Fix conversation history duplication and optimize file embedding

This major refactoring addresses critical bugs in conversation history management
and significantly improves token efficiency through intelligent file embedding:

**Key Improvements:**
• Fixed conversation history duplication bug by centralizing reconstruction in server.py
• Added intelligent file filtering to prevent re-embedding files already in conversation history
• Centralized file processing logic in BaseTool._prepare_file_content_for_prompt()
• Enhanced log monitoring with better categorization and file embedding visibility
• Updated comprehensive test suite to verify new architecture and edge cases

**Architecture Changes:**
• Removed duplicate conversation history reconstruction from tools/base.py
• Conversation history now handled exclusively by server.py:reconstruct_thread_context
• All tools now use centralized file processing with automatic deduplication
• Improved token efficiency by embedding unique files only once per conversation

**Performance Benefits:**
• Reduced token usage through smart file filtering
• Eliminated redundant file embeddings in continued conversations
• Better observability with detailed debug logging for file operations

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

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

tools/analyze.py

@@ -9,7 +9,6 @@ from pydantic import Field
 
 from config import TEMPERATURE_ANALYTICAL
 from prompts import ANALYZE_PROMPT
-from utils import read_files
 
 from .base import BaseTool, ToolRequest
 from .models import ToolOutput
@@ -132,11 +131,9 @@ class AnalyzeTool(BaseTool):
         if updated_files is not None:
             request.files = updated_files
 
-        # Read all files
-        file_content = read_files(request.files)
-
-        # Check token limits
-        self._validate_token_limit(file_content, "Files")
+        # Use centralized file processing logic
+        continuation_id = getattr(request, "continuation_id", None)
+        file_content = self._prepare_file_content_for_prompt(request.files, continuation_id, "Files")
 
         # Build analysis instructions
         analysis_focus = []