fix: Docker path translation for review_changes and code deduplication

- Fixed review_changes tool to properly translate host paths to container paths in Docker
- Prevents "No such file or directory" errors when running in Docker containers
- Added proper error handling with clear messages when paths are inaccessible

refactor: Centralized token limit validation across all tools
- Added _validate_token_limit method to BaseTool to eliminate code duplication
- Reduced ~25 lines of duplicated code across 5 tools (analyze, chat, debug_issue, review_code, think_deeper)
- Maintains exact same error messages and behavior

feat: Enhanced large prompt handling
- Added support for prompts >50K chars by requesting file-based input
- Preserves MCP's ~25K token capacity for responses
- All tools now check prompt size before processing

test: Added comprehensive Docker path integration tests
- Tests for path translation, security validation, and error handling
- Tests for review_changes tool specifically with Docker paths
- Fixed failing think_deeper test (updated default from "max" to "high")

chore: Code quality improvements
- Applied black formatting across all files
- Fixed import sorting with isort
- All tests passing (96 tests)
- Standardized error handling follows MCP TextContent format

The changes ensure consistent behavior across all environments while reducing code duplication and improving maintainability.

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

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

.env.example

@@ -1,15 +1,21 @@
-# Example .env file for Gemini MCP Server Docker setup
+# Example .env file for Gemini MCP Server
 # Copy this to .env and update with your actual values
 
 # Your Gemini API key (required)
 # Get one from: https://makersuite.google.com/app/apikey
 GEMINI_API_KEY=your-gemini-api-key-here
 
-# The absolute path to your project directory on the host machine
-# This will be mounted to /workspace in the container
+# Docker-specific environment variables (optional)
+# These are set automatically by the Docker setup scripts
+# You typically don't need to set these manually
+
+# WORKSPACE_ROOT: Used for Docker path translation
+# Automatically set when using Docker wrapper scripts
 # Example: /Users/username/my-project (macOS/Linux)
 # Example: C:\Users\username\my-project (Windows)
-WORKSPACE_ROOT=/path/to/your/project
+# WORKSPACE_ROOT=/path/to/your/project
 
-# Optional: Logging level (DEBUG, INFO, WARNING, ERROR)
-# LOG_LEVEL=INFO
+# MCP_PROJECT_ROOT: Restricts file access to a specific directory
+# If not set, defaults to user's home directory
+# Set this to limit file access to a specific project folder
+# MCP_PROJECT_ROOT=/path/to/allowed/directory