refactor: reorganize src/ structure - move bootstrap and network utilities

- Create src/bootstrap/ with app, container, help, logging modules
- Create src/testing/network/ with port_checker and port_usage_checker
- Update all imports across the codebase
- Update module exports in lib.rs, shared/mod.rs, testing/mod.rs
- Update bin executables to use new paths
- All tests pass successfully

Co-authored-by: josecelano <58816+josecelano@users.noreply.github.com>

Author: Copilot

src/bin/e2e_config_tests.rs

@@ -65,8 +65,8 @@ use torrust_tracker_deployer_lib::testing::e2e::tasks::run_configure_command::ru
 use tracing::{error, info};
 
 use torrust_tracker_deployer_lib::adapters::ssh::{SshCredentials, DEFAULT_SSH_PORT};
+use torrust_tracker_deployer_lib::bootstrap::logging::{LogFormat, LogOutput, LoggingBuilder};
 use torrust_tracker_deployer_lib::domain::{Environment, EnvironmentName};
-use torrust_tracker_deployer_lib::logging::{LogFormat, LogOutput, LoggingBuilder};
 use torrust_tracker_deployer_lib::shared::Username;
 use torrust_tracker_deployer_lib::testing::e2e::context::{TestContext, TestContextType};
 use torrust_tracker_deployer_lib::testing::e2e::tasks::{

src/bin/e2e_provision_and_destroy_tests.rs

@@ -54,8 +54,8 @@ use tracing::{error, info};
 
 // Import E2E testing infrastructure
 use torrust_tracker_deployer_lib::adapters::ssh::{SshCredentials, DEFAULT_SSH_PORT};
+use torrust_tracker_deployer_lib::bootstrap::logging::{LogFormat, LogOutput, LoggingBuilder};
 use torrust_tracker_deployer_lib::domain::{Environment, EnvironmentName};
-use torrust_tracker_deployer_lib::logging::{LogFormat, LogOutput, LoggingBuilder};
 use torrust_tracker_deployer_lib::shared::Username;
 use torrust_tracker_deployer_lib::testing::e2e::context::{TestContext, TestContextType};
 use torrust_tracker_deployer_lib::testing::e2e::tasks::virtual_machine::{

src/bin/e2e_tests_full.rs

@@ -61,8 +61,8 @@ use tracing::{error, info};
 
 // Import E2E testing infrastructure
 use torrust_tracker_deployer_lib::adapters::ssh::DEFAULT_SSH_PORT;
+use torrust_tracker_deployer_lib::bootstrap::logging::{LogFormat, LogOutput, LoggingBuilder};
 use torrust_tracker_deployer_lib::infrastructure::persistence::repository_factory::RepositoryFactory;
-use torrust_tracker_deployer_lib::logging::{LogFormat, LogOutput, LoggingBuilder};
 use torrust_tracker_deployer_lib::shared::{Clock, SystemClock};
 use torrust_tracker_deployer_lib::testing::e2e::context::{TestContext, TestContextType};
 use torrust_tracker_deployer_lib::testing::e2e::tasks::{

src/bin/test_logging.rs

@@ -31,7 +31,7 @@
 use std::path::PathBuf;
 
 use clap::Parser;
-use torrust_tracker_deployer_lib::logging::{LogFormat, LogOutput, LoggingBuilder};
+use torrust_tracker_deployer_lib::bootstrap::logging::{LogFormat, LogOutput, LoggingBuilder};
 use tracing::{debug, error, info, trace, warn};
 
 #[derive(Parser)]

src/app.rs src/bootstrap/app.rssrc/app.rs renamed to src/bootstrap/app.rs

@@ -20,7 +20,7 @@
 use clap::Parser;
 use tracing::info;
 
-use torrust_tracker_deployer_lib::{help, logging, presentation};
+use crate::{bootstrap, presentation};
 
 /// Main application entry point
 ///
@@ -42,7 +42,7 @@ pub fn run() {
 
     let logging_config = cli.global.logging_config();
 
-    logging::init_subscriber(logging_config);
+    bootstrap::logging::init_subscriber(logging_config);
 
     info!(
         app = "torrust-tracker-deployer",
@@ -62,7 +62,7 @@ pub fn run() {
             }
         }
         None => {
-            help::display_getting_started();
+            bootstrap::help::display_getting_started();
         }
     }
 

src/container.rs src/bootstrap/container.rssrc/container.rs renamed to src/bootstrap/container.rs

@@ -0,0 +1,21 @@
+//! Bootstrap Module
+//!
+//! This module contains application initialization and bootstrap concerns.
+//! It handles application lifecycle, dependency injection, logging setup,
+//! and help display.
+//!
+//! ## Modules
+//!
+//! - `app` - Main application bootstrap and entry point logic
+//! - `container` - Service container for dependency injection
+//! - `help` - Help and usage information display
+//! - `logging` - Logging configuration and initialization
+
+pub mod app;
+pub mod container;
+pub mod help;
+pub mod logging;
+
+// Re-export commonly used types for convenience
+pub use container::Services;
+pub use logging::{LogFormat, LogOutput, LoggingBuilder, LoggingConfig};

src/help.rs src/bootstrap/help.rssrc/help.rs renamed to src/bootstrap/help.rs

@@ -25,7 +25,7 @@ use std::path::PathBuf;
 /// Centralizes all deployment-related configuration including file paths,
 /// service connection details, and runtime behavior settings.
 ///
-/// Created once at deployment start and passed to [`Services::new()`](crate::container::Services::new).
+/// Created once at deployment start and passed to [`Services::new()`](crate::bootstrap::container::Services::new).
 pub struct Config {
     /// Directory containing template files for rendering configurations.
     ///