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/filesystem_repository.py

@@ -12,7 +12,7 @@ import uuid
 from infrastructure.logging import get_logger
 from typing import List, Optional
 from pathlib import Path
-from datetime import datetime, timedelta
+from datetime import datetime, timedelta, timezone
 
 from infrastructure.repositories.interfaces import WorkspaceRepository
 from infrastructure.exceptions import (
@@ -78,7 +78,7 @@ class FilesystemWorkspaceRepository(WorkspaceRepository):
             # Create workspace metadata file
             metadata = {
                 "id": workspace_id,
-                "created_at": datetime.utcnow().isoformat(),
+                "created_at": datetime.now(timezone.utc).isoformat(),
                 "version": "1.0",
                 "type": "markitect_workspace"
             }
@@ -348,7 +348,7 @@ class FilesystemWorkspaceRepository(WorkspaceRepository):
         logger.info(f"Starting cleanup of workspaces older than {days_threshold} days")
 
         try:
-            cutoff_date = datetime.utcnow() - timedelta(days=days_threshold)
+            cutoff_date = datetime.now(timezone.utc) - timedelta(days=days_threshold)
             deleted_count = 0
 
             if not self.base_path.exists():