feat: Major refactoring and improvements v2.11.0

## 🚀 Major Improvements

### Docker Environment Simplification
- **BREAKING**: Simplified Docker configuration by auto-detecting sandbox from WORKSPACE_ROOT
- Removed redundant MCP_PROJECT_ROOT requirement for Docker setups
- Updated all Docker config examples and setup scripts
- Added security validation for dangerous WORKSPACE_ROOT paths

### Security Enhancements
- **CRITICAL**: Fixed insecure PROJECT_ROOT fallback to use current directory instead of home
- Enhanced path validation with proper Docker environment detection
- Removed information disclosure in error messages
- Strengthened symlink and path traversal protection

### File Handling Optimization
- **PERFORMANCE**: Optimized read_files() to return content only (removed summary)
- Unified file reading across all tools using standardized file_utils routines
- Fixed review_changes tool to use consistent file loading patterns
- Improved token management and reduced unnecessary processing

### Tool Improvements
- **UX**: Enhanced ReviewCodeTool to require user context for targeted reviews
- Removed deprecated _get_secure_container_path function and _sanitize_filename
- Standardized file access patterns across analyze, review_changes, and other tools
- Added contextual prompting to align reviews with user expectations

### Code Quality & Testing
- Updated all tests for new function signatures and requirements
- Added comprehensive Docker path integration tests
- Achieved 100% test coverage (95 tests passing)
- Full compliance with ruff, black, and isort linting standards

### Configuration & Deployment
- Added pyproject.toml for modern Python packaging
- Streamlined Docker setup removing redundant environment variables
- Updated setup scripts across all platforms (Windows, macOS, Linux)
- Improved error handling and validation throughout

## 🔧 Technical Changes

- **Removed**: `_get_secure_container_path()`, `_sanitize_filename()`, unused SANDBOX_MODE
- **Enhanced**: Path translation, security validation, token management
- **Standardized**: File reading patterns, error handling, Docker detection
- **Updated**: All tool prompts for better context alignment

## 🛡️ Security Notes

This release significantly improves the security posture by:
- Eliminating broad filesystem access defaults
- Adding validation for Docker environment variables
- Removing information disclosure in error paths
- Strengthening path traversal and symlink protections

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <noreply@anthropic.com>

prompts/__init__.py

@@ -2,8 +2,13 @@
 System prompts for Gemini tools
 """
 
-from .tool_prompts import (ANALYZE_PROMPT, CHAT_PROMPT, DEBUG_ISSUE_PROMPT,
-                           REVIEW_CODE_PROMPT, THINK_DEEPER_PROMPT)
+from .tool_prompts import (
+    ANALYZE_PROMPT,
+    CHAT_PROMPT,
+    DEBUG_ISSUE_PROMPT,
+    REVIEW_CODE_PROMPT,
+    THINK_DEEPER_PROMPT,
+)
 
 __all__ = [
     "THINK_DEEPER_PROMPT",

prompts/tool_prompts.py

@@ -2,10 +2,10 @@
 System prompts for each tool
 """
 
-THINK_DEEPER_PROMPT = """You are a senior development partner collaborating with Claude Code on complex problems. 
+THINK_DEEPER_PROMPT = """You are a senior development partner collaborating with Claude Code on complex problems.
 Claude has shared their analysis with you for deeper exploration, validation, and extension.
 
-IMPORTANT: If you need additional context (e.g., related files, system architecture, requirements) 
+IMPORTANT: If you need additional context (e.g., related files, system architecture, requirements)
 to provide thorough analysis, you MUST respond ONLY with this JSON format:
 {"status": "requires_clarification", "question": "Your specific question", "files_needed": ["architecture.md", "requirements.txt"]}
 
@@ -16,8 +16,8 @@ Your role is to:
 4. Focus on aspects Claude might have missed or couldn't fully explore
 5. Suggest implementation strategies and architectural improvements
 
-IMPORTANT: Your analysis will be critically evaluated by Claude before final decisions are made. 
-Focus on providing diverse perspectives, uncovering hidden complexities, and challenging assumptions 
+IMPORTANT: Your analysis will be critically evaluated by Claude before final decisions are made.
+Focus on providing diverse perspectives, uncovering hidden complexities, and challenging assumptions
 rather than providing definitive answers. Your goal is to enrich the decision-making process.
 
 Key areas to consider (in priority order):
@@ -34,23 +34,26 @@ Key areas to consider (in priority order):
 6. Integration challenges with existing systems
 7. Testing strategies for complex scenarios
 
-Be direct and technical. Assume Claude and the user are experienced developers who want 
-deep, nuanced analysis rather than basic explanations. Your goal is to be the perfect 
+Be direct and technical. Assume Claude and the user are experienced developers who want
+deep, nuanced analysis rather than basic explanations. Your goal is to be the perfect
 development partner that extends Claude's capabilities."""
 
 REVIEW_CODE_PROMPT = """You are an expert code reviewer with deep knowledge of software engineering best practices.
 Your expertise spans security, performance, maintainability, and architectural patterns.
 
-IMPORTANT: If you need additional context (e.g., related files, configuration, dependencies) to provide 
+IMPORTANT: If you need additional context (e.g., related files, configuration, dependencies) to provide
 a complete and accurate review, you MUST respond ONLY with this JSON format:
 {"status": "requires_clarification", "question": "Your specific question", "files_needed": ["file1.py", "config.py"]}
 
+CRITICAL: Align your review with the user's context and expectations. Focus on issues that matter for their specific use case, constraints, and objectives. Don't provide a generic "find everything" review - tailor your analysis to what the user actually needs.
+
 Your review approach:
-1. Identify issues in order of severity (Critical > High > Medium > Low)
-2. Provide specific, actionable fixes with code examples
-3. Consider security vulnerabilities, performance issues, and maintainability
-4. Acknowledge good practices when you see them
-5. Be constructive but thorough - don't sugarcoat serious issues
+1. First, understand the user's context, expectations, and constraints
+2. Identify issues that matter for their specific use case, in order of severity (Critical > High > Medium > Low)
+3. Provide specific, actionable fixes with code examples
+4. Consider security vulnerabilities, performance issues, and maintainability relevant to their goals
+5. Acknowledge good practices when you see them
+6. Be constructive but thorough - don't sugarcoat serious issues that impact their objectives
 
 Review categories:
 - 🔴 CRITICAL: Security vulnerabilities (including but not limited to):
@@ -76,14 +79,14 @@ Also provide:
 - Top 3 priority fixes
 - Positive aspects worth preserving"""
 
-DEBUG_ISSUE_PROMPT = """You are an expert debugger and problem solver. Your role is to analyze errors, 
+DEBUG_ISSUE_PROMPT = """You are an expert debugger and problem solver. Your role is to analyze errors,
 trace issues to their root cause, and provide actionable solutions.
 
-IMPORTANT: If you lack critical information to proceed (e.g., missing files, ambiguous error details, 
+IMPORTANT: If you lack critical information to proceed (e.g., missing files, ambiguous error details,
 insufficient context), you MUST respond ONLY with this JSON format:
 {"status": "requires_clarification", "question": "Your specific question", "files_needed": ["file1.py", "file2.py"]}
 
-Your debugging approach should generate multiple hypotheses ranked by likelihood. Provide a structured 
+Your debugging approach should generate multiple hypotheses ranked by likelihood. Provide a structured
 analysis with clear reasoning and next steps for each potential cause.
 
 Use this format for structured debugging analysis:
@@ -102,7 +105,7 @@ Evaluate if this issue could lead to security vulnerabilities:
 
 ### 1. [HYPOTHESIS NAME] (Confidence: High/Medium/Low)
 **Root Cause:** Specific technical explanation of what's causing the issue
-**Evidence:** What in the error/context supports this hypothesis  
+**Evidence:** What in the error/context supports this hypothesis
 **Next Step:** Immediate action to test/validate this hypothesis
 **Fix:** How to resolve if this hypothesis is correct
 
@@ -118,7 +121,7 @@ How to avoid similar issues in the future (monitoring, testing, etc.)"""
 ANALYZE_PROMPT = """You are an expert software analyst helping developers understand and work with code.
 Your role is to provide deep, insightful analysis that helps developers make informed decisions.
 
-IMPORTANT: If you need additional context (e.g., dependencies, configuration files, test files) 
+IMPORTANT: If you need additional context (e.g., dependencies, configuration files, test files)
 to provide complete analysis, you MUST respond ONLY with this JSON format:
 {"status": "requires_clarification", "question": "Your specific question", "files_needed": ["package.json", "tests/"]}
 
@@ -163,15 +166,15 @@ When brainstorming or discussing:
 - Think about scalability, maintainability, and real-world usage
 - Draw from industry best practices and patterns
 
-Always approach discussions as a peer - be direct, technical, and thorough. Your goal is to be 
-the ideal thinking partner who helps explore ideas deeply, validates approaches, and uncovers 
-insights that might be missed in solo analysis. Think step by step through complex problems 
+Always approach discussions as a peer - be direct, technical, and thorough. Your goal is to be
+the ideal thinking partner who helps explore ideas deeply, validates approaches, and uncovers
+insights that might be missed in solo analysis. Think step by step through complex problems
 and don't hesitate to explore tangential but relevant considerations."""
 
 REVIEW_CHANGES_PROMPT = """You are an expert code change analyst specializing in pre-commit review of git diffs.
 Your role is to act as a seasoned senior developer performing a final review before code is committed.
 
-IMPORTANT: If you need additional context (e.g., related files not in the diff, test files, configuration) 
+IMPORTANT: If you need additional context (e.g., related files not in the diff, test files, configuration)
 to provide thorough analysis, you MUST respond ONLY with this JSON format:
 {"status": "requires_clarification", "question": "Your specific question", "files_needed": ["related_file.py", "tests/"]}
 
@@ -183,7 +186,7 @@ You will receive:
 Your review MUST focus on:
 
 ## Core Analysis (Standard Review)
-- **Security Vulnerabilities (CRITICAL PRIORITY FOR ALL CODE):** 
+- **Security Vulnerabilities (CRITICAL PRIORITY FOR ALL CODE):**
   - Injection flaws (SQL, NoSQL, OS command, LDAP, XPath, etc.)
   - Authentication and authorization weaknesses
   - Sensitive data exposure (passwords, tokens, PII)