Merge #60: Reorganize src/ structure: group bootstrap concerns and move network utilities to testing

bf81f0f fix: update doc test imports to use new bootstrap module paths (copilot-swe-agent[bot])
59b165f docs: update codebase-architecture.md for new module structure (copilot-swe-agent[bot])
1f320b9 refactor: reorganize src/ structure - move bootstrap and network utilities (copilot-swe-agent[bot])
8d48c22 Initial plan (copilot-swe-agent[bot])

Pull request description:

  ## Reorganize src/ structure: bootstrap and testing utilities ✅

  Successfully reorganized the src/ directory structure to improve code organization and semantic clarity.

  ### Changes Summary

  **1. Created `src/bootstrap/` module** - Groups application initialization concerns:
  - `app.rs` - Application bootstrap and entry point logic
  - `container.rs` - Dependency injection container (Services)
  - `help.rs` - Help and usage information display
  - `logging.rs` - Logging configuration and initialization
  - `mod.rs` - Module exports

  **2. Created `src/testing/network/` module** - Network testing utilities:
  - `port_checker.rs` - TCP port connectivity checking
  - `port_usage_checker.rs` - Port usage validation
  - `mod.rs` - Module exports

  **3. Updated all imports** across 24 files:
  - Binary executables (4 files)
  - Library modules (6 files)
  - Test infrastructure (6 files)
  - Presentation layer (1 file)
  - Documentation (2 files)
  - Integration test (1 file)

  **4. Fixed doc test imports** (latest commit):
  - Updated all doc comments in `bootstrap/logging.rs` to use correct paths
  - Updated doc comments in `bootstrap/help.rs`
  - Updated doc comments in `presentation/cli/args.rs`

  ### Benefits

  ✨ **Clearer src/ root**: Shows only main architectural layers (DDD + adapters + bootstrap + testing)
  ✨ **Semantic accuracy**: `shared/` truly contains pure utilities, not infrastructure code
  ✨ **Better discoverability**: Related bootstrap concerns grouped together
  ✨ **Honest organization**: Test utilities in `testing/`, not pretending to be shared production code

  ### Verification

  - ✅ **200 doc tests pass** - All documentation examples compile correctly
  - ✅ **987 unit tests pass** - All library tests successful
  - ✅ **No unused dependencies** - cargo machete clean
  - ✅ **Clippy clean** - No warnings or errors
  - ✅ **Build successful** - Compilation passes
  - ✅ **Documentation updated** - codebase-architecture.md reflects new structure

  ### File Changes

  ```
  26 files changed, 108 insertions(+), 59 deletions(-)
  ```

  All acceptance criteria from the issue have been met. The refactoring is complete and all tests pass.

  <!-- START COPILOT CODING AGENT SUFFIX -->

  <details>

  <summary>Original prompt</summary>

  ----

  *This section details on the original issue you should resolve*

  <issue_title>Reorganize `src/` structure: group bootstrap concerns and move network utilities to testing</issue_title>
  <issue_description>### 🎯 Motivation

  The current `src/` structure has some organizational inconsistencies:

  1. **Bootstrap concerns scattered in root**: Files like `app.rs`, `container.rs`, `logging.rs`, and `help.rs` are bootstrap/initialization concerns that clutter the `src/` root alongside the main DDD layers
  2. **Port checkers in wrong location**: `port_checker` and `port_usage_checker` are in `shared/` but they:
     - Are exclusively used in tests (not production code)
     - Perform infrastructure operations (network I/O)
     - Don't fit the semantic meaning of "shared utilities"

  ### 📋 Proposed Changes

  #### 1. Group Bootstrap Concerns in `src/bootstrap/`

  Move application initialization and setup files into a dedicated `bootstrap/` folder:

  ```
  src/app.rs            → src/bootstrap/app.rs
  src/container.rs      → src/bootstrap/container.rs
  src/logging.rs        → src/bootstrap/logging.rs
  src/help.rs           → src/bootstrap/help.rs
  ```

  **Rationale**:
  - Groups related concerns together (application lifecycle, DI container, logging setup, help display)
  - Cleans up `src/` root to show only the main architectural layers
  - Name "bootstrap" is clear and won't be confused with tracker setup/deployment

  #### 2. Move Port Checkers to `src/testing/network/`

  Move network testing utilities from shared to testing:

  ```
  src/shared/port_checker.rs        → src/testing/network/port_checker.rs
  src/shared/port_usage_checker.rs  → src/testing/network/port_usage_checker.rs
  ```

  **Rationale**:
  - These are **test-only utilities** (used exclusively in E2E and integration tests)
  - They perform **infrastructure operations** (network checks), not pure utility functions
  - Honest representation of their actual usage and purpose
  - Can be moved to `src/infrastructure/network/` later if needed in production

  ### 📊 Before and After

  **Current Structure**:
  ```
  src/
  ├── adapters/              ✅ Good
  ├── app.rs                ⚠️ Bootstrap concern
  ├── application/           ✅ DDD layer
  ├── bin/                  ✅ Standard location
  ├── config/               ✅ Configuration
  ├── container.rs          ⚠️ Bootstrap concern
  ├── domain/               ✅ DDD layer
  ├── help.rs               ⚠️ Bootstrap concern
  ├── infrastructure/        ✅ DDD layer
  ├── lib.rs                ✅ Library root
  ├── logging.rs            ⚠️ Bootstrap concern
  ├── main.rs               ✅ Entry point
  ├── presentation/          ✅ DDD layer
  ├── shared/               ⚠️ Mixing utilities with infrastructure
  │   ├── clock.rs
  │   ├── command/
  │   ├── error/
  │   ├── port_checker.rs   ❌ Test-only, infrastructure concern
  │   ├── port_usage_checker.rs ❌ Test-only, infrastructure concern
  │   └── username.rs
  └── testing/              ✅ Test utilities
  ```

  **Proposed Structure**:
  ```
  src/
  ├── adapters/              ✅ External tool wrappers
  ├── application/           ✅ DDD layer
  ├── bin/                  ✅ Binary executables
  ├── bootstrap/            ✨ NEW: Application initialization
  │   ├── app.rs
  │   ├── container.rs
  │   ├── help.rs
  │   └── logging.rs
  ├── config/               ✅ Configuration
  ├── domain/               ✅ DDD layer
  ├── infrastructure/        ✅ DDD layer
  ├── lib.rs                ✅ Library root
  ├── main.rs               ✅ Entry point
  ├── presentation/          ✅ DDD layer
  ├── shared/               ✅ Pure utilities only
  │   ├── clock.rs
  │   ├── command/
  │   ├── error/
  │   └── username.rs
  └── testing/              ✅ Test utilities
      ├── e2e/
      ├── fixtures.rs
      ├── integration/
      ├── mock_clock.rs
      └── network/          ✨ NEW: Network testing utilities
          ├── mod.rs
          ├── port_checker.rs
          └── port_usage_checker.rs
  ```

  ### 🔧 Migration Steps

  1. **Create new directories**:
     - `src/bootstrap/`
     - `src/testing/network/`

  2. **Move bootstrap files**:
     - Move `app.rs`, `container.rs`, `help.rs`, `logging.rs` to `bootstrap/`
     - Create `src/bootstrap/mod.rs` with appropriate exports

  3. **Move network utilities**:
     - Move `port_checker.rs` and `port_usage_checker.rs` to `testing/network/`
     - Create `src/testing/network/mod.rs` with appropriate exports

  4. **Update imports** throughout the codebase:
     - `crate::app` → `crate::bootstrap::app`
     - `crate::container` → `crate::bootstrap::container`
     - `crate::logging` → `crate::bootstrap::logging`
     - `crate::help` → `crate::bootstrap::help`
     - `crate::shared::PortChecker` → `crate::testing::network::PortChecker`
     - `crate::shared::port_usage_checker::PortUsageChecker` → `crate::testing::network::PortUsageChecker`

  5. **Update module exports** in:
     - `src/lib.rs` (add `bootstrap`, update `shared` and `testing` exports)
     - `src/shared/mod.rs` (remove port checker exports)
     - `src/testing/mod.rs` (add network module)

  6. **Update documentation**:
     - Update `docs/codebase-architecture.m...

  </details>

  - Fixes #44

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Top commit has no ACKs.

Tree-SHA512: 038566cc707d35704995da5c7caabdb8b650b63456b87f2ff695febbfbd247285eb80a55fbaacd1d007389023840860a098e304fbe8df640865c6e8cf451e457

Author: josecelano

docs/codebase-architecture.md

@@ -189,11 +189,19 @@ All modules include comprehensive `//!` documentation with:
 
 ### Core Infrastructure
 
+**Bootstrap Module:**
+
+Application initialization and lifecycle management:
+
+- ✅ `src/bootstrap/mod.rs` - Bootstrap module root with re-exports
+- ✅ `src/bootstrap/app.rs` - Main application bootstrap and entry point logic
+- ✅ `src/bootstrap/container.rs` - Dependency injection container (Services)
+- ✅ `src/bootstrap/help.rs` - Help and usage information display
+- ✅ `src/bootstrap/logging.rs` - Logging configuration and utilities
+
 **Root Level Files:**
 
 - ✅ `src/main.rs` - Main binary entry point
-- ✅ `src/container.rs` - Dependency injection container
-- ✅ `src/logging.rs` - Logging configuration and utilities
 - ✅ `src/lib.rs` - Library root module
 
 **Binary Files:**
@@ -359,20 +367,28 @@ Generic utilities used across all layers:
 - ✅ `src/shared/command/mod.rs` - Command execution utilities (used by all adapters)
 - ✅ `src/shared/clock.rs` - Time abstraction for deterministic testing
 - ✅ `src/shared/error/mod.rs` - Shared error types
-- ✅ `src/shared/port_checker.rs` - Network port checking
-- ✅ `src/shared/port_usage_checker.rs` - Port usage validation
 - ✅ `src/shared/username.rs` - Username value object
 
-Note: SSH and Docker adapters have been moved to `src/adapters/`
+Note: SSH and Docker adapters have been moved to `src/adapters/`. Network testing utilities (port_checker, port_usage_checker) have been moved to `src/testing/network/`.
 
 ### Testing Infrastructure
 
 **E2E Testing Framework:**
 
-- ✅ `src/e2e/mod.rs` - E2E testing framework coordination
-- ✅ `src/e2e/containers/mod.rs` - Container-based testing infrastructure
-- ✅ `src/e2e/containers/actions/` - E2E test actions
-- ✅ `src/e2e/containers/provisioned.rs` - Provisioned container management
+- ✅ `src/testing/mod.rs` - Testing framework root module
+- ✅ `src/testing/e2e/mod.rs` - E2E testing framework coordination
+- ✅ `src/testing/e2e/containers/mod.rs` - Container-based testing infrastructure
+- ✅ `src/testing/e2e/containers/actions/` - E2E test actions
+- ✅ `src/testing/e2e/containers/provisioned.rs` - Provisioned container management
+- ✅ `src/testing/integration/` - Integration testing utilities
+- ✅ `src/testing/fixtures.rs` - Reusable test fixtures
+- ✅ `src/testing/mock_clock.rs` - Mock clock implementation for deterministic testing
+
+**Network Testing Utilities:**
+
+- ✅ `src/testing/network/mod.rs` - Network testing utilities root
+- ✅ `src/testing/network/port_checker.rs` - TCP port connectivity checking
+- ✅ `src/testing/network/port_usage_checker.rs` - Port usage validation and process identification
 
 **Configuration:**
 

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

@@ -29,7 +29,7 @@
 /// # Example
 ///
 /// ```rust
-/// use torrust_tracker_deployer_lib::help;
+/// use torrust_tracker_deployer_lib::bootstrap::help;
 ///
 /// // Display help when user runs app without arguments
 /// help::display_getting_started();
@@ -73,7 +73,7 @@ pub fn display_getting_started() {
 /// # Example
 ///
 /// ```rust
-/// use torrust_tracker_deployer_lib::help;
+/// use torrust_tracker_deployer_lib::bootstrap::help;
 ///
 /// // Display troubleshooting info when user encounters issues
 /// help::display_troubleshooting();

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

@@ -27,7 +27,7 @@
 //!
 //! ```rust,no_run
 //! use std::path::Path;
-//! use torrust_tracker_deployer_lib::logging::{LogOutput, LogFormat, LoggingBuilder};
+//! use torrust_tracker_deployer_lib::bootstrap::logging::{LogOutput, LogFormat, LoggingBuilder};
 //!
 //! // Flexible builder API
 //! LoggingBuilder::new(Path::new("./data/logs"))
@@ -40,7 +40,7 @@
 //!
 //! ```rust,no_run
 //! use std::path::Path;
-//! use torrust_tracker_deployer_lib::logging::{LogOutput, init_compact};
+//! use torrust_tracker_deployer_lib::bootstrap::logging::{LogOutput, init_compact};
 //!
 //! // E2E tests - enable stderr visibility with production log location
 //! init_compact(Path::new("./data/logs"), LogOutput::FileAndStderr);
@@ -151,7 +151,7 @@ impl LoggingConfig {
 ///
 /// ```rust,no_run
 /// use std::path::Path;
-/// use torrust_tracker_deployer_lib::logging::{LogOutput, LogFormat, LoggingBuilder};
+/// use torrust_tracker_deployer_lib::bootstrap::logging::{LogOutput, LogFormat, LoggingBuilder};
 ///
 /// // Basic usage with defaults (Compact file format, Pretty stderr format, FileAndStderr output)
 /// LoggingBuilder::new(Path::new("./data/logs")).init();
@@ -314,7 +314,7 @@ impl LoggingBuilder {
 ///
 /// ```rust,no_run
 /// use std::path::PathBuf;
-/// use torrust_tracker_deployer_lib::logging::{LogFormat, LogOutput, LoggingConfig, init_subscriber};
+/// use torrust_tracker_deployer_lib::bootstrap::logging::{LogFormat, LogOutput, LoggingConfig, init_subscriber};
 ///
 /// let config = LoggingConfig::new(
 ///     PathBuf::from("./data/logs"),
@@ -589,7 +589,7 @@ fn create_log_file_appender(log_dir: &Path) -> tracing_appender::non_blocking::N
 /// # Example
 /// ```rust,no_run
 /// use std::path::Path;
-/// use torrust_tracker_deployer_lib::logging::{LogOutput, init};
+/// use torrust_tracker_deployer_lib::bootstrap::logging::{LogOutput, init};
 ///
 /// // E2E tests - enable stderr visibility with production location
 /// init(Path::new("./data/logs"), LogOutput::FileAndStderr);
@@ -632,7 +632,7 @@ pub fn init(log_dir: &Path, output: LogOutput) {
 /// # Example
 /// ```rust,no_run
 /// use std::path::Path;
-/// use torrust_tracker_deployer_lib::logging::{LogOutput, init_json};
+/// use torrust_tracker_deployer_lib::bootstrap::logging::{LogOutput, init_json};
 ///
 /// // E2E tests - enable stderr visibility with production location
 /// init_json(Path::new("./data/logs"), LogOutput::FileAndStderr);
@@ -675,7 +675,7 @@ pub fn init_json(log_dir: &Path, output: LogOutput) {
 /// # Example
 /// ```rust,no_run
 /// use std::path::Path;
-/// use torrust_tracker_deployer_lib::logging::{LogOutput, init_compact};
+/// use torrust_tracker_deployer_lib::bootstrap::logging::{LogOutput, init_compact};
 ///
 /// // E2E tests - enable stderr visibility with production location
 /// init_compact(Path::new("./data/logs"), LogOutput::FileAndStderr);
@@ -716,7 +716,7 @@ pub fn init_compact(log_dir: &Path, output: LogOutput) {
 /// # Example
 /// ```rust,no_run
 /// use std::path::Path;
-/// use torrust_tracker_deployer_lib::logging::{LogFormat, LogOutput, init_with_format};
+/// use torrust_tracker_deployer_lib::bootstrap::logging::{LogFormat, LogOutput, init_with_format};
 ///
 /// // Initialize with JSON format for E2E tests with production location
 /// init_with_format(Path::new("./data/logs"), LogOutput::FileAndStderr, &LogFormat::Json);

src/logging.rs src/bootstrap/logging.rssrc/logging.rs renamed to src/bootstrap/logging.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};