@paths.design/caws-cli 7.0.1 → 7.0.3

package/dist/templates/scripts/v3/analysis/todo_analyzer.py

@@ -0,0 +1,1997 @@
+#!/usr/bin/env python3
+"""
+Hidden TODO Pattern Analyzer
+
+@description: Hidden TODO analyzer with better accuracy, context awareness,
+and reduced false positives. Uses semantic analysis and context clues to
+distinguish between hidden TODOs and legitimate documentation.
+
+@parameters:
+- root_dir: The root directory to analyze.
+- min_confidence: The minimum confidence score to consider a TODO.
+- output_json: The path to save the JSON report.
+- output_md: The path to save the Markdown report.
+- verbose: Whether to print verbose output.
+- enable_code_stub_scan: Whether to enable code stub detection heuristics.
+
+For an example on how to improve the clarity of the TODOs that were found, see the following snippet:
+```rust
+    // TODO: Implement ANE initialization with the following requirements:
+    // 1. ANE initialization: Initialize Apple Neural Engine framework and resources
+    //    - Set up ANE device and computation resources
+    //    - Initialize ANE neural network computation capabilities
+    //    - Handle ANE initialization error handling and recovery
+    // 2. ANE resource setup: Set up ANE resources and memory
+    //    - Allocate ANE memory and computation buffers
+    //    - Set up ANE resource management and optimization
+    //    - Implement ANE resource validation and verification
+    // 3. ANE configuration: Configure ANE settings and parameters
+    //    - Set up ANE computation parameters and settings
+    //    - Configure ANE performance and optimization settings
+    //    - Handle ANE configuration validation and verification
+    // 4. ANE monitoring: Set up ANE monitoring and management
+    //    - Initialize ANE performance monitoring
+    //    - Set up ANE resource monitoring and management
+    //    - Implement ANE monitoring and reporting
+```
+
+The analyzer now includes engineering-grade TODO format suggestions. Use --engineering-suggestions to get
+recommendations for upgrading TODOs to the CAWS-compliant format with completion checklists, acceptance
+criteria, dependencies, and governance information.
+
+@author: @darianrosebrook
+@date: 2025-10-17
+@version: 2.0.0
+"""
+
+import os
+import re
+import json
+from pathlib import Path
+from collections import defaultdict, Counter
+from typing import Any, Dict, List, Set, Tuple, Optional
+
+
+class HiddenTodoAnalyzer:
+    def __init__(self, root_dir: str, *, enable_code_stub_scan: bool = True):
+        self.root_dir = Path(root_dir)
+        self.enable_code_stub_scan = enable_code_stub_scan
+
+        # Language-specific comment patterns
+        self.language_patterns = {
+            'rust': {
+                'extensions': ['.rs'],
+                'single_line': r'^\s*//',
+                'multi_line_start': r'^\s*/\*',
+                'multi_line_end': r'\*/',
+            },
+            'javascript': {
+                'extensions': ['.js', '.mjs', '.cjs'],
+                'single_line': r'^\s*//',
+                'multi_line_start': r'^\s*/\*',
+                'multi_line_end': r'\*/',
+            },
+            'typescript': {
+                'extensions': ['.ts', '.tsx', '.mts', '.cts'],
+                'single_line': r'^\s*//',
+                'multi_line_start': r'^\s*/\*',
+                'multi_line_end': r'\*/',
+            },
+            'python': {
+                'extensions': ['.py', '.pyi'],
+                'single_line': r'^\s*#',
+                'multi_line_start': r'^\s*"""',
+                'multi_line_end': r'"""',
+            },
+            'go': {
+                'extensions': ['.go'],
+                'single_line': r'^\s*//',
+                'multi_line_start': r'^\s*/\*',
+                'multi_line_end': r'\*/',
+            },
+            'java': {
+                'extensions': ['.java'],
+                'single_line': r'^\s*//',
+                'multi_line_start': r'^\s*/\*',
+                'multi_line_end': r'\*/',
+            },
+            'csharp': {
+                'extensions': ['.cs'],
+                'single_line': r'^\s*//',
+                'multi_line_start': r'^\s*/\*',
+                'multi_line_end': r'\*/',
+            },
+            'cpp': {
+                'extensions': ['.cpp', '.cc', '.cxx', '.c++', '.hpp', '.h', '.hxx'],
+                'single_line': r'^\s*//',
+                'multi_line_start': r'^\s*/\*',
+                'multi_line_end': r'\*/',
+            },
+            'c': {
+                'extensions': ['.c'],
+                'single_line': r'^\s*//',
+                'multi_line_start': r'^\s*/\*',
+                'multi_line_end': r'\*/',
+            },
+            'php': {
+                'extensions': ['.php'],
+                'single_line': r'^\s*//',
+                'multi_line_start': r'^\s*/\*',
+                'multi_line_end': r'\*/',
+            },
+            'ruby': {
+                'extensions': ['.rb'],
+                'single_line': r'^\s*#',
+                'multi_line_start': r'^\s*=begin',
+                'multi_line_end': r'=end',
+            },
+            'shell': {
+                'extensions': ['.sh', '.bash', '.zsh', '.fish'],
+                'single_line': r'^\s*#',
+                'multi_line_start': None,
+                'multi_line_end': None,
+            },
+            'yaml': {
+                'extensions': ['.yaml', '.yml'],
+                'single_line': r'^\s*#',
+                'multi_line_start': None,
+                'multi_line_end': None,
+            },
+            'json': {
+                'extensions': ['.json'],
+                'single_line': None,
+                'multi_line_start': None,
+                'multi_line_end': None,
+            },
+            'markdown': {
+                'extensions': ['.md', '.markdown'],
+                'single_line': r'^\s*<!--',
+                'multi_line_start': r'^\s*<!--',
+                'multi_line_end': r'-->',
+            },
+        }
+
+        # Comprehensive list of file patterns to ignore
+        self.ignored_file_patterns = [
+            # Test files
+            r'\btest\b',
+            r'\btests\b',
+            r'_test\.',
+            r'_tests\.',
+            r'\.test\.',
+            r'\.spec\.',
+            r'\.specs\.',
+
+            # Build artifacts and generated files
+            r'\btarget\b',
+            r'\bbuild\b',
+            r'\bout\b',
+            r'\bdist\b',
+            r'\bbin\b',
+            r'\.next\b',
+            r'generated\.',
+            r'bindgen\.',
+            r'private\.',
+            r'mime_types_generated\.',
+            r'named_entities\.',
+            r'ascii_case_insensitive_html_attributes\.',
+
+            # Package management and dependencies
+            r'\bnode_modules\b',
+            r'package-lock\.json$',
+            r'package\.json$',
+            r'yarn\.lock$',
+            r'pnpm-lock\.yaml$',
+            r'\bvenv\b',
+            r'\bpip\b',
+            r'requirements\.txt$',
+            r'Pipfile$',
+            r'Pipfile\.lock$',
+            r'poetry\.lock$',
+            r'Cargo\.lock$',
+            r'Cargo\.toml$',
+
+            # External libraries and frameworks
+            r'libtorch-cpu',
+            r'libtorch\b',
+            r'\.venv-whisper\b',
+            r'whisper_conversion_env',
+            r'\bsite-packages\b',
+            r'lib/python\d+\.\d+/site-packages',
+            r'whisperkit\b',
+            r'\.build\b',
+
+            # Model and data directories
+            r'models\b',
+            r'\bmodels/',
+            r'temp\.rs$',
+            r'todo_analyzer\.',
+
+            # Version control and IDE
+            r'\.git\b',
+            r'\.github\b',
+            r'\.vscode\b',
+            r'\.idea\b',
+            r'\.DS_Store$',
+            r'\.DS_Store\?$',
+            r'\._',
+            r'\.Spotlight-V100$',
+
+            # Documentation and examples
+            r'\bdocs\b',
+            r'\bexamples\b',
+            r'\bdoc\b',
+            r'\bexample\b',
+
+            # Temporary and cache files
+            r'\bcache\b',
+            r'\btmp\b',
+            r'\btemp\b',
+            r'\.tmp$',
+            r'\.temp$',
+            r'\.cache$',
+            
+            # Coverage and analysis reports
+            r'\bhtmlcov\b',
+            r'\bcoverage\b',
+            r'\.coverage$',
+            r'coverage\.xml$',
+            r'lcov\.info$',
+
+            # OS-specific files
+            r'Thumbs\.db$',
+            r'desktop\.ini$',
+            r'\.fseventsd$',
+            r'\.Trashes$',
+
+            # Language-specific build artifacts
+            r'\.rlib$',
+            r'\.rmeta$',
+            r'\.d$',
+            r'\.pdb$',
+            r'\.o$',
+            r'\.obj$',
+            r'\.exe$',
+            r'\.dll$',
+            r'\.so$',
+            r'\.dylib$',
+            r'\.pyc$',
+            r'\.pyo$',
+            r'__pycache__',
+            r'\.class$',
+            r'\.jar$',
+            r'\.war$',
+            r'\.ear$',
+
+            # Web assets
+            r'\.min\.js$',
+            r'\.min\.css$',
+            r'\.bundle\.js$',
+            r'\.chunk\.js$',
+            r'\.map$',
+
+            # Configuration files (often generated)
+            r'\.env\.local$',
+            r'\.env\.production$',
+            r'\.env\.development$',
+            r'config\.local\.',
+            r'config\.prod\.',
+            r'config\.dev\.',
+            
+            # Logs and reports
+            r'\blogs\b',
+            r'\.log$',
+            r'\breports\b',
+            r'\bartifacts\b',
+            r'\btemp\b',
+            
+            # IDE and editor files
+            r'\.swp$',
+            r'\.swo$',
+            r'~$',
+            r'\.bak$',
+            r'\.backup$',
+
+            # Additional exclusions from user's search
+            r'\.gitignore$',
+            r'\.json$',
+            r'\.md$',
+        ]
+
+        # Explicit TODO patterns (highest priority) - more restrictive
+        self.explicit_todo_patterns = {
+            'explicit_todos': [
+                r'\bTODO\b.*?:',
+                r'\bFIXME\b.*?:',
+                r'\bHACK\b.*?:',
+                r'\bXXX\b.*?:',
+                r'\bTEMP\b.*?:.*?(implement|fix|replace|complete|add)',
+                r'\bTEMPORARY\b.*?:.*?(implement|fix|replace|complete|add)',
+                # User's VSCode search patterns
+                r'\bTODO\b(?!(_|\.|anal|\sanal|s))',
+                r'\bin\s+a\s+real\b(?!(_|\.|anal|\sanal|s))',
+                r'\bsimplified\b(?!(_|\.|anal|\sanal|s))',
+                r'\bfor\s+now\b(?!(_|\.|anal|\sanal|s))',
+            ]
+        }
+
+        # High-confidence hidden TODO patterns (more specific and contextual)
+        self.high_confidence_patterns = {
+            'incomplete_implementation': [
+                r'\bnot\s+yet\s+implemented\b',
+                r'\bmissing\s+implementation\b',
+                r'\bincomplete\s+implementation\b',
+                r'\bpartial\s+implementation\b',
+                r'\bunimplemented\b',
+                r'\bnot\s+done\b',
+                r'\bpending\s+implementation\b',
+                r'\bto\s+be\s+implemented\b',
+                r'\bwill\s+be\s+implemented\b',
+            ],
+            
+            'placeholder_code': [
+                r'\bplaceholder\s+code\b',
+                r'\bplaceholder\s+implementation\b',
+                r'\bplaceholder\s+function\b',
+                r'\bplaceholder\s+value\b',
+                r'\bstub\s+implementation\b',
+                r'\bstub\s+function\b',
+                r'\bdummy\s+implementation\b',
+                r'\bfake\s+implementation\b',
+                r'\bexample\s+implementation\b',
+                r'\bdemo\s+implementation\b',
+                r'\bsample\s+implementation\b',
+                r'\btemplate\s+implementation\b',
+                r'\bstub\s+implementation\s+for\b',
+                r'\bsimplified\s+.*?\s+calculation\b',
+                r'\bsimplified\s+.*?\s+implementation\b',
+                r'\bfor\s+now\b.*?(just|simply|only)\s+(concatenate|return|use)',
+                r'\bin\s+practice\b.*?(would|should|will)\s+(intelligently|properly|correctly)',
+            ],
+            
+            'temporary_solutions': [
+                r'\btemporary\s+solution\b',
+                r'\btemporary\s+fix\b',
+                r'\btemporary\s+workaround\b',
+                r'\bquick\s+fix\b',
+                r'\bquick\s+hack\b',
+                r'\bworkaround\b',
+                r'\bhack\b.*?(fix|solution)',
+                r'\bpatch\b.*?(fix|solution)',
+                r'\bbypass\b.*?(fix|solution)',
+            ],
+            
+            'hardcoded_values': [
+                r'\bhardcoded\s+value\b',
+                r'\bhard-coded\s+value\b',
+                r'\bmagic\s+number\b',
+                r'\bmagic\s+string\b',
+                r'\bconstant\s+value\b.*?(replace|change|make\s+configurable)',
+                r'\bdefault\s+value\b.*?(replace|change|make\s+configurable)',
+                r'\bhardcoded\s+return\s+value\b',
+                r'\bhardcoded\s+result\b',
+                r'\bhardcoded\s+efficiency\b',
+                r'\bhardcoded\s+percentage\b',
+            ],
+            
+            'future_improvements': [
+                r'\bin\s+production\b.*?(implement|add|fix)',
+                r'\bin\s+a\s+real\s+implementation\b',
+                r'\beventually\b.*?(implement|add|fix)',
+                r'\blater\b.*?(implement|add|fix)',
+                r'\bshould\s+be\b.*?(implemented|added|fixed)',
+                r'\bwould\s+be\b.*?(implemented|added|fixed)',
+                r'\bcould\s+be\b.*?(implemented|added|fixed)',
+                r'\bwill\s+be\b.*?(implemented|added|fixed)',
+                r'\bin\s+practice\b.*?(would|should|will)\s+(analyze|merge|intelligently)',
+                r'\bin\s+practice\b.*?(this\s+would|this\s+should|this\s+will)',
+                r'\bfor\s+now\b.*?(just|simply|only)',
+            ],
+        }
+
+        # Medium-confidence patterns (context-dependent)
+        self.medium_confidence_patterns = {
+            'basic_implementations': [
+                r'\bbasic\s+implementation\b.*?(improve|enhance|replace)',
+                r'\bsimple\s+implementation\b.*?(improve|enhance|replace)',
+                r'\bminimal\s+implementation\b.*?(improve|enhance|replace)',
+                r'\bnaive\s+implementation\b.*?(improve|enhance|replace)',
+                r'\brough\s+implementation\b.*?(improve|enhance|replace)',
+                r'\bcrude\s+implementation\b.*?(improve|enhance|replace)',
+            ],
+        }
+
+        # Patterns to exclude (legitimate technical terms and documentation)
+        self.exclusion_patterns = [
+            # Performance and optimization terms
+            r'\bperformance\s+monitoring\b',
+            r'\bperformance\s+optimization\b',
+            r'\bperformance\s+analysis\b',
+            r'\bperformance\s+benchmark\b',
+            r'\boptimize\s+for\s+performance\b',
+            r'\boptimization\s+strategy\b',
+            r'\befficient\s+implementation\b',
+            
+            # Simulation and testing terms
+            r'\bsimulation\s+environment\b',
+            r'\bsimulate\s+network\s+conditions\b',
+            r'\bsimulate\s+.*?(behavior|response|data)\b',
+            r'\bsimulation\s+.*?(mode|environment)\b',
+            
+            # Fallback and error handling
+            r'\bfallback\s+mechanism\b',
+            r'\bfallback\s+strategy\b',
+            r'\bfallback\s+to\b.*?(method|function|implementation)',
+            
+            # Authentication and security
+            r'\bbasic\s+authentication\b',
+            r'\bbasic\s+configuration\b',
+            r'\bsimple\s+interface\b',
+            r'\bsimple\s+api\b',
+            
+            # Mock and testing
+            r'\bmock\s+object\b',
+            r'\bmock\s+service\b',
+            r'\bmock\s+data\b',
+            r'\bmock\s+response\b',
+            
+            # Documentation patterns
+            r'\bcurrent\s+implementation\b.*?(uses|provides|supports)',
+            r'\bthis\s+implementation\b.*?(uses|provides|supports)',
+            r'\bthe\s+implementation\b.*?(uses|provides|supports)',
+            r'\bimplementation\s+uses\b',
+            r'\bimplementation\s+provides\b',
+            r'\bimplementation\s+supports\b',
+            
+            # Architecture and design documentation
+            r'\barchitecture\s+note\b',
+            r'\bdesign\s+note\b',
+            r'\bpattern\s+note\b',
+            r'\bdependency\s+injection\b',
+            r'\bresource\s+management\b',
+            
+            # Console and logging
+            r'console\.(log|warn|error|info)',
+            r'\blogging\s+implementation\b',
+            
+            # TODO system documentation (false positives when documenting TODO system itself)
+            r'\btodo\s+template\s+system\b',
+            r'\btodo\s+template\b',
+            r'\btodo\s+instance\b',
+            r'\btodo\s+step\b',
+            r'\btodo\s+integration\b',
+            r'\btodo\s+system\b',
+            r'\btodotemplate\b',
+            r'\btodoinstance\b',
+            r'\btodostep\b',
+            r'\btodointegration\b',
+            r'\btodotemplatesystem\b',
+            r'\btodoprogress\b',
+            r'\btododependency\b',
+            r'\btodoqualityenforcer\b',
+            r'\btodoworkflowhooks\b',
+            r'\btodostatus\b',
+            r'\btodopriority\b',
+            r'\btodosteptype\b',
+            # Rust doc comment patterns when mentioning TODO system types
+            r'^\s*//[!]/.*\btodo\b.*(template|instance|step|integration|system)\b',
+            r'^\s*///.*\btodo\b.*(template|instance|step|integration|system)\b',
+        ]
+
+        # Engineering-grade TODO template patterns (for suggestions)
+        self.engineering_grade_patterns = {
+            'completion_checklist': [
+                r'COMPLETION CHECKLIST:',
+                r'COMPLETION CRITERIA:',
+                r'CHECKLIST:',
+                r'\[ \]',
+                r'\[x\]',
+            ],
+            'acceptance_criteria': [
+                r'ACCEPTANCE CRITERIA:',
+                r'ACCEPTANCE:',
+                r'CRITERIA:',
+                r'REQUIREMENTS:',
+            ],
+            'dependencies': [
+                r'DEPENDENCIES:',
+                r'DEPENDS ON:',
+                r'REQUIRES:',
+                r'BLOCKED BY:',
+            ],
+            'governance': [
+                r'CAWS TIER:',
+                r'TIER:',
+                r'PRIORITY:',
+                r'BLOCKING:',
+                r'ESTIMATED EFFORT:',
+                r'EFFORT:',
+                r'GOVERNANCE:',
+            ],
+            'structured_format': [
+                r'// TODO:.*?\n.*?//\s*COMPLETION',
+                r'// TODO:.*?\n.*?//\s*ACCEPTANCE',
+                r'// TODO:.*?\n.*?//\s*DEPENDENCIES',
+            ]
+        }
+
+        # Patterns that suggest a TODO needs engineering-grade format
+        self.needs_engineering_format_patterns = {
+            'vague_todos': [
+                r'\bTODO\b.*?(implement|add|fix|complete|do)\b.*?$',
+                r'\bFIXME\b.*?(implement|add|fix|complete|do)\b.*?$',
+                r'\bHACK\b.*?(implement|add|fix|complete|do)\b.*?$',
+            ],
+            'missing_structure': [
+                r'\bTODO\b.*?(?!.*COMPLETION CHECKLIST)(?!.*ACCEPTANCE CRITERIA)(?!.*DEPENDENCIES).*$',
+                r'\bFIXME\b.*?(?!.*COMPLETION CHECKLIST)(?!.*ACCEPTANCE CRITERIA)(?!.*DEPENDENCIES).*$',
+            ],
+            'single_line_todos': [
+                r'^\s*//\s*TODO\b.*?$',
+                r'^\s*#\s*TODO\b.*?$',
+            ],
+            'business_critical': [
+                r'\bTODO\b.*?(auth|security|payment|billing|database|persist|save|store)\b',
+                r'\bTODO\b.*?(critical|important|essential|required|must)\b',
+                r'\bFIXME\b.*?(auth|security|payment|billing|database|persist|save|store)\b',
+            ]
+        }
+
+        # Context clues that suggest documentation rather than TODO
+        self.documentation_indicators = [
+            r'@param',
+            r'@return',
+            r'@throws',
+            r'@author',
+            r'@date',
+            r'@version',
+            r'@description',
+            r'@example',
+            r'@see',
+            r'@since',
+            r'@deprecated',
+            r'\*\s*\*\s*\*',  # JSDoc comment blocks
+            r'^\s*/\*\*',     # Start of JSDoc
+            r'^\s*# ',        # Markdown headers
+            r'^\s*## ',       # Markdown subheaders
+            r'^\s*### ',      # Markdown sub-subheaders
+        ]
+
+        # Context clues that suggest actual TODO
+        self.todo_indicators = [
+            r'\btodo\b',
+            r'\bfixme\b',
+            r'\bhack\b',
+            r'\bneed\s+to\b',
+            r'\bshould\s+be\b',
+            r'\bmust\s+be\b',
+            r'\bhas\s+to\b',
+            r'\brequired\s+to\b',
+            r'\bmissing\b',
+            r'\bincomplete\b',
+            r'\bpartial\b',
+            r'\bunfinished\b',
+            r'\bwork\s+in\s+progress\b',
+            r'\bwip\b',
+        ]
+
+        self.results = defaultdict(list)
+        self.file_stats = defaultdict(int)
+        self.pattern_stats = defaultdict(int)
+
+        # Heuristic code stub patterns keyed by language
+        self.code_stub_patterns = {
+            'python': {
+                'function_stub': re.compile(r'^\s*def\s+\w+\(.*\):'),
+                'pass_stmt': re.compile(r'^\s*pass\s*$'),
+                'ellipsis_stmt': re.compile(r'^\s*\.\.\.\s*$'),
+                'raise_not_impl': re.compile(r'^\s*raise\s+NotImplementedError'),
+                'return_not_impl': re.compile(r'^\s*return\s+(None|NotImplemented)\s*$'),
+            },
+            'javascript': {
+                'function_stub': re.compile(r'^\s*(async\s+)?function\s+\w+\(.*\)\s*{'),
+                'arrow_stub': re.compile(r'^\s*const\s+\w+\s*=\s*\(.*\)\s*=>\s*{'),
+                'throw_not_impl': re.compile(r"^\s*throw\s+new\s+Error\((\"|')(TODO|Not\s+Implemented)"),
+                'return_todo': re.compile(r"^\s*return\s+(null|undefined);\s*//\s*TODO"),
+            },
+            'typescript': {
+                'function_stub': re.compile(r'^\s*(async\s+)?function\s+\w+\(.*\)\s*{'),
+                'arrow_stub': re.compile(r'^\s*const\s+\w+\s*=\s*\(.*\)\s*=>\s*{'),
+                'throw_not_impl': re.compile(r"^\s*throw\s+new\s+Error\((\"|')(TODO|Not\s+Implemented)"),
+                'return_todo': re.compile(r"^\s*return\s+(null|undefined);\s*//\s*TODO"),
+            },
+        }
+
+    def should_ignore_file(self, file_path: Path) -> bool:
+        """Check if a file should be ignored based on patterns."""
+        path_str = str(file_path)
+
+        # Check against ignored patterns
+        for pattern in self.ignored_file_patterns:
+            if re.search(pattern, path_str, re.IGNORECASE):
+                return True
+
+        return False
+
+    def detect_language(self, file_path: Path) -> Optional[str]:
+        """Detect the programming language of a file based on its extension."""
+        suffix = file_path.suffix.lower()
+
+        for language, config in self.language_patterns.items():
+            if suffix in config['extensions']:
+                return language
+
+        return None
+
+    def is_excluded_pattern(self, comment: str) -> bool:
+        """Check if a comment matches exclusion patterns (legitimate technical terms)."""
+        for pattern in self.exclusion_patterns:
+            if re.search(pattern, comment, re.IGNORECASE):
+                return True
+        return False
+
+    def is_documentation_comment(self, comment: str) -> bool:
+        """Check if a comment appears to be documentation rather than a TODO."""
+        for indicator in self.documentation_indicators:
+            if re.search(indicator, comment, re.IGNORECASE):
+                return True
+        
+        # Check for Rust doc comments (//! and ///) that mention TODO system types
+        todo_system_types = [
+            r'todo\s+template',
+            r'todo\s+instance',
+            r'todo\s+step',
+            r'todo\s+integration',
+            r'todo\s+system',
+            r'todotemplate',
+            r'todoinstance',
+            r'todostep',
+            r'todointegration',
+            r'todotemplatesystem',
+            r'todoprogress',
+            r'tododependency',
+        ]
+        
+        # If comment mentions TODO system types and appears to be documentation, exclude it
+        if any(re.search(pattern, comment, re.IGNORECASE) for pattern in todo_system_types):
+            # Check if it's describing the system rather than a TODO item
+            # If it contains "TODO:" followed by a colon, it's likely a real TODO
+            if not re.search(r'\bTODO\s*:\s*', comment, re.IGNORECASE):
+                return True
+        
+        return False
+
+    def has_todo_indicators(self, comment: str) -> bool:
+        """Check if a comment contains indicators that suggest it's an actual TODO."""
+        for indicator in self.todo_indicators:
+            if re.search(indicator, comment, re.IGNORECASE):
+                return True
+        return False
+
+    def calculate_context_score(self, comment: str, line_num: int, file_path: Path) -> float:
+        """Calculate a context score to help determine if this is a real TODO."""
+        score = 0.0
+        
+        # Check for documentation indicators (reduce score)
+        if self.is_documentation_comment(comment):
+            score -= 0.5
+        
+        # Check for TODO indicators (increase score)
+        if self.has_todo_indicators(comment):
+            score += 0.3
+        
+        # Check if it's in a generated file (reduce score)
+        if self.is_generated_file(file_path):
+            score -= 0.4
+        
+        # Check if comment is very short (likely not a TODO)
+        if len(comment.strip()) < 20 and not self.has_todo_indicators(comment):
+            score -= 0.2
+
+        # Check if comment starts with common documentation words
+        doc_starters = ['note:', 'current', 'this', 'the', 'implementation', 'method', 'function']
+        if any(comment.lower().startswith(starter) for starter in doc_starters):
+            score -= 0.2
+
+        score = round(score, 3)
+
+        return max(-1.0, min(1.0, score))  # Clamp between -1 and 1
+
+    def is_generated_file(self, file_path: Path) -> bool:
+        """Check if a file appears to be generated code."""
+        path_str = str(file_path)
+        generated_indicators = [
+            r'\.next\b',
+            r'generated',
+            r'build/',
+            r'dist/',
+            r'target/',
+            r'node_modules',
+            r'\.min\.',
+            r'\.bundle\.',
+            r'\.chunk\.',
+        ]
+        
+        for indicator in generated_indicators:
+            if re.search(indicator, path_str, re.IGNORECASE):
+                return True
+        return False
+
+    def extract_comments_from_file(self, file_path: Path) -> List[Tuple[int, str]]:
+        """Extract all comments from a file based on its language."""
+        language = self.detect_language(file_path)
+        if not language:
+            return []
+
+        config = self.language_patterns[language]
+        comments = []
+
+        try:
+            with open(file_path, 'r', encoding='utf-8') as f:
+                lines = f.readlines()
+
+            in_multiline = False
+            multiline_content = []
+
+            for line_num, line in enumerate(lines, 1):
+                original_line = line
+                line = line.strip()
+
+                # Skip empty lines
+                if not line:
+                    continue
+
+                # Handle multi-line comments / docstrings
+                start_pattern = config['multi_line_start']
+                end_pattern = config['multi_line_end']
+                if start_pattern and end_pattern:
+                    if not in_multiline:
+                        start_match = re.search(start_pattern, original_line)
+                        if start_match:
+                            in_multiline = True
+                            multiline_content = []
+                            after_start = original_line[start_match.end():]
+                            end_match_inline = re.search(end_pattern, after_start)
+
+                            if end_match_inline:
+                                body = after_start[:end_match_inline.start()].strip()
+                                if body:
+                                    multiline_content.append(body)
+                                combined = ' '.join(multiline_content).strip()
+                                if combined:
+                                    comments.append((line_num, combined))
+                                in_multiline = False
+                                multiline_content = []
+                            else:
+                                stripped_body = after_start.strip()
+                                if stripped_body:
+                                    multiline_content.append(stripped_body)
+                            continue
+                    else:
+                        end_match = re.search(end_pattern, original_line)
+                        if end_match:
+                            before_end = original_line[:end_match.start()].strip()
+                            if before_end:
+                                multiline_content.append(before_end)
+                            combined = ' '.join(multiline_content).strip()
+                            if combined:
+                                comments.append((line_num, combined))
+                            in_multiline = False
+                            multiline_content = []
+                            continue
+                        else:
+                            inner = original_line.strip()
+                            if inner:
+                                multiline_content.append(inner)
+                            continue
+
+                # Extract single-line comments (only if not in multi-line mode)
+                if not in_multiline and config['single_line'] and re.search(config['single_line'], line):
+                    # Remove comment prefix
+                    if language in ['rust', 'javascript', 'typescript', 'go', 'java', 'csharp', 'cpp', 'c', 'php']:
+                        comment = re.sub(r'^\s*//\s*', '', line)
+                    elif language in ['python', 'ruby', 'shell', 'yaml']:
+                        comment = re.sub(r'^\s*#\s*', '', line)
+                    elif language == 'markdown':
+                        comment = re.sub(r'^\s*<!--\s*', '', line)
+                        comment = re.sub(r'\s*-->$', '', comment)
+
+                    if comment:
+                        comments.append((line_num, comment))
+
+        except Exception as e:
+            print(f"Error reading {file_path}: {e}")
+
+        return comments
+
+    def detect_code_stubs(self, file_path: Path, language: str) -> List[Dict[str, Any]]:
+        """Detect code stub patterns beyond explicit comments."""
+        if not self.enable_code_stub_scan:
+            return []
+
+        patterns = self.code_stub_patterns.get(language)
+        if not patterns:
+            return []
+
+        try:
+            with open(file_path, 'r', encoding='utf-8') as f:
+                lines = f.readlines()
+        except Exception as e:
+            print(f"Error reading {file_path}: {e}")
+            return []
+
+        if language == 'python':
+            stubs = self._detect_python_code_stubs(lines, patterns)
+        elif language in ('javascript', 'typescript'):
+            stubs = self._detect_js_code_stubs(lines, patterns)
+        else:
+            stubs = []
+
+        for stub in stubs:
+            self.pattern_stats[stub['reason']] += 1
+
+        return stubs
+
+    def _detect_python_code_stubs(self, lines: List[str], patterns: Dict[str, re.Pattern]) -> List[Dict[str, Any]]:
+        stubs: List[Dict[str, Any]] = []
+
+        for idx, raw_line in enumerate(lines, 1):
+            stripped = raw_line.strip()
+            if not stripped:
+                continue
+
+            if patterns['function_stub'].match(raw_line):
+                stub_entry = self._scan_python_function_body(lines, idx, patterns)
+                if stub_entry:
+                    stubs.append(stub_entry)
+                continue
+
+            if patterns['raise_not_impl'].search(raw_line):
+                stubs.append({
+                    'line': idx,
+                    'reason': 'python_raise_not_implemented',
+                    'snippet': stripped,
+                    'confidence': 0.95,
+                    'context_score': 0.2,
+                })
+                continue
+
+            if patterns['ellipsis_stmt'].match(raw_line):
+                stubs.append({
+                    'line': idx,
+                    'reason': 'python_ellipsis_stub',
+                    'snippet': stripped,
+                    'confidence': 0.85,
+                    'context_score': 0.15,
+                })
+                continue
+
+        return stubs
+
+    def _scan_python_function_body(self, lines: List[str], start_index: int, patterns: Dict[str, re.Pattern]) -> Optional[Dict[str, Any]]:
+        """Inspect the first meaningful statement in a Python function for stub markers."""
+        func_line = lines[start_index - 1]
+        func_indent = len(func_line) - len(func_line.lstrip())
+
+        for idx in range(start_index + 1, len(lines) + 1):
+            raw_line = lines[idx - 1]
+            stripped = raw_line.strip()
+
+            if not stripped or stripped.startswith('#'):
+                continue
+
+            current_indent = len(raw_line) - len(raw_line.lstrip())
+            if current_indent <= func_indent:
+                break
+
+            if patterns['pass_stmt'].match(raw_line):
+                return {
+                    'line': idx,
+                    'reason': 'python_pass_stub',
+                    'snippet': stripped,
+                    'confidence': 0.82,
+                    'context_score': 0.1,
+                }
+
+            if patterns['ellipsis_stmt'].match(raw_line):
+                return {
+                    'line': idx,
+                    'reason': 'python_ellipsis_stub',
+                    'snippet': stripped,
+                    'confidence': 0.82,
+                    'context_score': 0.1,
+                }
+
+            if patterns['raise_not_impl'].search(raw_line):
+                return {
+                    'line': idx,
+                    'reason': 'python_raise_not_implemented',
+                    'snippet': stripped,
+                    'confidence': 0.95,
+                    'context_score': 0.25,
+                }
+
+            if patterns['return_not_impl'].match(raw_line):
+                return {
+                    'line': idx,
+                    'reason': 'python_return_placeholder',
+                    'snippet': stripped,
+                    'confidence': 0.8,
+                    'context_score': 0.1,
+                }
+
+            # First substantive line is real implementation
+            break
+
+        return None
+
+    def _detect_js_code_stubs(self, lines: List[str], patterns: Dict[str, re.Pattern]) -> List[Dict[str, Any]]:
+        stubs: List[Dict[str, Any]] = []
+        total_lines = len(lines)
+
+        for idx, raw_line in enumerate(lines, 1):
+            stripped = raw_line.strip()
+            if not stripped:
+                continue
+
+            if patterns['throw_not_impl'].search(stripped):
+                stubs.append({
+                    'line': idx,
+                    'reason': 'js_throw_not_implemented',
+                    'snippet': stripped,
+                    'confidence': 0.9,
+                    'context_score': 0.2,
+                })
+                continue
+
+            if patterns['return_todo'].search(stripped):
+                stubs.append({
+                    'line': idx,
+                    'reason': 'js_return_todo',
+                    'snippet': stripped,
+                    'confidence': 0.82,
+                    'context_score': 0.1,
+                })
+                continue
+
+            if patterns['function_stub'].match(raw_line) or patterns['arrow_stub'].match(raw_line):
+                stub_entry = self._scan_js_function_body(lines, idx, patterns)
+                if stub_entry:
+                    stubs.append(stub_entry)
+
+        return stubs
+
+    def _scan_js_function_body(self, lines: List[str], start_index: int, patterns: Dict[str, re.Pattern]) -> Optional[Dict[str, Any]]:
+        """Inspect the first executable statement in a JS/TS function body."""
+        opening_line = lines[start_index - 1]
+        initial_brace_count = opening_line.count('{') - opening_line.count('}')
+        brace_depth = max(initial_brace_count, 0)
+
+        for idx in range(start_index + 1, len(lines) + 1):
+            raw_line = lines[idx - 1]
+            stripped = raw_line.strip()
+
+            brace_depth += raw_line.count('{')
+            brace_depth -= raw_line.count('}')
+
+            if not stripped or stripped.startswith('//') or stripped.startswith('/*'):
+                continue
+
+            if brace_depth < 0:
+                break
+
+            if patterns['throw_not_impl'].search(stripped):
+                return {
+                    'line': idx,
+                    'reason': 'js_throw_not_implemented',
+                    'snippet': stripped,
+                    'confidence': 0.9,
+                    'context_score': 0.2,
+                }
+
+            if patterns['return_todo'].search(stripped):
+                return {
+                    'line': idx,
+                    'reason': 'js_return_todo',
+                    'snippet': stripped,
+                    'confidence': 0.82,
+                    'context_score': 0.1,
+                }
+
+            if brace_depth <= 0:
+                break
+
+            # Found non-stub statement
+            break
+
+        return None
+
+    def analyze_comment(self, comment: str, line_num: int, file_path: Path) -> Dict[str, Any]:
+        """Analyze a single comment for hidden TODO patterns with enhanced context awareness."""
+        normalized = comment.strip()
+        if not normalized:
+            return {}
+
+        comment = normalized
+        matches = defaultdict(list)
+        confidence_scores = []
+        
+        # Skip if this is an excluded pattern (legitimate technical term)
+        if self.is_excluded_pattern(comment):
+            return {}
+
+        # Calculate context score
+        context_score = self.calculate_context_score(comment, line_num, file_path)
+
+        # Check explicit TODO patterns (highest confidence)
+        for pattern in self.explicit_todo_patterns['explicit_todos']:
+            if re.search(pattern, comment, re.IGNORECASE):
+                matches['explicit_todos'].append(pattern)
+                # Adjust confidence based on context
+                base_confidence = 1.0
+                adjusted_confidence = min(1.0, max(0.1, base_confidence + context_score * 0.3))
+                confidence_scores.append(('explicit', adjusted_confidence))
+                self.pattern_stats[pattern] += 1
+
+        # Check high-confidence patterns
+        for category, patterns in self.high_confidence_patterns.items():
+            for pattern in patterns:
+                if re.search(pattern, comment, re.IGNORECASE):
+                    matches[category].append(pattern)
+                    # Adjust confidence based on context
+                    base_confidence = 0.9
+                    adjusted_confidence = min(1.0, max(0.1, base_confidence + context_score * 0.2))
+                    confidence_scores.append((category, adjusted_confidence))
+                    self.pattern_stats[pattern] += 1
+
+        # Check medium-confidence patterns
+        for category, patterns in self.medium_confidence_patterns.items():
+            for pattern in patterns:
+                if re.search(pattern, comment, re.IGNORECASE):
+                    matches[category].append(pattern)
+                    # Adjust confidence based on context
+                    base_confidence = 0.6
+                    adjusted_confidence = min(1.0, max(0.1, base_confidence + context_score * 0.1))
+                    confidence_scores.append((category, adjusted_confidence))
+                    self.pattern_stats[pattern] += 1
+
+        # Calculate overall confidence score
+        if not confidence_scores:
+            return {}
+
+        overall_confidence = max(score for _, score in confidence_scores)
+
+        return {
+            'matches': matches,
+            'confidence_score': overall_confidence,
+            'confidence_breakdown': confidence_scores,
+            'context_score': context_score
+        }
+
+    def analyze_engineering_grade_suggestions(self, comment: str, line_num: int, file_path: Path) -> Dict[str, Any]:
+        """Analyze a TODO comment to suggest engineering-grade format improvements."""
+        normalized = comment.strip()
+        if not normalized:
+            return {}
+
+        # Only analyze explicit TODOs
+        if not re.search(r'\b(TODO|FIXME|HACK)\b', normalized, re.IGNORECASE):
+            return {}
+
+        suggestions = {
+            'needs_engineering_format': False,
+            'missing_elements': [],
+            'suggested_tier': None,
+            'priority_level': 'Medium',
+            'template_suggestion': None,
+            'confidence': 0.0
+        }
+
+        # Check if already has engineering-grade structure
+        has_structure = False
+        for category, patterns in self.engineering_grade_patterns.items():
+            for pattern in patterns:
+                if re.search(pattern, normalized, re.IGNORECASE):
+                    has_structure = True
+                    break
+            if has_structure:
+                break
+
+        if not has_structure:
+            suggestions['needs_engineering_format'] = True
+            suggestions['confidence'] = 0.8
+
+            # Check what's missing
+            missing_elements = []
+            
+            # Check for completion checklist
+            if not any(re.search(pattern, normalized, re.IGNORECASE) for pattern in self.engineering_grade_patterns['completion_checklist']):
+                missing_elements.append('completion_checklist')
+            
+            # Check for acceptance criteria
+            if not any(re.search(pattern, normalized, re.IGNORECASE) for pattern in self.engineering_grade_patterns['acceptance_criteria']):
+                missing_elements.append('acceptance_criteria')
+            
+            # Check for dependencies
+            if not any(re.search(pattern, normalized, re.IGNORECASE) for pattern in self.engineering_grade_patterns['dependencies']):
+                missing_elements.append('dependencies')
+            
+            # Check for governance info
+            if not any(re.search(pattern, normalized, re.IGNORECASE) for pattern in self.engineering_grade_patterns['governance']):
+                missing_elements.append('governance')
+
+            suggestions['missing_elements'] = missing_elements
+
+            # Determine suggested CAWS tier based on content
+            if any(re.search(pattern, normalized, re.IGNORECASE) for pattern in self.needs_engineering_format_patterns['business_critical']):
+                suggestions['suggested_tier'] = 1
+                suggestions['priority_level'] = 'Critical'
+                suggestions['confidence'] = 0.9
+            elif any(re.search(pattern, normalized, re.IGNORECASE) for pattern in self.needs_engineering_format_patterns['vague_todos']):
+                suggestions['suggested_tier'] = 2
+                suggestions['priority_level'] = 'High'
+                suggestions['confidence'] = 0.7
+            else:
+                suggestions['suggested_tier'] = 3
+                suggestions['priority_level'] = 'Medium'
+                suggestions['confidence'] = 0.6
+
+            # Generate template suggestion
+            suggestions['template_suggestion'] = self._generate_template_suggestion(normalized, suggestions, file_path)
+
+        return suggestions
+
+    def _generate_template_suggestion(self, todo_text: str, suggestions: Dict[str, Any], file_path: Path) -> str:
+        """Generate a suggested engineering-grade TODO template based on the original TODO."""
+        # Extract the main TODO description
+        todo_match = re.search(r'\b(TODO|FIXME|HACK)\b[:\s]*(.*?)$', todo_text, re.IGNORECASE)
+        if not todo_match:
+            return ""
+        
+        todo_type = todo_match.group(1).upper()
+        description = todo_match.group(2).strip()
+        
+        # Determine language-specific comment prefix
+        language = self.detect_language(file_path)
+        if language in ['rust', 'javascript', 'typescript', 'go', 'java', 'csharp', 'cpp', 'c']:
+            comment_prefix = "//"
+        elif language in ['python', 'ruby', 'shell', 'yaml']:
+            comment_prefix = "#"
+        else:
+            comment_prefix = "//"
+
+        tier = suggestions.get('suggested_tier', 2)
+        priority = suggestions.get('priority_level', 'Medium')
+        
+        template = f"""{comment_prefix} {todo_type}: {description}
+{comment_prefix}       <One-sentence context & why this exists>
+{comment_prefix}
+{comment_prefix} COMPLETION CHECKLIST:
+{comment_prefix} [ ] Primary functionality implemented
+{comment_prefix} [ ] API/data structures defined & stable
+{comment_prefix} [ ] Error handling + validation aligned with error taxonomy
+{comment_prefix} [ ] Tests: Unit ≥80% branch coverage (≥50% mutation if enabled)
+{comment_prefix} [ ] Integration tests for external systems/contracts
+{comment_prefix} [ ] Documentation: public API + system behavior
+{comment_prefix} [ ] Performance/profiled against SLA (CPU/mem/latency throughput)
+{comment_prefix} [ ] Security posture reviewed (inputs, authz, sandboxing)
+{comment_prefix} [ ] Observability: logs (debug), metrics (SLO-aligned), tracing
+{comment_prefix} [ ] Configurability and feature flags defined if relevant
+{comment_prefix} [ ] Failure-mode cards documented (degradation paths)
+{comment_prefix}
+{comment_prefix} ACCEPTANCE CRITERIA:
+{comment_prefix} - <User-facing measurable behavior>
+{comment_prefix} - <Invariant or schema contract requirements>
+{comment_prefix} - <Performance/statistical bounds>
+{comment_prefix} - <Interoperation requirements or protocol contract>
+{comment_prefix}
+{comment_prefix} DEPENDENCIES:
+{comment_prefix} - <System or feature this relies on> (Required/Optional)
+{comment_prefix} - <Interop/contract references>
+{comment_prefix} - File path(s)/module links to dependent code
+{comment_prefix}
+{comment_prefix} ESTIMATED EFFORT: <Number + confidence range>
+{comment_prefix} PRIORITY: {priority}
+{comment_prefix} BLOCKING: {{Yes/No}} – If Yes: explicitly list what it blocks
+{comment_prefix}
+{comment_prefix} GOVERNANCE:
+{comment_prefix} - CAWS Tier: {tier} (impacts rigor, provenance, review policy)
+{comment_prefix} - Change Budget: <LOC or file count> (if relevant)
+{comment_prefix} - Reviewer Requirements: <Roles or domain expertise>"""
+
+        return template
+
+    def analyze_file(self, file_path: Path) -> Dict:
+        """Analyze a single file for hidden TODO patterns."""
+        language = self.detect_language(file_path)
+        if not language:
+            return {}
+
+        # Skip ignored files
+        if self.should_ignore_file(file_path):
+            return {}
+
+        comments = self.extract_comments_from_file(file_path)
+        try:
+            relative_path = str(file_path.relative_to(self.root_dir))
+        except ValueError:
+            relative_path = str(file_path)
+
+        file_analysis = {
+            'file_path': relative_path,
+            'language': language,
+            'total_comments': len(comments),
+            'total_lines': self._count_file_lines(file_path),
+            'comment_lines': len(comments),
+            'hidden_todos': defaultdict(list),
+            'all_comments': []
+        }
+
+        for line_num, comment in comments:
+            analysis = self.analyze_comment(comment, line_num, file_path)
+            engineering_suggestions = self.analyze_engineering_grade_suggestions(comment, line_num, file_path)
+
+            if analysis and analysis['matches']:
+                todo_data = {
+                    'comment': comment,
+                    'matches': analysis['matches'],
+                    'confidence_score': analysis['confidence_score'],
+                    'confidence_breakdown': analysis['confidence_breakdown'],
+                    'context_score': analysis['context_score']
+                }
+                
+                # Add engineering-grade suggestions if available
+                if engineering_suggestions and engineering_suggestions.get('needs_engineering_format'):
+                    todo_data['engineering_suggestions'] = engineering_suggestions
+                
+                file_analysis['hidden_todos'][line_num] = todo_data
+
+            # Store all comments for analysis
+            file_analysis['all_comments'].append({
+                'line': line_num,
+                'comment': comment
+            })
+
+        # Detect stub implementations in code bodies
+        for stub in self.detect_code_stubs(file_path, language):
+            line_num = stub['line']
+            reason = stub['reason']
+            snippet = stub['snippet']
+            confidence = stub['confidence']
+            context = stub.get('context_score', 0.0)
+
+            # Attempt to merge with nearby comment within 3 lines above
+            nearby_comment_line = None
+            for existing_line in sorted(file_analysis['hidden_todos'].keys()):
+                if existing_line == line_num:
+                    nearby_comment_line = existing_line
+                    break
+                if existing_line < line_num and line_num - existing_line <= 3:
+                    nearby_comment_line = existing_line
+
+            target_line = nearby_comment_line if nearby_comment_line is not None else line_num
+
+            if target_line in file_analysis['hidden_todos']:
+                entry = file_analysis['hidden_todos'][target_line]
+                entry['matches'].setdefault('code_stubs', []).append(reason)
+                entry['confidence_score'] = max(entry['confidence_score'], confidence)
+                entry['confidence_breakdown'].append(('code_stub', confidence))
+                entry['context_score'] = max(entry['context_score'], context)
+                if target_line != line_num:
+                    related = entry.setdefault('related_stub_lines', [])
+                    if line_num not in related:
+                        related.append(line_num)
+            else:
+                file_analysis['hidden_todos'][target_line] = {
+                    'comment': snippet,
+                    'matches': defaultdict(list, {'code_stubs': [reason]}),
+                    'confidence_score': confidence,
+                    'confidence_breakdown': [('code_stub', confidence)],
+                    'context_score': context,
+                }
+                file_analysis['all_comments'].append({
+                    'line': line_num,
+                    'comment': snippet
+                })
+
+        return file_analysis
+
+    def _count_file_lines(self, file_path: Path) -> int:
+        """Count total lines in a file."""
+        try:
+            with open(file_path, 'r', encoding='utf-8', errors='ignore') as f:
+                return sum(1 for _ in f)
+        except Exception:
+            return 0
+
+    def analyze_directory(self, languages: Optional[List[str]] = None, min_confidence: float = 0.7, v3_only: bool = False) -> Dict:
+        """Analyze all files in the directory for hidden TODO patterns with improved accuracy."""
+        print(f"Analyzing files with improved patterns in: {self.root_dir}")
+        print(f"Minimum confidence threshold: {min_confidence}")
+
+        # Get all files with supported extensions
+        all_files = []
+        for language, config in self.language_patterns.items():
+            if languages and language not in languages:
+                continue
+            for ext in config['extensions']:
+                if v3_only:
+                    # Only analyze files in iterations/v3/ directory
+                    v3_dir = self.root_dir / 'iterations' / 'v3'
+                    if v3_dir.exists():
+                        all_files.extend(v3_dir.rglob(f'*{ext}'))
+                else:
+                    all_files.extend(self.root_dir.rglob(f'*{ext}'))
+
+        # Filter out ignored files
+        non_ignored_files = [
+            f for f in all_files if not self.should_ignore_file(f)]
+
+        print(f"Found {len(all_files)} total files")
+        print(f"Found {len(non_ignored_files)} non-ignored files")
+
+        # Count by language
+        language_counts = defaultdict(int)
+        for file_path in non_ignored_files:
+            language = self.detect_language(file_path)
+            if language:
+                language_counts[language] += 1
+
+        print("Files by language:")
+        for lang, count in sorted(language_counts.items()):
+            print(f"  {lang}: {count} files")
+
+        # Reset pattern statistics for this run
+        self.pattern_stats = defaultdict(int)
+
+        all_results = {
+            'summary': {
+                'total_files': len(all_files),
+                'non_ignored_files': len(non_ignored_files),
+                'ignored_files': len(all_files) - len(non_ignored_files),
+                'language_counts': dict(language_counts),
+                'files_with_hidden_todos': 0,
+                'total_hidden_todos': 0,
+                'high_confidence_todos': 0,
+                'medium_confidence_todos': 0,
+                'low_confidence_todos': 0,
+                'code_stub_todos': 0,
+                'pattern_counts': {},
+                'min_confidence_threshold': min_confidence,
+            },
+            'files': {},
+            'patterns': defaultdict(list)
+        }
+
+        for file_path in non_ignored_files:
+            print(f"Analyzing: {file_path.relative_to(self.root_dir)}")
+            file_analysis = self.analyze_file(file_path)
+
+            if file_analysis and file_analysis['hidden_todos']:
+                # Filter by confidence threshold
+                filtered_todos = {}
+                for line_num, data in file_analysis['hidden_todos'].items():
+                    if data['confidence_score'] >= min_confidence:
+                        filtered_todos[line_num] = data
+                        
+                        # Count by confidence level
+                        if data['confidence_score'] >= 0.9:
+                            all_results['summary']['high_confidence_todos'] += 1
+                        elif data['confidence_score'] >= 0.6:
+                            all_results['summary']['medium_confidence_todos'] += 1
+                        else:
+                            all_results['summary']['low_confidence_todos'] += 1
+
+                if filtered_todos:
+                    file_analysis['hidden_todos'] = filtered_todos
+                    all_results['files'][file_analysis['file_path']] = file_analysis
+                    all_results['summary']['files_with_hidden_todos'] += 1
+                    all_results['summary']['total_hidden_todos'] += len(filtered_todos)
+
+                    # Group by patterns
+                    for line_num, data in filtered_todos.items():
+                        for category, patterns in data['matches'].items():
+                            all_results['patterns'][category].append({
+                                'file': file_analysis['file_path'],
+                                'language': file_analysis['language'],
+                                'line': line_num,
+                                'comment': data['comment'],
+                                'patterns': patterns,
+                                'confidence_score': data['confidence_score'],
+                                'context_score': data['context_score']
+                            })
+                            if category == 'code_stubs':
+                                all_results['summary']['code_stub_todos'] += 1
+
+        all_results['summary']['pattern_counts'] = dict(self.pattern_stats)
+
+        return all_results
+
+    def analyze_files(self, file_paths: List[str], min_confidence: float = 0.7) -> Dict:
+        """Analyze specific files for hidden TODO patterns."""
+        print(f"Analyzing {len(file_paths)} specific files with improved patterns")
+        print(f"Minimum confidence threshold: {min_confidence}")
+
+        # Convert string paths to Path objects and filter valid files
+        valid_files = []
+        for file_path in file_paths:
+            path = Path(file_path)
+            if path.exists() and path.is_file():
+                valid_files.append(path)
+            else:
+                print(f"Warning: File not found or not accessible: {file_path}")
+
+        if not valid_files:
+            print("No valid files to analyze")
+            return {
+                'summary': {
+                    'total_files': 0,
+                    'non_ignored_files': 0,
+                    'ignored_files': 0,
+                    'language_counts': {},
+                    'files_with_hidden_todos': 0,
+                    'total_hidden_todos': 0,
+                    'high_confidence_todos': 0,
+                    'medium_confidence_todos': 0,
+                    'low_confidence_todos': 0,
+                    'code_stub_todos': 0,
+                    'pattern_counts': {},
+                    'min_confidence_threshold': min_confidence,
+                },
+                'files': {},
+                'patterns': defaultdict(list)
+            }
+
+        # Reset pattern statistics for this run
+        self.pattern_stats = defaultdict(int)
+
+        # Count languages
+        language_counts = Counter()
+        non_ignored_files = []
+
+        for file_path in valid_files:
+            language = self.detect_language(file_path)
+            if language:
+                language_counts[language] += 1
+                # Skip ignored files
+                if not self.should_ignore_file(file_path):
+                    non_ignored_files.append(file_path)
+
+        all_results = {
+            'summary': {
+                'total_files': len(valid_files),
+                'non_ignored_files': len(non_ignored_files),
+                'ignored_files': len(valid_files) - len(non_ignored_files),
+                'language_counts': dict(language_counts),
+                'files_with_hidden_todos': 0,
+                'total_hidden_todos': 0,
+                'high_confidence_todos': 0,
+                'medium_confidence_todos': 0,
+                'low_confidence_todos': 0,
+                'code_stub_todos': 0,
+                'pattern_counts': {},
+                'min_confidence_threshold': min_confidence,
+            },
+            'files': {},
+            'patterns': defaultdict(list)
+        }
+
+        for file_path in non_ignored_files:
+            print(f"Analyzing: {file_path}")
+            file_analysis = self.analyze_file(file_path)
+
+            if file_analysis and file_analysis['hidden_todos']:
+                # Filter by confidence threshold
+                filtered_todos = {}
+                for line_num, data in file_analysis['hidden_todos'].items():
+                    if data['confidence_score'] >= min_confidence:
+                        filtered_todos[line_num] = data
+
+                        # Count by confidence level
+                        if data['confidence_score'] >= 0.9:
+                            all_results['summary']['high_confidence_todos'] += 1
+                        elif data['confidence_score'] >= 0.6:
+                            all_results['summary']['medium_confidence_todos'] += 1
+                        else:
+                            all_results['summary']['low_confidence_todos'] += 1
+
+                        # Count patterns
+                        for pattern in data.get('matches', []):
+                            self.pattern_stats[pattern] += 1
+
+                if filtered_todos:
+                    all_results['summary']['files_with_hidden_todos'] += 1
+                    all_results['summary']['total_hidden_todos'] += len(filtered_todos)
+                    all_results['files'][str(file_path)] = {
+                        'language': file_analysis['language'],
+                        'hidden_todos': filtered_todos,
+                        'total_lines': file_analysis['total_lines'],
+                        'comment_lines': file_analysis['comment_lines']
+                    }
+
+                    # Add to patterns
+                    for line_num, data in filtered_todos.items():
+                        for pattern in data.get('matches', []):
+                            all_results['patterns'][pattern].append({
+                                'file': str(file_path),
+                                'language': file_analysis['language'],
+                                'line': line_num,
+                                'comment': data['comment'],
+                                'patterns': [pattern],
+                                'confidence_score': data['confidence_score'],
+                                'context_score': data.get('context_score', 0.0)
+                            })
+
+        # Finalize pattern counts
+        all_results['summary']['pattern_counts'] = dict(self.pattern_stats)
+
+        return all_results
+
+    def analyze_staged_files_with_dependencies(self, min_confidence: float = 0.7, 
+                                             dependency_resolution: bool = True) -> Dict:
+        """
+        Analyze staged files for hidden TODOs with dependency resolution.
+        
+        This method:
+        1. Gets staged files from git
+        2. Analyzes them for hidden TODOs
+        3. Resolves dependencies to determine if TODOs are blocking
+        4. Returns results with dependency information
+        """
+        import subprocess
+        
+        try:
+            # Get staged files
+            result = subprocess.run(['git', 'diff', '--cached', '--name-only'], 
+                                  capture_output=True, text=True, check=True)
+            staged_files = [f.strip() for f in result.stdout.split('\n') if f.strip()]
+            
+            # Filter for supported file types
+            supported_extensions = set()
+            for lang_config in self.language_patterns.values():
+                supported_extensions.update(lang_config['extensions'])
+            
+            staged_files = [f for f in staged_files 
+                          if any(f.endswith(ext) for ext in supported_extensions)]
+            
+            if not staged_files:
+                return {
+                    'summary': {
+                        'staged_files': 0,
+                        'analyzed_files': 0,
+                        'total_hidden_todos': 0,
+                        'blocking_todos': 0,
+                        'non_blocking_todos': 0,
+                        'dependency_resolution_enabled': dependency_resolution
+                    },
+                    'files': {},
+                    'dependencies': {},
+                    'blocking_analysis': {}
+                }
+            
+            print(f"Found {len(staged_files)} staged files to analyze")
+            
+            # Analyze staged files
+            analysis_results = self.analyze_files(staged_files, min_confidence)
+            
+            # Add dependency resolution if enabled
+            if dependency_resolution:
+                dependency_info = self._resolve_todo_dependencies(analysis_results)
+                analysis_results['dependencies'] = dependency_info
+                analysis_results['blocking_analysis'] = self._analyze_blocking_todos(
+                    analysis_results, dependency_info)
+            
+            # Update summary with staged file info
+            analysis_results['summary']['staged_files'] = len(staged_files)
+            analysis_results['summary']['analyzed_files'] = len(staged_files)
+            analysis_results['summary']['dependency_resolution_enabled'] = dependency_resolution
+            
+            return analysis_results
+            
+        except subprocess.CalledProcessError as e:
+            print(f"Error getting staged files: {e}")
+            return {
+                'summary': {
+                    'staged_files': 0,
+                    'analyzed_files': 0,
+                    'total_hidden_todos': 0,
+                    'blocking_todos': 0,
+                    'non_blocking_todos': 0,
+                    'dependency_resolution_enabled': False,
+                    'error': str(e)
+                },
+                'files': {},
+                'dependencies': {},
+                'blocking_analysis': {}
+            }
+
+    def _resolve_todo_dependencies(self, analysis_results: Dict) -> Dict:
+        """
+        Resolve dependencies for TODOs found in staged files.
+        
+        Returns dependency information for each TODO.
+        """
+        dependencies = {}
+        
+        for file_path, file_data in analysis_results['files'].items():
+            file_deps = {}
+            
+            for line_num, todo_data in file_data['hidden_todos'].items():
+                todo_text = todo_data['comment']
+                todo_deps = self._extract_dependencies_from_todo(todo_text, file_path)
+                file_deps[line_num] = todo_deps
+            
+            if file_deps:
+                dependencies[file_path] = file_deps
+        
+        return dependencies
+
+    def _extract_dependencies_from_todo(self, todo_text: str, file_path: str) -> Dict:
+        """
+        Extract dependency information from TODO text using the engineering-grade template.
+        
+        Looks for:
+        - DEPENDENCIES section
+        - BLOCKING status
+        - CAWS Tier
+        - Required/Optional dependencies
+        """
+        dependencies = {
+            'blocking': False,
+            'caws_tier': None,
+            'required_deps': [],
+            'optional_deps': [],
+            'estimated_effort': None,
+            'priority': 'Medium'
+        }
+        
+        # Look for DEPENDENCIES section
+        deps_match = re.search(r'DEPENDENCIES:\s*\n((?:- .*\n?)*)', todo_text, re.MULTILINE)
+        if deps_match:
+            deps_text = deps_match.group(1)
+            for line in deps_text.split('\n'):
+                line = line.strip()
+                if line.startswith('- '):
+                    dep_text = line[2:].strip()
+                    if '(Required)' in dep_text:
+                        dependencies['required_deps'].append(dep_text.replace('(Required)', '').strip())
+                    elif '(Optional)' in dep_text:
+                        dependencies['optional_deps'].append(dep_text.replace('(Optional)', '').strip())
+                    else:
+                        # Default to required if not specified
+                        dependencies['required_deps'].append(dep_text)
+        
+        # Look for BLOCKING status
+        blocking_match = re.search(r'BLOCKING:\s*{Yes|No}', todo_text)
+        if blocking_match:
+            dependencies['blocking'] = 'Yes' in blocking_match.group(0)
+        
+        # Look for CAWS Tier
+        tier_match = re.search(r'CAWS Tier:\s*(\d+)', todo_text)
+        if tier_match:
+            dependencies['caws_tier'] = int(tier_match.group(1))
+        
+        # Look for PRIORITY
+        priority_match = re.search(r'PRIORITY:\s*{Critical|High|Medium|Low}', todo_text)
+        if priority_match:
+            dependencies['priority'] = priority_match.group(0).split(':')[1].strip()
+        
+        # Look for ESTIMATED EFFORT
+        effort_match = re.search(r'ESTIMATED EFFORT:\s*([^\\n]+)', todo_text)
+        if effort_match:
+            dependencies['estimated_effort'] = effort_match.group(1).strip()
+        
+        return dependencies
+
+    def _analyze_blocking_todos(self, analysis_results: Dict, dependency_info: Dict) -> Dict:
+        """
+        Analyze which TODOs are blocking based on dependency resolution.
+        """
+        blocking_analysis = {
+            'blocking_todos': [],
+            'non_blocking_todos': [],
+            'critical_blockers': [],
+            'dependency_summary': {
+                'total_required_deps': 0,
+                'resolved_deps': 0,
+                'unresolved_deps': 0
+            }
+        }
+        
+        for file_path, file_data in analysis_results['files'].items():
+            file_deps = dependency_info.get(file_path, {})
+            
+            for line_num, todo_data in file_data['hidden_todos'].items():
+                todo_deps = file_deps.get(line_num, {})
+                
+                # Determine if TODO is blocking
+                is_blocking = self._is_todo_blocking(todo_deps, file_path)
+                
+                todo_info = {
+                    'file': file_path,
+                    'line': line_num,
+                    'text': todo_data['comment'],
+                    'confidence': todo_data['confidence_score'],
+                    'dependencies': todo_deps,
+                    'blocking': is_blocking
+                }
+                
+                if is_blocking:
+                    blocking_analysis['blocking_todos'].append(todo_info)
+                    
+                    # Check if it's critical
+                    if todo_deps.get('priority') == 'Critical' or todo_deps.get('caws_tier') == 1:
+                        blocking_analysis['critical_blockers'].append(todo_info)
+                else:
+                    blocking_analysis['non_blocking_todos'].append(todo_info)
+                
+                # Update dependency summary
+                required_deps = todo_deps.get('required_deps', [])
+                blocking_analysis['dependency_summary']['total_required_deps'] += len(required_deps)
+                # For now, assume all dependencies are unresolved (would need actual resolution logic)
+                blocking_analysis['dependency_summary']['unresolved_deps'] += len(required_deps)
+        
+        return blocking_analysis
+
+    def _is_todo_blocking(self, todo_deps: Dict, file_path: str) -> bool:
+        """
+        Determine if a TODO is blocking based on its dependencies and context.
+        """
+        # Explicit blocking flag
+        if todo_deps.get('blocking', False):
+            return True
+        
+        # High priority or critical tier
+        if todo_deps.get('priority') in ['Critical', 'High']:
+            return True
+        
+        if todo_deps.get('caws_tier') == 1:
+            return True
+        
+        # Has required dependencies (simplified check)
+        if todo_deps.get('required_deps'):
+            return True
+        
+        return False
+
+    def generate_report(self, results: Dict) -> str:
+        """Generate a comprehensive report with enhanced accuracy information."""
+        report = []
+        report.append("# Improved Hidden TODO Analysis Report (v2.0)")
+        report.append("=" * 60)
+        report.append("")
+
+        # Summary
+        summary = results['summary']
+        report.append("## Summary")
+        report.append(f"- Total files: {summary['total_files']}")
+        report.append(f"- Non-ignored files: {summary['non_ignored_files']}")
+        report.append(f"- Ignored files: {summary['ignored_files']}")
+        report.append(f"- Files with hidden TODOs: {summary['files_with_hidden_todos']}")
+        report.append(f"- Total hidden TODOs found: {summary['total_hidden_todos']}")
+        report.append(f"- Code stub detections: {summary.get('code_stub_todos', 0)}")
+        report.append(f"- High confidence TODOs (≥0.9): {summary['high_confidence_todos']}")
+        report.append(f"- Medium confidence TODOs (≥0.6): {summary['medium_confidence_todos']}")
+        report.append(f"- Low confidence TODOs (<0.6): {summary['low_confidence_todos']}")
+        report.append(f"- Minimum confidence threshold: {summary['min_confidence_threshold']}")
+        report.append("")
+
+        # Language breakdown
+        report.append("## Files by Language")
+        for lang, count in sorted(summary['language_counts'].items()):
+            report.append(f"- **{lang}**: {count} files")
+        report.append("")
+
+        # Pattern statistics
+        if summary['pattern_counts']:
+            report.append("## Pattern Statistics")
+            for pattern, count in sorted(summary['pattern_counts'].items(), key=lambda x: x[1], reverse=True):
+                if count > 0:
+                    report.append(f"- `{pattern}`: {count} occurrences")
+            report.append("")
+
+        # Files with most high-confidence hidden TODOs
+        if results['files']:
+            report.append("## Files with High-Confidence Hidden TODOs")
+            file_todo_counts = []
+            for file_path, data in results['files'].items():
+                high_conf_count = sum(1 for todo in data['hidden_todos'].values() 
+                                    if todo['confidence_score'] >= 0.9)
+                if high_conf_count > 0:
+                    file_todo_counts.append((file_path, data['language'], high_conf_count))
+
+            file_todo_counts.sort(key=lambda x: x[2], reverse=True)
+            for file_path, language, count in file_todo_counts:
+                report.append(f"- `{file_path}` ({language}): {count} high-confidence TODOs")
+            report.append("")
+
+        # Engineering-grade TODO suggestions
+        engineering_suggestions = []
+        for file_path, file_data in results['files'].items():
+            for line_num, todo_data in file_data['hidden_todos'].items():
+                if 'engineering_suggestions' in todo_data:
+                    suggestions = todo_data['engineering_suggestions']
+                    if suggestions.get('needs_engineering_format'):
+                        engineering_suggestions.append({
+                            'file': file_path,
+                            'line': line_num,
+                            'language': file_data['language'],
+                            'original_comment': todo_data['comment'],
+                            'suggestions': suggestions
+                        })
+
+        if engineering_suggestions:
+            report.append("## Engineering-Grade TODO Suggestions")
+            report.append("")
+            report.append("The following TODOs should be upgraded to the engineering-grade format:")
+            report.append("")
+            
+            for suggestion in engineering_suggestions[:10]:  # Limit to top 10
+                report.append(f"### `{suggestion['file']}:{suggestion['line']}` ({suggestion['language']})")
+                report.append(f"**Original:** {suggestion['original_comment'][:100]}...")
+                report.append(f"**Suggested Tier:** {suggestion['suggestions']['suggested_tier']}")
+                report.append(f"**Priority:** {suggestion['suggestions']['priority_level']}")
+                report.append(f"**Missing Elements:** {', '.join(suggestion['suggestions']['missing_elements'])}")
+                report.append("")
+                report.append("**Suggested Template:**")
+                report.append("```")
+                report.append(suggestion['suggestions']['template_suggestion'])
+                report.append("```")
+                report.append("")
+            
+            if len(engineering_suggestions) > 10:
+                report.append(f"... and {len(engineering_suggestions) - 10} more TODOs need engineering-grade format")
+                report.append("")
+
+        # Pattern categories with confidence scores
+        if results['patterns']:
+            report.append("## Pattern Categories by Confidence")
+            for category, items in results['patterns'].items():
+                if items:
+                    high_conf_items = [item for item in items if 'confidence_score' in item and item['confidence_score'] >= 0.9]
+                    medium_conf_items = [item for item in items if 'confidence_score' in item and 0.6 <= item['confidence_score'] < 0.9]
+                    low_conf_items = [item for item in items if 'confidence_score' in item and item['confidence_score'] < 0.6]
+                    
+                    if high_conf_items or medium_conf_items:
+                        report.append(f"### {category.replace('_', ' ').title()} ({len(items)} items)")
+                        
+                        if high_conf_items:
+                            report.append(f"#### High Confidence ({len(high_conf_items)} items)")
+                            for item in high_conf_items[:3]:
+                                context_info = f" (context: {item['context_score']:.1f})" if 'context_score' in item else ""
+                                report.append(f"- `{item['file']}:{item['line']}` ({item['language']}, conf: {item['confidence_score']:.1f}{context_info}): {item['comment'][:80]}...")
+                            if len(high_conf_items) > 3:
+                                report.append(f"- ... and {len(high_conf_items) - 3} more high-confidence items")
+                        
+                        if medium_conf_items:
+                            report.append(f"#### Medium Confidence ({len(medium_conf_items)} items)")
+                            for item in medium_conf_items[:2]:
+                                context_info = f" (context: {item['context_score']:.1f})" if 'context_score' in item else ""
+                                report.append(f"- `{item['file']}:{item['line']}` ({item['language']}, conf: {item['confidence_score']:.1f}{context_info}): {item['comment'][:80]}...")
+                            if len(medium_conf_items) > 2:
+                                report.append(f"- ... and {len(medium_conf_items) - 2} more medium-confidence items")
+                        
+                        if low_conf_items:
+                            report.append(f"#### Low Confidence ({len(low_conf_items)} items) - *Consider reviewing for false positives*")
+                        
+                        report.append("")
+
+        return "\n".join(report)
+
+
+HiddenTodoAnalyzer = HiddenTodoAnalyzer
+
+
+def main():
+    import argparse
+
+    parser = argparse.ArgumentParser(
+        description='Analyze files for hidden TODO patterns with improved accuracy')
+    parser.add_argument('--root', default='.',
+                        help='Root directory to analyze (default: current directory)')
+    parser.add_argument('--files', nargs='+',
+                        help='Specific files to analyze (instead of scanning directory)')
+    parser.add_argument('--languages', nargs='+',
+                        help='Specific languages to analyze (e.g., rust python javascript)')
+    parser.add_argument(
+        '--output-json', help='Output JSON file for detailed results')
+    parser.add_argument('--output-md', help='Output Markdown report file')
+    parser.add_argument('--min-confidence', type=float, default=0.7,
+                        help='Minimum confidence threshold (0.0-1.0, default: 0.7)')
+    parser.add_argument('--verbose', '-v',
+                        action='store_true', help='Verbose output')
+    parser.add_argument('--disable-code-stub-scan',
+                        action='store_true', help='Disable code stub detection heuristics')
+    parser.add_argument('--ci-mode',
+                        action='store_true', help='CI mode - exit with error code if hidden TODOs found')
+    parser.add_argument('--warn-only',
+                        action='store_true', help='Warning mode - only warn, never fail')
+    parser.add_argument('--v3-only',
+                        action='store_true', help='Only analyze v3 folder (matches user search scope)')
+    parser.add_argument('--staged-only',
+                        action='store_true', help='Only analyze staged files with dependency resolution')
+    parser.add_argument('--disable-dependency-resolution',
+                        action='store_true', help='Disable dependency resolution for staged files')
+    parser.add_argument('--engineering-suggestions',
+                        action='store_true', help='Include engineering-grade TODO format suggestions')
+
+    args = parser.parse_args()
+
+    analyzer = HiddenTodoAnalyzer(
+        args.root,
+        enable_code_stub_scan=not args.disable_code_stub_scan,
+    )
+
+    # Analyze staged files with dependency resolution
+    if args.staged_only:
+        results = analyzer.analyze_staged_files_with_dependencies(
+            args.min_confidence, 
+            dependency_resolution=not args.disable_dependency_resolution
+        )
+    # Analyze specific files or entire directory
+    elif args.files:
+        results = analyzer.analyze_files(args.files, args.min_confidence)
+    else:
+        results = analyzer.analyze_directory(args.languages, args.min_confidence, args.v3_only)
+
+    # Print summary
+    summary = results['summary']
+    print(f"\n{'='*60}")
+    print("IMPROVED HIDDEN TODO ANALYSIS COMPLETE (v2.0)")
+    print(f"{'='*60}")
+    print(f"Total files: {summary['total_files']}")
+    print(f"Non-ignored files: {summary['non_ignored_files']}")
+    print(f"Ignored files: {summary['ignored_files']}")
+    print(f"Files with hidden TODOs: {summary['files_with_hidden_todos']}")
+    print(f"Total hidden TODOs: {summary['total_hidden_todos']}")
+    print(f"High confidence (≥0.9): {summary['high_confidence_todos']}")
+    print(f"Medium confidence (≥0.6): {summary['medium_confidence_todos']}")
+    print(f"Low confidence (<0.6): {summary['low_confidence_todos']}")
+    print(f"Confidence threshold: {summary['min_confidence_threshold']}")
+
+    print(f"\nFiles by language:")
+    for lang, count in sorted(summary['language_counts'].items()):
+        print(f"  {lang}: {count} files")
+
+    if summary['pattern_counts']:
+        print(f"\nTop patterns found:")
+        for pattern, count in sorted(summary['pattern_counts'].items(), key=lambda x: x[1], reverse=True)[:15]:
+            if count > 0:
+                print(f"  {pattern}: {count}")
+
+    # Save reports
+    if args.output_json:
+        with open(args.output_json, 'w') as f:
+            json.dump(results, f, indent=2)
+        print(f"\nDetailed results saved to: {args.output_json}")
+
+    if args.output_md:
+        report = analyzer.generate_report(results)
+        with open(args.output_md, 'w') as f:
+            f.write(report)
+        print(f"Report saved to: {args.output_md}")
+    else:
+        # Print report to console
+        try:
+            print("\n" + analyzer.generate_report(results))
+        except Exception as e:
+            print(f"⚠️  Could not generate report: {e}")
+
+    # Handle CI mode and warn-only mode
+    summary = results['summary']
+    total_hidden_todos = summary['total_hidden_todos']
+
+    if total_hidden_todos > 0:
+        if args.ci_mode:
+            print(f"\n❌ CI MODE: Found {total_hidden_todos} hidden TODOs - blocking commit/push")
+            exit(1)
+        elif args.warn_only:
+            print(f"\n⚠️  WARN MODE: Found {total_hidden_todos} hidden TODOs - proceeding anyway")
+        else:
+            print(f"\n⚠️  Found {total_hidden_todos} hidden TODOs - consider addressing them")
+    else:
+        print(f"\n✅ No hidden TODOs found - good job!")
+
+
+if __name__ == '__main__':
+    main()