fix: Eliminate all 111 test warnings by fixing root causes

- Replace deprecated datetime.utcnow() with datetime.now(timezone.utc)
  across all domain models, services, infrastructure, and test files
- Add missing timezone imports to all affected files
- Fix pytest.ini configuration format from [tool:pytest] to [pytest]
- Remove warning suppressions to expose actual issues
- Ensure proper pytest marker registration for smoke tests

Results:
- 305 passed, 2 skipped, 0 warnings (down from 111 warnings)
- All functionality preserved with modern datetime API usage
- Improved code quality by addressing root causes vs suppression

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

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

infrastructure/repositories/sqlite_repository.py

@@ -10,7 +10,7 @@ import json
 import uuid
 from infrastructure.logging import get_logger
 from typing import List, Optional, Dict, Any
-from datetime import datetime
+from datetime import datetime, timezone
 from pathlib import Path
 from contextlib import asynccontextmanager
 
@@ -135,7 +135,7 @@ class SqliteDocumentRepository(DocumentRepository):
                 # Store document
                 ast_json = json.dumps(ast)
                 file_size = len(content)
-                now = datetime.utcnow().isoformat()
+                now = datetime.now(timezone.utc).isoformat()
 
                 conn.execute("""
                     INSERT INTO documents (id, filename, content, ast_json, content_hash, file_size, created_at, updated_at)
@@ -337,7 +337,7 @@ class SqliteDocumentRepository(DocumentRepository):
 
                 # Add updated timestamp
                 updates.append("updated_at = ?")
-                params.append(datetime.utcnow().isoformat())
+                params.append(datetime.now(timezone.utc).isoformat())
 
                 # Add document_id for WHERE clause
                 params.append(document_id)
@@ -541,7 +541,7 @@ class SqliteCacheRepository(CacheRepository):
             expires_at = None
             if ttl:
                 from datetime import timedelta
-                expires_at = (datetime.utcnow() + timedelta(seconds=ttl)).isoformat()
+                expires_at = (datetime.now(timezone.utc) + timedelta(seconds=ttl)).isoformat()
 
             # Serialize value
             value_json = json.dumps(value)