fix: address critical deprecation and doctor fix issues

- Remove duplicate deprecation warnings between wrapper and core Agent
- Fix CLI command reference from 'praisonai doctor --fix' to 'praisonai doctor fix --execute'
- Remove unimplemented 'allow_legacy_runtime_pin=True' reference
- Fix duplicate file processing in doctor handler by deduplicating yaml_files
- Add proper error handling with exit codes in doctor fix command
- Remove unused imports and variables in doctor handler
- Fix CLI flag mapping from --config to --file for handler compatibility
- Remove test fixture from repository root

These fixes address all critical bugs identified by previous reviewers.

Co-authored-by: Mervin Praison <MervinPraison@users.noreply.github.com>

Author: praisonai-triage-agent[bot]

src/praisonai-agents/praisonaiagents/agent/agent.py

@@ -2041,8 +2041,7 @@ def __init__(
                 warnings.warn(
                     "Agent-level 'cli_backend' parameter is deprecated when model configuration is available. "
                     "Consider using model-scoped runtime configuration instead. "
-                    "Use 'allow_legacy_runtime_pin=True' to suppress this warning. "
-                    "For migration assistance, run: praisonai doctor --fix",
+                    "For migration assistance, run: praisonai doctor fix --execute",
                     DeprecationWarning,
                     stacklevel=2
                 )

src/praisonai/praisonai/agent.py

@@ -30,20 +30,7 @@ def __init__(self, *args, cli_backend: Optional[Union[str, Any]] = None, **kwarg
                 - None: No CLI backend
             **kwargs: Keyword arguments for core Agent
         """
-        # Check for deprecation warning in wrapper layer
-        if cli_backend is not None:
-            # Check if model/llm is specified in kwargs
-            if 'model' in kwargs or 'llm' in kwargs:
-                import warnings
-                warnings.warn(
-                    "Agent-level 'cli_backend' parameter is deprecated when model configuration is available. "
-                    "Consider using model-scoped runtime configuration instead. "
-                    "Use 'allow_legacy_runtime_pin=True' to suppress this warning. "
-                    "For migration assistance, run: praisonai doctor --fix",
-                    DeprecationWarning,
-                    stacklevel=2
-                )
-        
+        # Deprecation warning will be emitted by the core Agent class
         # Resolve CLI backend configuration using unified resolver
         if cli_backend is not None and not self._is_protocol_instance(cli_backend):
             from .cli_backends import resolve_cli_backend_config

src/praisonai/praisonai/cli/commands/doctor.py

@@ -356,7 +356,7 @@ def doctor_fix(
     if not backup:
         args.append("--no-backup") 
     if config_path:
-        args.extend(["--config", config_path])
+        args.extend(["--file", config_path])
     raise typer.Exit(_run_doctor(args))
 
 

src/praisonai/praisonai/cli/features/doctor/handler.py

@@ -315,7 +315,6 @@ def _run_fix_mode(self, config: DoctorConfig) -> int:
         import os
         import yaml
         import glob
-        from pathlib import Path
 
         if not config.quiet:
             print("🔧 PraisonAI Configuration Migration Tool")
@@ -330,6 +329,7 @@ def _run_fix_mode(self, config: DoctorConfig) -> int:
             patterns = ["*.yaml", "*.yml", "agents.yaml", "config.yaml"]
             for pattern in patterns:
                 yaml_files.extend(glob.glob(pattern))
+            yaml_files = list(dict.fromkeys(yaml_files))  # Remove duplicates while preserving order
 
         if not yaml_files:
             if not config.quiet:
@@ -338,6 +338,7 @@ def _run_fix_mode(self, config: DoctorConfig) -> int:
 
         issues_found = 0
         files_modified = 0
+        files_failed = 0
 
         for yaml_file in yaml_files:
             if not os.path.exists(yaml_file):
@@ -348,7 +349,6 @@ def _run_fix_mode(self, config: DoctorConfig) -> int:
                     data = yaml.safe_load(f)
 
                 # Check for deprecated cli_backend usage
-                modified = False
                 if self._has_deprecated_cli_backend(data):
                     issues_found += 1
                     if not config.quiet:
@@ -375,9 +375,10 @@ def _run_fix_mode(self, config: DoctorConfig) -> int:
                             print(f"✅ Migrated: {yaml_file}")
                     else:
                         if not config.quiet:
-                            print(f"   Run with --execute to apply migration")
+                            print("   Run with --execute to apply migration")
 
             except Exception as e:
+                files_failed += 1
                 if not config.quiet:
                     print(f"❌ Error processing {yaml_file}: {e}")
 
@@ -391,7 +392,7 @@ def _run_fix_mode(self, config: DoctorConfig) -> int:
                 if not config.execute and issues_found > 0:
                     print("\n💡 To apply migrations, run: praisonai doctor fix --execute")
 
-        return 0
+        return 1 if files_failed > 0 else 0
 
     def _has_deprecated_cli_backend(self, data: dict) -> bool:
         """Check if YAML config has deprecated cli_backend usage."""