diff --git a/.gitignore b/.gitignore
index c249249..6b8e127 100644
--- a/.gitignore
+++ b/.gitignore
@@ -4,3 +4,4 @@ best.pt
 .venv
 .venv-formatters
 autonomy/src/autonomy.egg-info
+hydrus_software_stack.egg-info
diff --git a/hydrus_software_stack.egg-info/PKG-INFO b/hydrus_software_stack.egg-info/PKG-INFO
new file mode 100644
index 0000000..93c0108
--- /dev/null
+++ b/hydrus_software_stack.egg-info/PKG-INFO
@@ -0,0 +1,120 @@
+Metadata-Version: 2.4
+Name: hydrus-software-stack
+Version: 0.1.0
+Summary: Autonomous underwater vehicle software stack with computer vision and navigation capabilities
+Home-page: https://github.com/your-username/hydrus-software-stack
+Author: Cesar
+Author-email: cesar@example.com
+Project-URL: Bug Reports, https://github.com/your-username/hydrus-software-stack/issues
+Project-URL: Source, https://github.com/your-username/hydrus-software-stack
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: opencv-python
+Requires-Dist: numpy
+Requires-Dist: matplotlib
+Requires-Dist: requests
+Requires-Dist: colorama
+Requires-Dist: pyserial
+Requires-Dist: fastapi
+Requires-Dist: Flask
+Requires-Dist: black>=23.0.0
+Requires-Dist: isort>=5.12.0
+Requires-Dist: flake8>=6.0.0
+Requires-Dist: pre-commit>=3.0.0
+Requires-Dist: mypy>=1.0.0
+Provides-Extra: depth-estimation
+Requires-Dist: onnx; extra == "depth-estimation"
+Requires-Dist: onnxruntime-gpu; extra == "depth-estimation"
+Requires-Dist: onnxscript; extra == "depth-estimation"
+Requires-Dist: onnxslim; extra == "depth-estimation"
+Requires-Dist: torch; extra == "depth-estimation"
+Requires-Dist: torchvision; extra == "depth-estimation"
+Requires-Dist: tqdm; extra == "depth-estimation"
+Requires-Dist: typer; extra == "depth-estimation"
+Provides-Extra: all
+Requires-Dist: onnx; extra == "all"
+Requires-Dist: onnxruntime-gpu; extra == "all"
+Requires-Dist: onnxscript; extra == "all"
+Requires-Dist: onnxslim; extra == "all"
+Requires-Dist: torch; extra == "all"
+Requires-Dist: torchvision; extra == "all"
+Requires-Dist: tqdm; extra == "all"
+Requires-Dist: typer; extra == "all"
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: license-file
+Dynamic: project-url
+Dynamic: provides-extra
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
+
+<div align="center" style="text-align: center;">
+
+<h1>🌊 Hydrus Software Stack</h1>
+
+<p>
+  <b>A comprehensive ROS-based toolkit for autonomous underwater vehicles.</b>
+  <br>
+  Built for RobSub competitions with maintainability and usability at its core.
+</p>
+
+<h3>
+  <a href="PHILOSOPHY.md">Philosophy</a>
+  <span> · </span>
+  <a href="autonomy/README.md">Autonomy Docs</a>
+  <span> · </span>
+  <a href="../../issues">Issues</a>
+  <span> · </span>
+  <a href="docker/README.md">Docker Setup</a>
+  <span> · </span>
+  <a href="https://github.com/Rumarino-Team/hydrus-software-stack">GitHub</a>
+</h3>
+
+Quick start: `./doctor.sh && ./docker/hydrus-docker/hocker`
+
+[![Tests](https://img.shields.io/badge/tests-passing-brightgreen.svg)](./run_tests.sh)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](LICENSE)
+[![ROS](https://img.shields.io/badge/ROS-Melodic-blue.svg)](http://wiki.ros.org/melodic)
+[![Docker](https://img.shields.io/badge/Docker-Enabled-blue.svg)](docker/README.md)
+
+</div>
+
+
+To start developing Hydrus
+------
+
+Hydrus is developed by [Rumarino Team](https://github.com/Rumarino-Team). We welcome both pull requests and issues on [GitHub](https://github.com/Rumarino-Team/hydrus-software-stack).
+
+* Read our [Philosophy & Contributing Guide](PHILOSOPHY.md)
+* Check out the [autonomy system documentation](autonomy/README.md)
+* Explore the [Docker deployment options](docker/README.md)
+* Join discussions in [GitHub Issues](../../issues)
+
+Want to contribute? Check our [open issues](../../issues) and follow our [contribution guidelines](PHILOSOPHY.md).
+
+<details>
+<summary>MIT Licensed</summary>
+
+Hydrus is released under the MIT license. Some parts of the software are released under other licenses as specified.
+
+Any user of this software shall indemnify and hold harmless the Rumarino Team and its members from and against all allegations, claims, actions, suits, demands, damages, liabilities, obligations, losses, settlements, judgments, costs and expenses which arise out of, relate to or result from any use of this software by user.
+
+**THIS IS ALPHA QUALITY SOFTWARE FOR RESEARCH AND COMPETITION PURPOSES ONLY. THIS IS NOT A PRODUCT.
+YOU ARE RESPONSIBLE FOR COMPLYING WITH LOCAL LAWS AND REGULATIONS.
+NO WARRANTY EXPRESSED OR IMPLIED.**
+</details>
diff --git a/hydrus_software_stack.egg-info/SOURCES.txt b/hydrus_software_stack.egg-info/SOURCES.txt
new file mode 100644
index 0000000..c0797ff
--- /dev/null
+++ b/hydrus_software_stack.egg-info/SOURCES.txt
@@ -0,0 +1,45 @@
+LICENSE
+README.md
+pyproject.toml
+setup.py
+autonomy/__init__.py
+autonomy/arduino_simulator.py
+autonomy/setup.py
+autonomy/test_controller.py
+autonomy/scripts/__init__.py
+autonomy/scripts/profiler/__init__.py
+autonomy/scripts/profiler/profiling_decorators.py
+autonomy/scripts/profiler/profiling_test.py
+autonomy/scripts/profiler/ros_profiler.py
+autonomy/scripts/profiler/ros_profiler_demo.py
+autonomy/scripts/web/__init__.py
+autonomy/scripts/web/detection_viewer.py
+autonomy/src/__init__.py
+autonomy/src/api_server.py
+autonomy/src/controllers.py
+autonomy/src/custom_types.py
+autonomy/src/cv_publishers.py
+autonomy/src/mission_planner/__init__.py
+autonomy/src/mission_planner/base_mission.py
+autonomy/src/mission_planner/gate_mission.py
+autonomy/src/mission_planner/gate_mission_tester.py
+autonomy/src/mission_planner/gate_tester_visualizer.py
+autonomy/src/mission_planner/mission_manager.py
+autonomy/src/mission_planner/mission_tree.py
+autonomy/src/mission_planner/prequalification_mission.py
+autonomy/src/mission_planner/slalom_mission.py
+autonomy/src/mission_planner/slalom_visualizer.py
+autonomy/src/mission_planner/tagging_mission.py
+autonomy/src/mission_planner/tagging_mission_test.py
+autonomy/src/mission_planner/task_parameters.py
+autonomy/src/mission_planner/test_gate_mission.py
+autonomy/src/mission_planner/test_slalom.py
+autonomy/src/mission_planner/test_slalom_integration.py
+autonomy/src/mission_planner/types.py
+hydrus_software_stack.egg-info/PKG-INFO
+hydrus_software_stack.egg-info/SOURCES.txt
+hydrus_software_stack.egg-info/dependency_links.txt
+hydrus_software_stack.egg-info/entry_points.txt
+hydrus_software_stack.egg-info/not-zip-safe
+hydrus_software_stack.egg-info/requires.txt
+hydrus_software_stack.egg-info/top_level.txt
\ No newline at end of file
diff --git a/hydrus_software_stack.egg-info/dependency_links.txt b/hydrus_software_stack.egg-info/dependency_links.txt
new file mode 100644
index 0000000..8b13789
--- /dev/null
+++ b/hydrus_software_stack.egg-info/dependency_links.txt
@@ -0,0 +1 @@
+
diff --git a/hydrus_software_stack.egg-info/entry_points.txt b/hydrus_software_stack.egg-info/entry_points.txt
new file mode 100644
index 0000000..f06db19
--- /dev/null
+++ b/hydrus_software_stack.egg-info/entry_points.txt
@@ -0,0 +1,2 @@
+[console_scripts]
+hydrus-depth-estimator = autonomy.src.computer_vision.depth_estimation:main
diff --git a/hydrus_software_stack.egg-info/not-zip-safe b/hydrus_software_stack.egg-info/not-zip-safe
new file mode 100644
index 0000000..8b13789
--- /dev/null
+++ b/hydrus_software_stack.egg-info/not-zip-safe
@@ -0,0 +1 @@
+
diff --git a/hydrus_software_stack.egg-info/requires.txt b/hydrus_software_stack.egg-info/requires.txt
new file mode 100644
index 0000000..3af6dfa
--- /dev/null
+++ b/hydrus_software_stack.egg-info/requires.txt
@@ -0,0 +1,33 @@
+opencv-python
+numpy
+matplotlib
+requests
+colorama
+pyserial
+fastapi
+Flask
+black>=23.0.0
+isort>=5.12.0
+flake8>=6.0.0
+pre-commit>=3.0.0
+mypy>=1.0.0
+
+[all]
+onnx
+onnxruntime-gpu
+onnxscript
+onnxslim
+torch
+torchvision
+tqdm
+typer
+
+[depth-estimation]
+onnx
+onnxruntime-gpu
+onnxscript
+onnxslim
+torch
+torchvision
+tqdm
+typer
diff --git a/hydrus_software_stack.egg-info/top_level.txt b/hydrus_software_stack.egg-info/top_level.txt
new file mode 100644
index 0000000..342156a
--- /dev/null
+++ b/hydrus_software_stack.egg-info/top_level.txt
@@ -0,0 +1 @@
+autonomy
diff --git a/scripts/cli.py b/scripts/cli.py
index e5d849b..0b1fc61 100755
--- a/scripts/cli.py
+++ b/scripts/cli.py
@@ -6,6 +6,7 @@
 from .commands.ros import ros_app
 from .commands.test import test_app
 from .commands.tmux import tmux_command
+from .commands.todo import todo_app
 
 app = typer.Typer()
 
@@ -19,6 +20,7 @@
 app.add_typer(ros_app, name="ros", help="ROS workspace and utilities management")
 app.add_typer(test_app, name="test", help="Test suite management and execution")
 app.add_typer(tmux_command, name="tmux", help="Tmux session management commands")
+app.add_typer(todo_app, name="todo", help="TODO and FIXME tracker for code analysis")
 
 
 @app.command()
diff --git a/scripts/commands/todo.py b/scripts/commands/todo.py
new file mode 100644
index 0000000..196a1c3
--- /dev/null
+++ b/scripts/commands/todo.py
@@ -0,0 +1,429 @@
+#!/usr/bin/env python3
+"""
+TODO and FIXME tracker for the Hydrus Software Stack.
+
+This module provides functionality to scan the repository for TODO, FIXME,
+HACK, NOTE, and XXX comments, generate reports, and optionally link them
+to GitHub issues.
+"""
+
+import json
+import os
+import re
+from collections import defaultdict
+from pathlib import Path
+from typing import Dict, List, Optional, Tuple
+
+import typer
+from rich.console import Console
+from rich.table import Table
+
+# Create the todo subcommand app
+todo_app = typer.Typer()
+
+console = Console()
+
+# Default file extensions to search
+DEFAULT_EXTENSIONS = [
+    '.py', '.cpp', '.c', '.h', '.hpp', '.js', '.ts', '.md', '.yaml', '.yml',
+    '.launch', '.xml', '.sh', '.bash', '.json', '.txt', '.rst'
+]
+
+# Default comment patterns to search for
+DEFAULT_PATTERNS = ['TODO', 'FIXME', 'HACK', 'NOTE', 'XXX', 'BUG']
+
+
+class TodoItem:
+    """Represents a TODO/FIXME item found in the codebase."""
+    
+    def __init__(self, file_path: str, line_number: int, content: str, 
+                 pattern: str, context: str = "", issue_number: Optional[int] = None):
+        self.file_path = file_path
+        self.line_number = line_number
+        self.content = content.strip()
+        self.pattern = pattern
+        self.context = context.strip()
+        self.issue_number = issue_number
+        
+    def to_dict(self) -> dict:
+        """Convert to dictionary for JSON serialization."""
+        return {
+            'file_path': self.file_path,
+            'line_number': self.line_number,
+            'content': self.content,
+            'pattern': self.pattern,
+            'context': self.context,
+            'issue_number': self.issue_number
+        }
+
+
+class TodoTracker:
+    """Main class for scanning and tracking TODO items."""
+    
+    def __init__(self, root_path: str = ".", 
+                 extensions: List[str] = None,
+                 patterns: List[str] = None):
+        self.root_path = Path(root_path).resolve()
+        self.extensions = extensions or DEFAULT_EXTENSIONS
+        self.patterns = patterns or DEFAULT_PATTERNS
+        self.exclude_dirs = {'.git', '__pycache__', '.venv', 'venv', 'node_modules', 
+                           'build', 'dist', '.pytest_cache', 'hydrus_software_stack.egg-info'}
+        
+    def _should_exclude_path(self, path: Path) -> bool:
+        """Check if a path should be excluded from scanning."""
+        for part in path.parts:
+            if part in self.exclude_dirs or part.startswith('.'):
+                return True
+        
+        # Exclude the todo.py file itself to avoid self-references
+        if path.name == 'todo.py':
+            return True
+            
+        return False
+    
+    def _extract_issue_number(self, content: str) -> Optional[int]:
+        """Extract GitHub issue number from comment if present."""
+        # Look for patterns like #123, issue #123, fixes #123, etc.
+        issue_patterns = [
+            r'#(\d+)',
+            r'issue\s*#?(\d+)',
+            r'fixes?\s*#?(\d+)', 
+            r'closes?\s*#?(\d+)',
+            r'resolves?\s*#?(\d+)'
+        ]
+        
+        for pattern in issue_patterns:
+            match = re.search(pattern, content, re.IGNORECASE)
+            if match:
+                return int(match.group(1))
+        return None
+    
+    def _scan_file(self, file_path: Path) -> List[TodoItem]:
+        """Scan a single file for TODO patterns."""
+        todos = []
+        
+        try:
+            with open(file_path, 'r', encoding='utf-8', errors='ignore') as f:
+                lines = f.readlines()
+                
+            for line_num, line in enumerate(lines, 1):
+                line_clean = line.strip()
+                if not line_clean:
+                    continue
+                    
+                # Check for any of our patterns
+                for pattern in self.patterns:
+                    # Create case-insensitive pattern matching for comment-style TODO/FIXME
+                    # Look for the pattern preceded by comment markers and optionally followed by a colon
+                    regex_pattern = rf'(?i)(?://|#|\*|<!--)\s*{pattern}(?:\s*:?\s*(.*))?'
+                    match = re.search(regex_pattern, line_clean)
+                    
+                    if match:
+                        content = match.group(1) if match.group(1) else line_clean
+                        issue_number = self._extract_issue_number(content)
+                        
+                        # Get context (previous and next line if available)
+                        context_lines = []
+                        if line_num > 1:
+                            context_lines.append(f"{line_num-1}: {lines[line_num-2].strip()}")
+                        context_lines.append(f"{line_num}: {line.strip()}")
+                        if line_num < len(lines):
+                            context_lines.append(f"{line_num+1}: {lines[line_num].strip()}")
+                        
+                        context = "\n".join(context_lines)
+                        
+                        todo_item = TodoItem(
+                            file_path=str(file_path.relative_to(self.root_path)),
+                            line_number=line_num,
+                            content=content,
+                            pattern=pattern.upper(),
+                            context=context,
+                            issue_number=issue_number
+                        )
+                        todos.append(todo_item)
+                        break  # Only match one pattern per line
+                        
+        except Exception as e:
+            console.print(f"[yellow]Warning: Could not read {file_path}: {e}[/yellow]")
+            
+        return todos
+    
+    def scan_repository(self) -> List[TodoItem]:
+        """Scan the entire repository for TODO items."""
+        todos = []
+        
+        for root, dirs, files in os.walk(self.root_path):
+            root_path = Path(root)
+            
+            # Filter out excluded directories
+            dirs[:] = [d for d in dirs if not self._should_exclude_path(root_path / d)]
+            
+            for file in files:
+                file_path = root_path / file
+                
+                # Check if file has a supported extension
+                if file_path.suffix.lower() in self.extensions:
+                    if not self._should_exclude_path(file_path):
+                        todos.extend(self._scan_file(file_path))
+                        
+        return todos
+    
+    def generate_report(self, todos: List[TodoItem]) -> Dict:
+        """Generate a comprehensive report from TODO items."""
+        report = {
+            'summary': {
+                'total_todos': len(todos),
+                'by_pattern': defaultdict(int),
+                'by_directory': defaultdict(int),
+                'by_file_type': defaultdict(int),
+                'with_issues': 0
+            },
+            'todos': [todo.to_dict() for todo in todos]
+        }
+        
+        for todo in todos:
+            # Count by pattern
+            report['summary']['by_pattern'][todo.pattern] += 1
+            
+            # Count by directory
+            dir_path = os.path.dirname(todo.file_path) or '.'
+            report['summary']['by_directory'][dir_path] += 1
+            
+            # Count by file type
+            ext = Path(todo.file_path).suffix or 'no_extension'
+            report['summary']['by_file_type'][ext] += 1
+            
+            # Count items with issue references
+            if todo.issue_number:
+                report['summary']['with_issues'] += 1
+                
+        # Convert defaultdicts to regular dicts for JSON serialization
+        report['summary']['by_pattern'] = dict(report['summary']['by_pattern'])
+        report['summary']['by_directory'] = dict(report['summary']['by_directory'])
+        report['summary']['by_file_type'] = dict(report['summary']['by_file_type'])
+        
+        return report
+
+
+def _print_summary_table(report: Dict):
+    """Print a summary table to the console."""
+    summary = report['summary']
+    
+    # Overall summary
+    console.print(f"\n[bold cyan]📋 TODO Tracker Summary[/bold cyan]")
+    console.print(f"Total items found: [bold]{summary['total_todos']}[/bold]")
+    console.print(f"Items with GitHub issues: [bold]{summary['with_issues']}[/bold]")
+    
+    # Pattern breakdown
+    if summary['by_pattern']:
+        console.print(f"\n[bold yellow]🏷️  By Pattern:[/bold yellow]")
+        pattern_table = Table()
+        pattern_table.add_column("Pattern", style="cyan")
+        pattern_table.add_column("Count", style="magenta")
+        
+        for pattern, count in sorted(summary['by_pattern'].items(), 
+                                   key=lambda x: x[1], reverse=True):
+            pattern_table.add_row(pattern, str(count))
+        console.print(pattern_table)
+    
+    # Directory breakdown  
+    if summary['by_directory']:
+        console.print(f"\n[bold yellow]📁 By Directory:[/bold yellow]")
+        dir_table = Table()
+        dir_table.add_column("Directory", style="cyan")
+        dir_table.add_column("Count", style="magenta")
+        
+        for directory, count in sorted(summary['by_directory'].items(), 
+                                     key=lambda x: x[1], reverse=True):
+            dir_table.add_row(directory, str(count))
+        console.print(dir_table)
+
+
+def _print_detailed_todos(todos: List[TodoItem], limit: Optional[int] = None):
+    """Print detailed TODO items."""
+    if not todos:
+        console.print("[green]🎉 No TODO items found![/green]")
+        return
+        
+    console.print(f"\n[bold cyan]📝 TODO Items Detail:[/bold cyan]")
+    
+    displayed_todos = todos[:limit] if limit else todos
+    
+    for i, todo in enumerate(displayed_todos, 1):
+        console.print(f"\n[bold]{i}. {todo.pattern}[/bold] in [cyan]{todo.file_path}[/cyan]:[magenta]{todo.line_number}[/magenta]")
+        console.print(f"   💬 {todo.content}")
+        
+        if todo.issue_number:
+            console.print(f"   🔗 Related to issue #{todo.issue_number}")
+            
+    if limit and len(todos) > limit:
+        console.print(f"\n[dim]... and {len(todos) - limit} more items. Use --limit to see more.[/dim]")
+
+
+@todo_app.command("scan")
+def scan_todos(
+    path: str = typer.Option(".", "--path", "-p", help="Path to scan (default: current directory)"),
+    patterns: str = typer.Option(
+        ",".join(DEFAULT_PATTERNS), 
+        "--patterns", 
+        help="Comma-separated list of patterns to search for"
+    ),
+    extensions: str = typer.Option(
+        ",".join(DEFAULT_EXTENSIONS),
+        "--extensions", "-e",
+        help="Comma-separated list of file extensions to scan"
+    ),
+    output_format: str = typer.Option(
+        "console", 
+        "--format", "-f",
+        help="Output format: console, json, markdown"
+    ),
+    output_file: Optional[str] = typer.Option(
+        None,
+        "--output", "-o", 
+        help="Output file path (optional)"
+    ),
+    limit: Optional[int] = typer.Option(
+        None,
+        "--limit", "-l",
+        help="Limit number of detailed items to show"
+    ),
+    no_summary: bool = typer.Option(
+        False,
+        "--no-summary",
+        help="Skip summary output"
+    )
+):
+    """Scan repository for TODO, FIXME, and other patterns."""
+    
+    pattern_list = [p.strip().upper() for p in patterns.split(",") if p.strip()]
+    extension_list = [e.strip() if e.startswith('.') else f'.{e.strip()}' 
+                     for e in extensions.split(",") if e.strip()]
+    
+    console.print(f"[bold green]🔍 Scanning {path} for patterns: {', '.join(pattern_list)}[/bold green]")
+    
+    tracker = TodoTracker(path, extension_list, pattern_list)
+    todos = tracker.scan_repository()
+    report = tracker.generate_report(todos)
+    
+    # Output based on format
+    if output_format.lower() == "json":
+        output_content = json.dumps(report, indent=2)
+        if output_file:
+            with open(output_file, 'w') as f:
+                f.write(output_content)
+            console.print(f"[green]✅ JSON report saved to {output_file}[/green]")
+        else:
+            console.print(output_content)
+            
+    elif output_format.lower() == "markdown":
+        # Generate markdown output
+        md_lines = [
+            "# TODO Tracker Report",
+            f"\nGenerated on: {__import__('datetime').datetime.now().strftime('%Y-%m-%d %H:%M:%S')}",
+            f"\n## Summary",
+            f"- **Total items:** {report['summary']['total_todos']}",
+            f"- **Items with GitHub issues:** {report['summary']['with_issues']}"
+        ]
+        
+        if report['summary']['by_pattern']:
+            md_lines.append("\n### By Pattern")
+            for pattern, count in sorted(report['summary']['by_pattern'].items(), 
+                                       key=lambda x: x[1], reverse=True):
+                md_lines.append(f"- **{pattern}:** {count}")
+                
+        if report['summary']['by_directory']:
+            md_lines.append("\n### By Directory")
+            for directory, count in sorted(report['summary']['by_directory'].items(), 
+                                         key=lambda x: x[1], reverse=True):
+                md_lines.append(f"- **{directory}:** {count}")
+        
+        if todos:
+            md_lines.append("\n## Detailed Items")
+            for todo in todos:
+                md_lines.append(f"\n### {todo.pattern} in `{todo.file_path}:{todo.line_number}`")
+                md_lines.append(f"{todo.content}")
+                if todo.issue_number:
+                    md_lines.append(f"*Related to issue #{todo.issue_number}*")
+        
+        output_content = "\n".join(md_lines)
+        if output_file:
+            with open(output_file, 'w') as f:
+                f.write(output_content)
+            console.print(f"[green]✅ Markdown report saved to {output_file}[/green]")
+        else:
+            console.print(output_content)
+            
+    else:  # console format
+        if not no_summary:
+            _print_summary_table(report)
+        _print_detailed_todos(todos, limit)
+        
+        if output_file:
+            # Save console output as text
+            with open(output_file, 'w') as f:
+                f.write(f"TODO Tracker Report - {__import__('datetime').datetime.now()}\n")
+                f.write("=" * 50 + "\n\n")
+                f.write(f"Total items: {report['summary']['total_todos']}\n")
+                f.write(f"Items with issues: {report['summary']['with_issues']}\n\n")
+                
+                for todo in todos:
+                    f.write(f"{todo.pattern} in {todo.file_path}:{todo.line_number}\n")
+                    f.write(f"  {todo.content}\n")
+                    if todo.issue_number:
+                        f.write(f"  Related to issue #{todo.issue_number}\n")
+                    f.write("\n")
+            console.print(f"[green]✅ Text report saved to {output_file}[/green]")
+
+
+@todo_app.command("stats")
+def show_stats(
+    path: str = typer.Option(".", "--path", "-p", help="Path to analyze"),
+    patterns: str = typer.Option(
+        ",".join(DEFAULT_PATTERNS), 
+        "--patterns", 
+        help="Comma-separated list of patterns to search for"
+    )
+):
+    """Show statistics about TODO items in the repository."""
+    
+    pattern_list = [p.strip().upper() for p in patterns.split(",") if p.strip()]
+    
+    tracker = TodoTracker(path, patterns=pattern_list)
+    todos = tracker.scan_repository()
+    report = tracker.generate_report(todos)
+    
+    _print_summary_table(report)
+
+
+@todo_app.command("issues")
+def show_linked_issues(
+    path: str = typer.Option(".", "--path", "-p", help="Path to scan")
+):
+    """Show TODO items that reference GitHub issues."""
+    
+    tracker = TodoTracker(path)
+    todos = tracker.scan_repository()
+    
+    linked_todos = [todo for todo in todos if todo.issue_number]
+    
+    if not linked_todos:
+        console.print("[yellow]No TODO items with GitHub issue references found.[/yellow]")
+        return
+        
+    console.print(f"[bold cyan]🔗 TODO Items linked to GitHub Issues ({len(linked_todos)} found):[/bold cyan]")
+    
+    # Group by issue number
+    by_issue = defaultdict(list)
+    for todo in linked_todos:
+        by_issue[todo.issue_number].append(todo)
+    
+    for issue_num in sorted(by_issue.keys()):
+        console.print(f"\n[bold magenta]Issue #{issue_num}:[/bold magenta]")
+        for todo in by_issue[issue_num]:
+            console.print(f"  📁 {todo.file_path}:{todo.line_number} ({todo.pattern})")
+            console.print(f"     💬 {todo.content}")
+
+
+if __name__ == "__main__":
+    todo_app()
\ No newline at end of file