current project state accurately

The tree view now provides accurate navigation guidance for contributors.

Author: josecelano

.github/copilot-instructions.md

@@ -1,7 +1,33 @@
 # Torrust Tracker Demo - Contributor Guide
 
+> **📋 CRITICAL: Keep This Document Updated**
+>
+> This document is the **primary entry point** for all contributors, AI assistants, and newcomers to the project. It must be kept synchronized with repository changes at all times.
+>
+> **When making any repository changes, review and update this document if needed.** Check these areas for accuracy:
+>
+> - **Repository Structure** (`📁 Repository Structure` section): Verify folder structure and descriptions match current state
+> - **Available Commands** (`🛠️ Development Workflow` section): Ensure all `make` commands are current and accurate
+> - **Architecture Decision Records** (`📁 Repository Structure` → `Key Components` → ADR table): Add new ADRs to the table
+> - **User Guides** (`📁 Repository Structure` → `Key Components` → User guides table): Add new guides to the table
+> - **Testing Commands** (`📋 Conventions and Standards` → `Testing Requirements`): Verify all test commands work
+> - **Development Workflow** (`🛠️ Development Workflow`): Update commands, workflows, and environment requirements
+> - **Configuration Examples** (throughout document): Ensure examples reflect current configuration templates
+> - **Tool Requirements** (`🚀 Getting Started`): Update dependencies, extensions, and setup requirements
+>
+> **Validation Checklist**:
+>
+> - [ ] Run `make help` and verify all documented commands exist
+> - [ ] Check `docs/adr/` for new ADRs to include in the table
+> - [ ] Check `docs/guides/` for new guides to include in the table
+> - [ ] Test key commands mentioned in the development workflow
+> - [ ] Verify environment variable names match current template files
+> - [ ] Ensure testing layer architecture description is accurate
+> - [ ] Update any outdated tool versions or installation instructions
+
 ## Table of Contents
 
+- [📋 Document Maintenance](#-document-maintenance)
 - [🎯 Project Overview](#-project-overview)
   - [Current Major Initiative](#current-major-initiative)
 - [📁 Repository Structure](#-repository-structure)
@@ -21,7 +47,7 @@
   - [For AI Assistants](#for-ai-assistants)
 - [📖 Additional Resources](#-additional-resources)
 
-## 🎯 Project Overview
+## 📋 Document Maintenance
 
 **Torrust Tracker Demo** is the complete production deployment configuration for running a live [Torrust Tracker](https://github.com/torrust/torrust-tracker) instance. This repository provides:
 
@@ -50,7 +76,7 @@ This project implements a complete twelve-factor app architecture with clear sep
 ┌─────────────────────────────────────────────────────────────┐
 │                 Configuration Management                    │
 ├─────────────────────────────────────────────────────────────┤
-│  • Environment Templates (local.env.tpl, production.env.tpl)  │
+│  • Environment Templates (local.env.tpl, production.env.tpl)│
 │  • Configuration Processing (configure-env.sh)              │
 │  • Template Rendering (.tpl → actual configs)               │
 └─────────────────────────────────────────────────────────────┘
@@ -86,17 +112,23 @@ This project implements a complete twelve-factor app architecture with clear sep
 
 ```text
 torrust-tracker-demo/
+├── .editorconfig           # Editor configuration
 ├── .github/
-│   ├── workflows/           # GitHub Actions CI/CD pipelines
-│   ├── prompts/             # AI assistant prompts and templates
+│   ├── workflows/          # GitHub Actions CI/CD pipelines
+│   ├── prompts/            # AI assistant prompts and templates
 │   └── copilot-instructions.md  # This contributor guide
+├── .gitignore              # Global git ignore rules
+├── .markdownlint.json      # Markdown linting configuration
+├── .markdownlint.md        # Markdown lint rules documentation
+├── .taplo.toml             # TOML formatting configuration
+├── .vscode/                # VS Code workspace settings
+├── .yamllint-ci.yml        # YAML linting configuration for CI
+├── cspell.json             # Spell checking configuration
+├── project-words.txt       # Project-specific word list
+├── repomix-output.xml      # Repomix generated project summary
 ├── docs/
 │   ├── adr/                # Architecture Decision Records
-│   │   └── 001-makefile-location.md  # Makefile location decision
 │   ├── guides/             # User and developer guides
-│   │   ├── integration-testing-guide.md  # Testing guide
-│   │   ├── quick-start.md  # Fast setup guide
-│   │   └── smoke-testing-guide.md  # End-to-end testing
 │   ├── infrastructure/     # Infrastructure-specific documentation
 │   ├── issues/             # Issue documentation and analysis
 │   ├── plans/              # Project planning documentation
@@ -105,59 +137,64 @@ torrust-tracker-demo/
 │   └── README.md           # Cross-cutting documentation index
 ├── infrastructure/         # Infrastructure as Code
 │   ├── terraform/          # OpenTofu/Terraform configurations
-│   │   ├── main.tf         # VM and infrastructure definition
-│   │   └── terraform.tfvars.example  # Example configuration
 │   ├── cloud-init/         # VM provisioning templates
-│   │   ├── user-data.yaml.tpl     # Main system configuration
+│   │   ├── user-data.yaml.tpl       # Main system configuration
 │   │   ├── user-data-minimal.yaml.tpl  # Debug configuration
 │   │   ├── meta-data.yaml  # VM metadata
-│   │   └── network-config.yaml    # Network setup
+│   │   └── network-config.yaml      # Network setup
 │   ├── config/             # Infrastructure configuration templates
 │   │   ├── environments/   # Environment-specific configs
 │   │   └── templates/      # Configuration templates
 │   ├── scripts/            # Infrastructure automation scripts
-│   │   ├── deploy-app.sh   # Application deployment script
-│   │   ├── provision-infrastructure.sh  # Infrastructure provisioning
-│   │   └── health-check.sh # Health validation script
 │   ├── tests/              # Infrastructure validation tests
 │   ├── docs/               # Infrastructure documentation
-│   │   ├── quick-start.md  # Fast setup guide
-│   │   ├── local-testing-setup.md  # Detailed setup
-│   │   ├── infrastructure-overview.md  # Architecture overview
+│   │   ├── bugs/           # Bug documentation
 │   │   ├── refactoring/    # Refactoring documentation
 │   │   ├── testing/        # Testing documentation
 │   │   ├── third-party/    # Third-party setup guides
-│   │   └── bugs/           # Bug documentation
+│   │   ├── configuration-architecture.md  # Config system docs
+│   │   ├── flexible-environment-system.md # Environment system
+│   │   ├── infrastructure-overview.md     # Architecture overview
+│   │   ├── local-testing-setup.md         # Detailed setup
+│   │   └── quick-start.md  # Fast setup guide
 │   ├── .gitignore          # Infrastructure-specific ignores
 │   └── README.md           # Infrastructure overview
 ├── application/            # Application deployment and services
 │   ├── config/             # Application configuration
 │   │   └── templates/      # Configuration templates
 │   ├── share/
 │   │   ├── bin/            # Deployment and utility scripts
-│   │   ├── container/      # Docker service configurations
 │   │   ├── dev/            # Development configs
 │   │   └── grafana/        # Grafana dashboards
 │   ├── storage/            # Persistent data storage
-│   │   ├── certbot/        # SSL certificate storage
-│   │   ├── dhparam/        # DH parameters
+│   │   ├── compose/        # Docker Compose environment files
 │   │   ├── prometheus/     # Prometheus data
 │   │   ├── proxy/          # Nginx proxy configs
 │   │   └── tracker/        # Tracker data
 │   ├── docs/               # Application documentation
-│   │   ├── production-setup.md    # Production deployment docs
-│   │   ├── deployment.md          # Deployment procedures
+│   │   ├── media/          # Screenshots and diagrams
+│   │   ├── backups.md      # Backup procedures
+│   │   ├── deployment.md   # Deployment procedures
 │   │   ├── firewall-requirements.md # Application firewall requirements
-│   │   ├── useful-commands.md     # Operational commands
-│   │   └── media/          # Screenshots and diagrams
+│   │   ├── production-setup.md      # Production deployment docs
+│   │   ├── rollbacks.md    # Rollback procedures
+│   │   └── useful-commands.md       # Operational commands
+│   ├── tests/              # Application tests
 │   ├── compose.yaml        # Docker Compose for services
-│   ├── .env                # Local environment configuration
 │   ├── .gitignore          # Application-specific ignores
 │   └── README.md           # Application overview
 ├── scripts/                # Project-wide utility scripts
-│   └── lint.sh             # Linting script for all file types
+│   ├── lint.sh             # Linting script for all file types
+│   ├── manage-hetzner-dns.sh # DNS management script
+│   └── shell-utils.sh      # Common shell utilities
+├── tests/                  # Project-wide tests
+│   ├── test-ci.sh          # CI test orchestrator
+│   ├── test-e2e.sh         # End-to-end integration tests
+│   ├── test-unit-project.sh # Project structure tests
+│   └── README.md           # Testing documentation
+├── LICENSE                 # Project license
 ├── Makefile                # Main automation interface
-└── *.md                    # Project root documentation
+└── README.md               # Project root documentation
 ```
 
 ### Key Components
@@ -196,6 +233,23 @@ Key design decisions are documented in `docs/adr/`. Contributors should review r
 | [ADR-006](../docs/adr/006-ssl-certificate-generation-strategy.md)                   | SSL Certificate Generation Strategy      | Approach for SSL certificate management                               |
 | [ADR-007](../docs/adr/007-two-level-environment-variable-structure.md)              | Two-Level Environment Variable Structure | Security-focused separation of infrastructure and container variables |
 
+#### User Guides
+
+Comprehensive deployment, configuration, and testing guides are available in `docs/guides/`. These provide step-by-step instructions for various scenarios:
+
+| Guide                                                                      | Purpose                         | Time   | Use Case            |
+| -------------------------------------------------------------------------- | ------------------------------- | ------ | ------------------- |
+| [Cloud Deployment Guide](../docs/guides/cloud-deployment-guide.md)         | General cloud deployment        | 30 min | First deployment    |
+| [Integration Testing Guide](../docs/guides/integration-testing-guide.md)   | Complete infrastructure testing | 15 min | Development         |
+| [Smoke Testing Guide](../docs/guides/smoke-testing-guide.md)               | Quick functionality validation  | 5 min  | Post-deployment     |
+| [DNS Setup for Testing](../docs/guides/dns-setup-for-testing.md)           | DNS configuration               | 10 min | Domain setup        |
+| [Grafana Setup Guide](../docs/guides/grafana-setup-guide.md)               | Monitoring dashboard setup      | 20 min | Monitoring          |
+| [Grafana Subdomain Setup](../docs/guides/grafana-subdomain-setup.md)       | Subdomain configuration         | 15 min | Advanced monitoring |
+| [SSL Testing Guide](../docs/guides/ssl-testing-guide.md)                   | Certificate testing             | 10 min | Security validation |
+| [Database Backup Testing](../docs/guides/database-backup-testing-guide.md) | Backup validation procedures    | 10 min | Data persistence    |
+
+**Provider-Specific Guides**: Cloud provider deployment guides are organized in `docs/guides/providers/` for Hetzner, AWS, and other providers.
+
 ## 🛠️ Development Workflow
 
 ### Quick Start for Contributors
@@ -208,8 +262,8 @@ cd torrust-tracker-demo
 # 2. Install dependencies (Ubuntu/Debian)
 make install-deps
 
-# 3. Setup SSH key for VMs
-make infra-config-local
+# 3. Setup development environment configuration
+make infra-config-development PROVIDER=libvirt
 
 # 4. Test twelve-factor deployment workflow locally
 make infra-apply  # Provision infrastructure (platform setup)
@@ -223,6 +277,26 @@ make test-e2e     # Full infrastructure test
 make lint         # Syntax validation only
 ```
 
+### Development Convenience Commands
+
+For faster development iteration, use these convenience commands:
+
+```bash
+# Complete development setup (first time)
+make dev-setup    # Install deps + configure development environment
+
+# Full deployment workflow
+make dev-deploy   # Complete infra-apply + app-deploy workflow
+
+# Quick validation
+make dev-test     # Syntax + unit tests (no VM required)
+
+# Complete cleanup
+make dev-clean    # Clean up all resources and temporary files
+```
+
+These commands combine multiple steps and use sensible defaults (development environment with libvirt provider).
+
 ### Main Commands
 
 #### Twelve-Factor Workflow (Recommended)
@@ -256,10 +330,13 @@ make lint         # Syntax validation only
 
 #### Testing and Validation
 
-| Command         | Purpose                           |
-| --------------- | --------------------------------- |
-| `make test-e2e` | Run complete infrastructure tests |
-| `make lint`     | Run syntax validation only        |
+| Command              | Purpose                                     |
+| -------------------- | ------------------------------------------- |
+| `make test-e2e`      | Run complete infrastructure tests           |
+| `make test-ci`       | Run project-wide CI tests (global concerns) |
+| `make lint`          | Run syntax validation only                  |
+| `make infra-test-ci` | Run infrastructure-only CI tests            |
+| `make app-test-ci`   | Run application-only CI tests               |
 
 #### Legacy Commands (Deprecated)
 
@@ -548,7 +625,7 @@ The project implements intelligent sudo cache management to improve the user exp
 
    ```bash
    make install-deps  # Install dependencies
-   make infra-config-local # Configure SSH access
+   make infra-config-development PROVIDER=libvirt # Configure development environment
    make infra-test-prereq   # Verify setup
    ```
 
@@ -764,7 +841,7 @@ ssh torrust@<VM_IP> "cd /home/torrust/github/torrust/torrust-tracker-demo/applic
 **Pre-commit Testing Requirement**: ALWAYS run the CI test suite before committing any changes:
 
 ```bash
-make infra-test-ci
+make test-ci
 ```
 
 This command runs all unit tests that don't require a virtual machine, including: