test/test_context_memory.py:29

• Import of 'Pattern' is not used.
  Import of 'Suggestion' is not used.
  test/test_error_parser.py:16
• Import of 'ErrorAnalysis' is not used.
  test/test_installation_history.py:20
• Import of 'PackageSnapshot' is not used.
  Import of 'InstallationRecord' is not used.
  test/test_installation_verifier.py:16
• Import of 'VerificationTest' is not used.
  test/test_llm_router.py:19
• Import of 'tempfile' is not used.
  test/test_llm_router.py:22
• Import of 'Path' is not used.
  test/test_llm_router.py:23
• Import of 'MagicMock' is not used.
  test/test_llm_router.py:24
• Import of 'datetime' is not used.
  test/test_llm_router.py:35
• Import of 'RoutingDecision' is not used.
  test/test_llm_router.py:18
• This import of module unittest is redundant, as it was previously imported on line 10.

cortex/cli.py (2)

289-420: Config subcommand implementation is solid; a few polish opportunities

The config() handler correctly delegates to PreferencesManager for:

• list → list_all() + get_config_info()
• get / set → get() / set() + save()
• reset (all or key) → reset()
• validate → validate()
• info → get_config_info()
• export / import → export_json() / import_json()

and wraps operations in a try/except ValueError block to surface schema issues cleanly. That aligns well with the manager API.

Minor refactors you might consider:

• For get, relying on value is None to detect “missing key” ties behavior to current schemas (where no preference is legitimately None). If you later add a nullable pref, this will misclassify it; an explicit default sentinel could make this more robust.
• For export/import, you can reuse the module-level Path import instead of re-importing inside the method.
• For import, a more specific error message for a missing file (e.g., FileNotFoundError) would be nicer than the generic “Configuration error: ...”.

Functionally this is fine as-is; these are just cleanups.

---

401-420: Value parsing is adequate for current keys; consider extending if you add numeric fields

_parse_config_value() covers booleans, integers, simple comma-separated lists, and strings, which matches the current schema (bool/int/list/string fields in PreferencesManager.set()).

If you later introduce float-valued preferences (e.g., temperatures or thresholds), you’ll likely want to extend this helper with a float branch before falling back to string, and perhaps tighten the “list if contains comma” rule for keys known to expect lists.

docs/USER_PREFERENCES_IMPLEMENTATION.md (1)

50-54: Minor Markdown polish (languages and bare URLs)

A few small doc cleanups you may want to do:

• Add explicit languages to fenced code blocks that are shell or tree listings, e.g.:

```bash
cortex config list

~/.config/cortex/preferences.yaml

cortex/
├── user_preferences.py
...

- Optionally wrap bare URLs in Markdown link syntax (`[text](url)`) to satisfy MD034, though the current style is still readable.

These are non-functional but will keep markdownlint quiet.




Also applies to: 356-365, 721-723

</blockquote></details>
<details>
<summary>cortex/user_preferences.py (1)</summary><blockquote>

`142-244`: **Persistence and backup behavior are reasonable; error wrapping could preserve original tracebacks**

`PreferencesManager`:

- Ensures the config directory exists in `__init__`/`_ensure_config_directory`.
- Creates timestamped backups via `_create_backup()` when saving over an existing file.
- Handles missing and empty config files in `load()`, creating defaults when needed.
- Differentiates YAML parse errors (`ValueError`) from other IO problems (`IOError`).

Functionally this is sound. To aid debugging and align with modern style, you might tweak the exception wrapping to preserve the original traceback, e.g.:

```diff
-        except Exception as e:
-            raise IOError(f"Failed to create backup: {str(e)}")
+        except Exception as exc:
+            raise IOError(f"Failed to create backup: {exc}") from exc
...
-        except Exception as e:
-            raise IOError(f"Failed to load config file: {str(e)}")
+        except Exception as exc:
+            raise IOError(f"Failed to load config file: {exc}") from exc
...
-        except Exception as e:
-            raise IOError(f"Failed to save config file: {str(e)}")
+        except Exception as exc:
+            raise IOError(f"Failed to save config file: {exc}") from exc

This keeps your custom messages while retaining the original stack context.

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Plan: Pro

cortex/user_preferences.py (1)

444-461: Refine writable detection in get_config_info()

Right now get_config_info() reports writability based on the directory only:

"writable": os.access(self.config_dir, os.W_OK),

This can report True even when the file itself is read-only, which slightly misleads users inspecting config health.

A small refinement would be:

-        info = {
-            "config_path": str(self.config_path),
-            "exists": self.config_path.exists(),
-            "writable": os.access(self.config_dir, os.W_OK),
-        }
+        exists = self.config_path.exists()
+        writable = (
+            os.access(self.config_path, os.W_OK)
+            if exists
+            else os.access(self.config_dir, os.W_OK)
+        )
+        info = {
+            "config_path": str(self.config_path),
+            "exists": exists,
+            "writable": writable,
+        }

That preserves the current behavior when the file doesn’t exist but reports more accurate writability once it does.

cortex/cli.py (1)

24-32: Consider logging (even at debug) when preference/credential load fails

In __init__ and _load_creds() you catch Exception and silently pass:

try:
    self.prefs_manager.load()
except Exception:
    # Silently ignore preference loading errors; defaults will be used
    pass
...
try:
    p = self._cred_path()
    if p.exists():
        return json.loads(p.read_text(encoding="utf-8"))
except Exception:
    # Return empty dict if credentials can't be loaded (file corrupted, etc.)
    pass

Swallowing all exceptions is understandable for resilience, but it also makes debugging broken configs or corrupted credential files harder.

I’d suggest at least emitting a low-noise log/print (e.g., [INFO] Falling back to defaults due to config error: ... or behind an env-guarded debug mode), while still continuing with defaults/empty creds.

Also applies to: 34-49

test/test_user_preferences.py (2)

15-18: Avoid mutating sys.path inside tests if possible

Adjusting sys.path in the test module can hide real packaging/import issues and makes test behavior differ from normal package usage. If your test runner is invoked from the project root with the package installed (or in editable mode), this block is typically unnecessary.

-import sys
-import os
-sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..'))
-
-from cortex.user_preferences import (
+import sys
+import os
+
+from cortex.user_preferences import (

If you still need direct execution of this file, consider relying on the package being installed/editable instead of manually tweaking sys.path.

---

243-275: Tests directly mutate private _preferences; consider using public surfaces

The validation tests (e.g., Lines 250–272) set invalid states via self.manager._preferences.... This works but tightly couples the tests to the internal representation of PreferencesManager.

If you want these tests to be more future-proof, consider driving invalid states via public APIs, for example:

• Importing from JSON with deliberately bad values and then calling validate(), or
• Introducing a small helper factory in tests that builds a UserPreferences instance and passes it into the manager via a dedicated setter (if you decide to expose one).

Not mandatory, but it would reduce reliance on internals if PreferencesManager evolves.

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docs/USER_PREFERENCES_IMPLEMENTATION.md (1)

441-445: File permission claim is inaccurate.

The documentation states config files are "created with user-only read/write (600)" but the implementation does not explicitly set file permissions - it relies on the OS umask defaults. Either update the implementation to set permissions explicitly using os.chmod(path, 0o600) after creation, or revise this documentation to reflect the actual behavior.

test/test_user_preferences.py (1)

1-5: Remove unnecessary shebang from test module.

This test file has a shebang (#!/usr/bin/env python3) but is not intended to be executed directly as a script - it's run via the test runner. Ruff flags this as EXE001.

-#!/usr/bin/env python3
 """
 Comprehensive tests for User Preferences & Settings System
 Tests all preference categories, validation, import/export, and persistence
 """

cortex/user_preferences.py (1)

197-231: Unknown nested keys are silently accepted but not persisted.

The set() method uses setattr without validating that the attribute exists on nested dataclasses. For example, set("ai.models", "gpt-4") (typo: "models" vs "model") will:

1. Dynamically add a models attribute to AISettings
2. Return successfully
3. Not persist the value because asdict() only serializes declared dataclass fields

This creates confusing "appears to succeed but doesn't stick" behavior.

Add validation before setattr:

         # Set the final attribute
         attr_name = parts[-1]
+        if not hasattr(obj, attr_name):
+            raise AttributeError(f"Unknown preference key: {key}")
         current_value = getattr(obj, attr_name)

test/test_user_preferences.py (2)

15-16: Prefer project-level test configuration over sys.path manipulation.

Modifying sys.path directly in test files is fragile. Consider configuring pytest/unittest properly via pyproject.toml or setup.py so imports work naturally, or use relative imports if the test is part of a package.

---

359-366: Atomic write test only verifies cleanup, not atomicity.

The test verifies no .tmp file remains after save, but doesn't verify atomicity under failure conditions. Consider adding a test that simulates a write failure (e.g., via mocking) to ensure the temp file is properly cleaned up and the original file remains intact.

cortex/cli.py (4)

284-286: Checking value is None is unreliable for detecting missing keys.

manager.get(key) returns None both for missing keys AND for keys that legitimately have None as a value (though none currently do). More importantly, the get() method returns the default parameter when the key doesn't exist. Since you pass no default, it returns None. This works now but is fragile.

Consider using a sentinel value or catching AttributeError instead:

-                value = manager.get(key)
-                if value is None:
+                _MISSING = object()
+                value = manager.get(key, default=_MISSING)
+                if value is _MISSING:

---

341-487: Refactor edit_pref to reduce cognitive complexity.

SonarCloud flags this method with cognitive complexity of 39 (limit: 15). Consider extracting each action into separate handler methods.

def edit_pref(self, action: str, key: Optional[str] = None, value: Optional[str] = None):
    """Edit user preferences"""
    manager = self._get_prefs_manager()
    
    handlers = {
        'set': self._handle_set_pref,
        'add': self._handle_set_pref,
        'update': self._handle_set_pref,
        'delete': self._handle_delete_pref,
        'remove': self._handle_delete_pref,
        'reset-key': self._handle_delete_pref,
        'list': lambda m, k, v: self.check_pref(),
        'show': lambda m, k, v: self.check_pref(),
        'display': lambda m, k, v: self.check_pref(),
        'reset-all': self._handle_reset_all,
        'validate': self._handle_validate,
        'export': self._handle_export,
        'import': self._handle_import,
    }
    
    handler = handlers.get(action)
    if handler:
        return handler(manager, key, value)
    else:
        self._print_error(f"Unknown action: {action}")
        # ... print available actions
        return 1

---

479-487: Improve exception handling: remove unused variable and use exception chaining.

The AttributeError handler captures e but doesn't use it. Also, the broad Exception catch should ideally use exception chaining when re-raising or be more specific.

-        except AttributeError as e:
+        except AttributeError:
             self._print_error(f"Invalid preference key: {key}")
             print("Use 'cortex check-pref' to see available keys")
             return 1
         except Exception as e:
-            self._print_error(f"Failed to edit preferences: {str(e)}")
-            import traceback
-            traceback.print_exc()
+            self._print_error(f"Failed to edit preferences: {e!s}")
+            if os.environ.get('DEBUG'):
+                import traceback
+                traceback.print_exc()
             return 1

---

415-424: Interactive confirmation blocks non-interactive usage.

Using input() for confirmation prevents this command from being used in scripts or CI pipelines. Consider adding a --yes or --force flag to bypass confirmation.

cortex/user_preferences.py (3)

1-1: Remove shebang from library module.

This is a library module, not an executable script. The shebang is unnecessary and triggers Ruff EXE001.

-#!/usr/bin/env python3
 """
 User Preferences & Settings System
 Manages persistent user preferences and configuration for Cortex Linux
 """

---

132-135: Broad exception catch swallows specific errors.

Catching all Exception types here will mask issues like PermissionError, yaml.YAMLError, etc. Consider catching more specific exceptions or at minimum logging the exception type.

-        except Exception as e:
-            print(f"[WARNING] Could not load preferences: {e}")
+        except (yaml.YAMLError, ValueError, TypeError) as e:
+            print(f"[WARNING] Could not load preferences ({type(e).__name__}): {e}")
             print("[INFO] Using default preferences")
             return self.preferences

---

328-337: Double stat() call is inefficient.

get_config_info() calls self.config_path.stat() twice when the file exists. Cache the stat result.

     def get_config_info(self) -> Dict[str, Any]:
         """Get configuration metadata"""
+        exists = self.config_path.exists()
+        stat_info = self.config_path.stat() if exists else None
         return {
             'config_path': str(self.config_path),
-            'config_exists': self.config_path.exists(),
-            'config_size_bytes': self.config_path.stat().st_size if self.config_path.exists() else 0,
+            'config_exists': exists,
+            'config_size_bytes': stat_info.st_size if stat_info else 0,
             'last_modified': datetime.fromtimestamp(
-                self.config_path.stat().st_mtime
-            ).isoformat() if self.config_path.exists() else None
+                stat_info.st_mtime
+            ).isoformat() if stat_info else None
         }

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docs/USER_PREFERENCES_IMPLEMENTATION.md (1)

257-268: Windows path separator remains in test command example.

The test command still uses Windows backslash syntax which won't work on Linux/macOS. This was previously flagged but not yet addressed.

cortex/cli.py (2)

479-481: Remove unused exception variable.

The exception variable e is captured but never used. Remove it or log it for debugging purposes.

-        except AttributeError as e:
+        except AttributeError:
             self._print_error(f"Invalid preference key: {key}")

---

341-487: Consider extracting action handlers to reduce complexity.

This method has cognitive complexity of 39 vs the recommended 15. While each action branch is relatively straightforward, extracting them into separate methods (e.g., _edit_pref_set, _edit_pref_delete, _edit_pref_export) would improve maintainability and testability.

This is a suggested refactor for future improvement rather than a blocking issue.

cortex/user_preferences.py (2)

1-1: Shebang unnecessary for library module.

The shebang is present but the file is not executable and is primarily imported as a module. While the if __name__ == "__main__" block provides a demo, consider removing the shebang or making the file executable if it's intended as a runnable script.

---

202-236: Validate attribute existence before setting.

The set() method uses getattr to retrieve the current value (line 219) which will raise AttributeError if the key doesn't exist, but this only works for the final attribute. For nested keys, if a typo is made in the final part, getattr at line 219 will raise an error, so the validation is actually present.

However, the error message from a failed getattr may not be clear to users. Consider catching AttributeError and re-raising with a more helpful message.

     def set(self, key: str, value: Any) -> None:
         """
         Set preference value by dot notation key
         
         Args:
             key: Dot notation key (e.g., 'ai.model')
             value: Value to set
         """
         parts = key.split('.')
         obj = self.preferences
         
-        # Navigate to parent object
-        for part in parts[:-1]:
-            obj = getattr(obj, part)
-        
-        # Set the final attribute
-        attr_name = parts[-1]
-        current_value = getattr(obj, attr_name)
+        try:
+            # Navigate to parent object
+            for part in parts[:-1]:
+                obj = getattr(obj, part)
+            
+            # Set the final attribute
+            attr_name = parts[-1]
+            current_value = getattr(obj, attr_name)
+        except AttributeError:
+            raise PreferencesError(f"Unknown preference key: {key}")
         
         # Type coercion
         if isinstance(current_value, bool):

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