fix: critical conversation history bug and improve Docker integration

This commit addresses several critical issues and improvements:

🔧 Critical Fixes:
- Fixed conversation history not being included when using continuation_id in AI-to-AI conversations
- Fixed test mock targeting issues preventing proper conversation memory validation
- Fixed Docker debug logging functionality with Gemini tools

🐛 Bug Fixes:
- Docker compose configuration for proper container command execution
- Test mock import targeting from utils.conversation_memory.* to tools.base.*
- Version bump to 3.1.0 reflecting significant improvements

🚀 Improvements:
- Enhanced Docker environment configuration with comprehensive logging setup
- Added cross-tool continuation documentation and examples in README
- Improved error handling and validation across all tools
- Better logging configuration with LOG_LEVEL environment variable support
- Enhanced conversation memory system documentation

🧪 Testing:
- Added comprehensive conversation history bug fix tests
- Added cross-tool continuation functionality tests
- All 132 tests now pass with proper conversation history validation
- Improved test coverage for AI-to-AI conversation threading

✨ Code Quality:
- Applied black, isort, and ruff formatting across entire codebase
- Enhanced inline documentation for conversation memory system
- Cleaned up temporary files and improved repository hygiene
- Better test descriptions and coverage for critical functionality

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

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

tests/test_collaboration.py

@@ -235,9 +235,9 @@ class TestCollaborationWorkflow:
         )
 
         response = json.loads(result[0].text)
-        assert response["status"] == "requires_clarification", (
-            "Should request clarification when asked about dependencies without package files"
-        )
+        assert (
+            response["status"] == "requires_clarification"
+        ), "Should request clarification when asked about dependencies without package files"
 
         clarification = json.loads(response["content"])
         assert "package.json" in str(clarification["files_needed"]), "Should specifically request package.json"