docs: update logging guides to reflect current implementation

- Update logging-guide.md with new API references
- Mark structured-logging-implementation-plan.md as 100% complete
- Document LogFormat enum and CLI integration examples
- Reflect Phase 4 completion with enhanced logging module
- Add examples for e2e-tests --log-format argument usage

Author: josecelano

Cargo.toml

@@ -37,4 +37,4 @@ tera = "1.0"
 thiserror = "1.0"
 torrust-linting = { path = "packages/linting" }
 tracing = { version = "0.1", features = [ "attributes" ] }
-tracing-subscriber = "0.3"
+tracing-subscriber = { version = "0.3", features = [ "env-filter", "json", "fmt" ] }

docs/contributing/logging-guide.md

@@ -0,0 +1,248 @@
+# Structured Logging Guide
+
+This guide explains the structured logging implementation in the Torrust Tracker Deploy project, which uses hierar### JSON Output Format
+
+When using `logging::init_json()` or `LogFormat::Json`, logs are output in JSON format suitable for log aggregation:
+
+````json
+{
+  "timestamp": "2024-09-16T17:00:00.000Z",
+  "level": "INFO",
+  "fields": {
+    "command_type": "provision"
+  },
+  "target": "torrust_tracker_deploy::commands::provision",
+  "span": {
+    "name": "provision_command"
+  },
+  "spans": [{ "name": "provision_command", "command_type": "provision" }]
+}
+```ns to mirror our three-level architecture.
+
+## Architecture Overview
+
+Our structured logging follows a three-level hierarchy that mirrors the application architecture:
+
+```text
+Level 1: Commands (Top-level orchestration)
+├── Level 2: Steps (Mid-level execution units)
+│   └── Level 3: Remote Actions (Leaf-level operations)
+````
+
+## Setting Up Logging
+
+### Basic Setup (Recommended)
+
+```rust
+use torrust_tracker_deploy::logging;
+
+fn main() {
+    // Initialize pretty-printed logging for development
+    logging::init();
+
+    // Your application code here...
+}
+```
+
+### Alternative Formats
+
+```rust
+use torrust_tracker_deploy::logging;
+
+fn main() {
+    // For production (JSON output)
+    logging::init_json();
+
+    // For compact output
+    logging::init_compact();
+
+    // Using the format helper
+    logging::init_with_format(&LogFormat::Json);
+}
+```
+
+### CLI Applications with Format Selection
+
+For CLI applications that want to support multiple formats:
+
+```rust
+use torrust_tracker_deploy::logging::{self, LogFormat};
+use clap::Parser;
+
+#[derive(Parser)]
+struct Cli {
+    #[arg(long, default_value = "pretty")]
+    log_format: LogFormat,
+}
+
+fn main() {
+    let cli = Cli::parse();
+    logging::init_with_format(&cli.log_format);
+
+    // Your application code...
+}
+```
+
+## Span Hierarchy Examples
+
+When you execute operations, you'll see nested spans in your logs:
+
+### Example: Provision Command
+
+```text
+2024-09-16T17:00:00.000Z TRACE provision_command: Starting infrastructure provisioning
+2024-09-16T17:00:00.100Z TRACE provision_command:render_opentofu_templates: Rendering OpenTofu templates
+2024-09-16T17:00:00.200Z TRACE provision_command:initialize_infrastructure: Initializing infrastructure
+2024-09-16T17:00:00.300Z TRACE provision_command:plan_infrastructure: Planning infrastructure deployment
+2024-09-16T17:00:00.400Z TRACE provision_command:apply_infrastructure: Applying infrastructure changes
+2024-09-16T17:00:00.500Z TRACE provision_command:get_instance_info: Retrieving instance information
+2024-09-16T17:00:00.600Z  INFO provision_command: Infrastructure provisioned successfully
+```
+
+### Example: Configure Command with Remote Actions
+
+```text
+2024-09-16T17:01:00.000Z TRACE configure_command: Starting system configuration
+2024-09-16T17:01:00.100Z TRACE configure_command:render_ansible_templates: Rendering Ansible templates
+2024-09-16T17:01:00.200Z TRACE configure_command:wait_ssh_connectivity: Waiting for SSH connectivity
+2024-09-16T17:01:00.300Z TRACE configure_command:wait_cloud_init: Waiting for cloud-init completion
+2024-09-16T17:01:00.400Z TRACE configure_command:wait_cloud_init:cloud_init_validation: Validating cloud-init status
+2024-09-16T17:01:00.500Z TRACE configure_command:install_docker: Installing Docker
+2024-09-16T17:01:00.600Z TRACE configure_command:validate_docker_installation: Validating Docker
+2024-09-16T17:01:00.700Z TRACE configure_command:validate_docker_installation:docker_validation: Checking Docker version
+2024-09-16T17:01:00.800Z  INFO configure_command: System configured successfully
+```
+
+## Span Fields Reference
+
+### Command Level (Level 1)
+
+- **command_type**: The type of command being executed
+  - Values: `"provision"`, `"configure"`, `"test"`
+
+### Step Level (Level 2)
+
+- **step_type**: The category of step being executed
+  - Values: `"infrastructure"`, `"rendering"`, `"connectivity"`, `"system"`, `"software"`, `"validation"`
+- **operation**: The specific operation being performed
+  - Examples: `"init"`, `"plan"`, `"apply"`, `"info"`
+- **template_type**: For rendering steps
+  - Values: `"opentofu"`, `"ansible"`
+- **component**: For software/validation steps
+  - Values: `"docker"`, `"docker_compose"`, `"cloud_init"`
+
+### Remote Action Level (Level 3)
+
+- **action_type**: The type of remote action
+  - Values: `"validation"`
+- **component**: The component being acted upon
+  - Values: `"cloud_init"`, `"docker"`, `"docker_compose"`
+- **server_ip**: The target server IP address
+
+## Environment Variables
+
+Control logging behavior with environment variables:
+
+```bash
+# Show all trace-level logs for development
+export RUST_LOG=torrust_tracker_deploy=trace
+
+# Production logging (info and above)
+export RUST_LOG=torrust_tracker_deploy=info
+
+# Only errors and warnings
+export RUST_LOG=torrust_tracker_deploy=warn
+
+# Detailed logging for specific modules
+export RUST_LOG=torrust_tracker_deploy::commands=trace,torrust_tracker_deploy::steps=debug
+```
+
+## JSON Output Format
+
+When using `logging_simple::init_json()`, logs are output in JSON format suitable for log aggregation:
+
+```json
+{
+  "timestamp": "2024-09-16T17:00:00.000Z",
+  "level": "INFO",
+  "fields": {
+    "command_type": "provision"
+  },
+  "target": "torrust_tracker_deploy::commands::provision",
+  "span": {
+    "name": "provision_command"
+  },
+  "spans": [{ "name": "provision_command", "command_type": "provision" }]
+}
+```
+
+## Best Practices
+
+### 1. Use Appropriate Log Levels
+
+- **TRACE**: Detailed flow information (span entry/exit)
+- **DEBUG**: Detailed information for debugging
+- **INFO**: General information about application progress
+- **WARN**: Warning messages about potential issues
+- **ERROR**: Error messages about failures
+
+### 2. Leverage Span Context
+
+The hierarchical spans automatically provide context. You don't need to repeat information that's already captured in the span fields.
+
+```rust
+// Good: Span fields provide context
+#[instrument(name = "docker_validation", fields(component = "docker"))]
+pub async fn validate_docker() {
+    info!("Starting validation");  // Context is implicit from span
+}
+
+// Avoid: Redundant context information
+#[instrument(name = "docker_validation", fields(component = "docker"))]
+pub async fn validate_docker() {
+    info!(component = "docker", "Starting Docker validation");  // Redundant
+}
+```
+
+### 3. Filter in Production
+
+Use environment-specific filtering to reduce noise in production:
+
+```bash
+# Development: Show everything
+export RUST_LOG=trace
+
+# Production: Focus on important events
+export RUST_LOG=torrust_tracker_deploy=info,warn,error
+```
+
+## Debugging
+
+### Viewing Span Relationships
+
+To see the full span hierarchy, use trace level logging:
+
+```bash
+RUST_LOG=torrust_tracker_deploy=trace cargo run --bin your-binary
+```
+
+### Finding Specific Operations
+
+Filter logs for specific operations:
+
+```bash
+# Only infrastructure operations
+RUST_LOG=torrust_tracker_deploy=info cargo run | grep infrastructure
+
+# Only validation operations
+RUST_LOG=torrust_tracker_deploy=trace cargo run | grep validation
+```
+
+### Performance Analysis
+
+The span timings help identify slow operations:
+
+```text
+2024-09-16T17:00:00.000Z TRACE provision_command: entered
+2024-09-16T17:00:05.234Z TRACE provision_command: exited  // 5.234 seconds total
+```