cortex/installation_history.py:177

• Good security improvement: The regex pattern has been changed from \(.*?\) to \([^)]*\) to prevent ReDoS (Regular Expression Denial of Service) attacks. The new pattern avoids nested quantifiers and backtracking, making it safer. This is a security best practice.
  cortex/installation_history.py:256
• Good security clarification: The comment correctly clarifies that MD5 is being used for non-cryptographic purposes (generating unique IDs), not for security. This is appropriate for this use case. MD5 is fast and sufficient for collision-resistant ID generation when security is not a concern.
  cortex/dependency_resolver.py:152
• Good security improvement: Similar to the other file, the regex pattern has been updated from \(.*?\) to \([^)]*\) to prevent ReDoS attacks. This is a consistent security improvement across the codebase.
  test/test_context_memory.py:24
• 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:25
• Import of 'RoutingDecision' is not used.

test/test_installation_verifier.py (1)

73-73: Remove redundant import.

The os module is already imported at the module level (line 8), making this import statement redundant.

Apply this diff:

-        import os

docs/USER_PREFERENCES_IMPLEMENTATION.md (1)

48-53: Minor Markdown hygiene for better tooling support

The doc is thorough and matches the implemented system. A few small cleanups would make linters happier and improve readability:

• Add explicit languages to “fenced” code blocks that currently have none (e.g., the ~/.config/cortex/preferences.yaml and file-structure snippets) to satisfy MD040.
• Consider wrapping bare URLs in Markdown links (e.g., [link](https://...)) for the references section.
• Optional: some style guides prefer November 18, 2025, with a trailing comma; you can adjust or ignore depending on your house style.

Also applies to: 356-365, 671-684, 736-737, 721-723

test/test_conflict_ui.py (1)

7-74: Conflict UI tests provide good coverage; only minor polish opportunities

The test scenarios align well with _resolve_conflicts_interactive and _ask_save_preference:

• Keep-first/keep-second paths assert the correct package ends up in resolutions['remove'] and that user-facing messages are printed.
• Cancel path asserts SystemExit and checks the cancellation message.
• Save-preference test verifies conflicts.saved_resolutions is written with the sorted key and that save() is called.
• Saved-preference test confirms the fast-path is used without prompting, and the output reflects the stored choice.

Only optional cleanups:

• Several patched arguments (mock_input, mock_stdout) are not referenced directly; you could rename them to _mock_input / _mock_stdout to quiet linters without changing behavior.
• If you want to avoid constructing a real CortexCLI in tests, you could inject a minimal stub just for conflict resolution, but this is not necessary given current scope.

cortex/cli.py (5)

23-33: Preference manager initialization is reasonable; consider logging on load failure

Initializing PreferencesManager in __init__ and attempting a best-effort load() makes sense so the rest of the CLI can assume preferences are present. Swallowing all exceptions keeps the CLI usable if the config is corrupt or unreadable, but completely silent failures may make diagnosing broken configs harder.

Consider logging a brief warning (to stderr or via a logger) when load() fails, ideally including the config path, while still proceeding with defaults.

Also applies to: 34-49

---

34-49: Credentials helpers are currently unused

_cred_path() and _load_creds() are defined but not yet wired into _get_api_key() or any other flow. If credential files are part of a planned follow-up, this is fine; otherwise, you might either:

• Integrate _load_creds() into _get_api_key() as a secondary source after env vars, or
• Remove these helpers for now to avoid dead code.

---

84-145: Interactive conflict resolution + saved preferences logic looks sound

The conflict UI and preference-saving logic are coherent and match the tests and ConflictSettings schema:

• Saved resolutions are keyed using f"{min(pkg1, pkg2)}:{max(pkg1, pkg2)}", ensuring that a conflict between pkgA/pkgB is recognized regardless of order.
• When a saved preference is present, the code computes the package to remove and prints a clear “Using saved preference: …” message without prompting, which is what the tests assert.
• New choices (1/2) correctly add the opposite package to resolutions['remove'] and delegate to _ask_save_preference if selected.
• Choice 3 cancels the installation via sys.exit(1), which matches the test expectations.

Given this is used in an interactive CLI, exiting from here is acceptable, but if you ever want to reuse _resolve_conflicts_interactive programmatically (e.g., from a higher-level orchestration layer), you may eventually prefer raising a custom exception instead of calling sys.exit() directly.

---

159-223: DependencyResolver integration for conflict checks is safe but could log resolver failures

The install flow’s conflict-check integration is conservative:

• It uses a simple heuristic (target_package = software.split()[0]) to pick a package to resolve, which is acceptable as a first cut for the UI demo.
• If DependencyResolver.resolve_dependencies() finds conflicts, they’re passed through the interactive resolver and any chosen removals are prepended as apt-get remove commands unless already present.
• Broadly catching Exception around the resolver and silently continuing avoids breaking installs when the resolver can’t handle a package, but you lose diagnostic visibility.

Consider logging a warning when resolver calls fail (e.g., missing apt-cache data or unsupported packages), so users and developers can see why conflict checks were skipped while still proceeding with the install.

Also applies to: 204-223

---

402-513: Config subcommand behavior and value parsing are coherent; consider surfacing validation on set

The config() method plus _parse_config_value() provide a straightforward interface:

• list uses list_all() and prints YAML plus config metadata.
• get/set/reset/validate/info/export/import map cleanly onto the PreferencesManager API.
• _parse_config_value() handles booleans (true/false-like strings), ints, and simple comma-separated lists, and otherwise returns a string—sufficient for current preference types.

Two optional improvements:

1. After a successful set, you could optionally run validate() and warn if the new value makes the config invalid (e.g., auto_update.frequency_hours = 0), instead of relying on a separate config validate step.
2. For reset without a key, you currently ask for confirmation via input("Continue? (y/n): "). That’s good; just be aware this introduces interactivity into config reset that might surprise scripts. A --force flag at the argparse level could be a future enhancement if scripting becomes common.

Overall, the implementation matches the documented CLI usage.

Also applies to: 514-533

cortex/user_preferences.py (4)

156-258: load()/save() behavior and backup handling are reasonable

PreferencesManager.load():

• Creates a default UserPreferences object and immediately saves it if the config file doesn’t exist, ensuring subsequent operations always have a concrete config.
• Uses yaml.safe_load() and handles empty files by treating them as {}, which is robust.

save():

• Requires _preferences to be non-None (enforcing a load() first).
• Optionally creates a timestamped backup using with_suffix(".backup.<timestamp>") when a config already exists.
• Dumps YAML with stable formatting (no flow style, no key sorting).

This is a solid, conservative approach. One optional enhancement would be to narrow the broad except Exception in load()/save()-related helpers (_create_backup, load) to more specific exceptions where practical, but it’s not strictly necessary.

---

259-387: Dot-notation get/set/reset behavior is consistent; conflicts.saved_resolutions is handled correctly

Key points:

• get() walks the UserPreferences.to_dict() structure using dot notation and returns the provided default if any segment is missing. This is what the CLI and conflict UI expect.
• set() validates per top-level section:
  • verbosity and ai.creativity restricted to known enum values.
  • Type checks for booleans/ints/lists/dicts as appropriate (e.g., auto_update.frequency_hours, ai.max_suggestions, packages.default_sources, conflicts.saved_resolutions).
  • For conflicts.saved_resolutions, requiring a dict lines up with how _ask_save_preference() passes in a Python dict of normalized keys to package names.
• reset() either:
  • Replaces the entire preferences object with defaults and saves, or
  • For specific keys, derives the default value from a fresh UserPreferences().to_dict() and then calls set(key, default_value) followed by save().

This all matches how cortex.cli.config uses the manager. Only minor caveat: resetting a non-leaf key like "ai" would currently fail (since set() expects "ai.something"), but the documented and tested flows all use leaf keys (ai.model, etc.), so this is acceptable.

---

389-423: Validation rules are sensible and match the documented configuration options

The validate() method checks:

• verbosity is within the VerbosityLevel enum.
• ai.creativity is within AICreativity.
• ai.model is one of ["claude-sonnet-4", "gpt-4", "gpt-4-turbo", "claude-3-opus"], which matches the docs.
• auto_update.frequency_hours >= 1.
• At least one package source in packages.default_sources.

This provides clear, actionable error messages and is sufficient for the current config surface. If/when you expand models or strategies (e.g. conflicts.default_strategy beyond "interactive"), this is a good place to enforce those constraints as well.

---

498-535: Embedded demo main() is fine but could be gated or moved later

The main() function at the bottom offers a handy demonstration of the preferences manager. It’s harmless in normal use (only runs under python -m cortex.user_preferences), but in some projects, such demos are moved to separate examples or guarded in documentation.

No need to change this now; just something to consider if the module grows further or if packaging policies prefer modules without executable demos.

test/test_user_preferences.py (2)

1-5: Resolve Ruff EXE001 by dropping the shebang (or making the file executable).

Ruff correctly notes the shebang on Line 1 but the file isn’t executable and is already invoked via python -m unittest / the __main__ guard. Simplest fix is to remove the shebang so the module just starts with the docstring.

-#!/usr/bin/env python3
-"""
-Unit tests for the User Preferences System
-Tests all functionality of the PreferencesManager class
-"""
+"""
+Unit tests for the User Preferences System
+Tests all functionality of the PreferencesManager class
+"""

Also applies to: 499-501

---

132-415: PreferencesManager tests are thorough; consider adding coverage for conflicts.saved_resolutions.

The suite here is strong: you cover default creation, load/save round‑trip, dot‑notation get/set, reset (all and specific), validation, backup creation, JSON export/import (valid and invalid), YAML parsing, basic concurrent access, invalid YAML, and directory creation. This gives very solid confidence in the manager’s behavior.

Given PreferencesManager.set has explicit handling for conflicts.saved_resolutions, it would be worth adding at least one positive round‑trip test (and optionally a type‑validation negative test) to keep the new conflict‑resolution preferences covered:

 class TestPreferencesManager(unittest.TestCase):
@@
     def test_import_invalid_json(self):
         """Test importing invalid JSON raises error"""
@@
         with self.assertRaises(ValueError):
             self.manager.import_json(import_path)
+
+    def test_conflicts_saved_resolutions_roundtrip(self):
+        """Test saving and reloading conflicts.saved_resolutions"""
+        self.manager.load()
+        resolutions = {"example_conflict": "example_resolution"}
+        self.manager.set("conflicts.saved_resolutions", resolutions)
+        self.manager.save()
+
+        reloaded = PreferencesManager(config_path=self.config_path)
+        reloaded.load()
+        self.assertEqual(
+            reloaded.get("conflicts.saved_resolutions"),
+            resolutions,
+        )

Configuration used: CodeRabbit UI

Review profile: CHILL

Plan: Pro

test/test_conflict_ui.py (1)

438-450: Align test_preference_validation with PreferencesManager.validate() behavior

This test assumes that setting prefs.ai.max_suggestions = -999 will cause validate() to return at least one error. At present, validate() does not check max_suggestions, so errors remains empty and the assertion will fail.

Once validate() is extended to enforce a lower bound on max_suggestions (e.g., >= 1), this test will pass as written. If you decide not to constrain max_suggestions, this test will need to be relaxed accordingly.

cortex/user_preferences.py (2)

283-355: PreferencesManager.set() is very branch-heavy; consider splitting into helpers

The set() method encodes all preference families (verbosity, confirmations, auto_update, ai, packages, conflicts, theme/language/timezone) in a single nested if/elif chain, which Sonar flags for high cognitive complexity and will be hard to extend.

Consider refactoring to dedicated helpers per top-level section, e.g.:

def set(self, key: str, value: Any) -> bool:
    if self._preferences is None:
        self.load()
    parts = key.split(".")
    if parts[0] == "verbosity":
        self._set_verbosity(value)
    elif parts[0] == "confirmations":
        self._set_confirmations(parts[1:], value)
    # ...

This will make new preference sections (or extra validation rules) much easier to add and reason about.

---

193-199: Broad except Exception and re-wrapped errors hide root causes

Several methods (_create_backup, load, save, set, import_json) catch bare Exception and immediately raise a new IOError/ValueError with a stringified message, without preserving the original traceback (raise ... from e). This pattern makes debugging configuration problems harder and is what Ruff/Sonar are complaining about.

It would be safer to:

• Narrow the caught exceptions where possible (e.g., OSError, yaml.YAMLError, json.JSONDecodeError).
• Re-raise with raise ... from e so the original stack is preserved.
• Optionally log the error before rethrowing.

Functionality is fine as-is, but tightening this would improve diagnostics without changing behavior.

Also applies to: 222-225, 243-257, 353-355, 448-450

test/test_conflict_ui.py (1)

61-62: Remove unused result assignments in assertRaises blocks

In test_interactive_conflict_resolution_skip and test_conflict_detected_triggers_ui, result = self.cli._resolve_conflicts_interactive(conflicts) is assigned but never used inside a with self.assertRaises(SystemExit) block.

You can drop the assignment and just call the method:

-        with self.assertRaises(SystemExit):
-            result = self.cli._resolve_conflicts_interactive(conflicts)
+        with self.assertRaises(SystemExit):
+            self.cli._resolve_conflicts_interactive(conflicts)

This will clear the Ruff/Sonar warnings without changing test behavior.

Also applies to: 362-363

docs/IMPLEMENTATION_SUMMARY.md (1)

73-85: Minor markdownlint issues: add code fence languages and avoid emphasis-as-heading

markdownlint is flagging:

• Fenced blocks without a language (e.g., the “Example Output” and workflow snippets).
• The “PR Title” line using bold emphasis instead of a proper heading.

To quiet this without changing meaning:

• Add languages, e.g. text for console output blocks and bash for shell command examples.
• Replace emphasized headings like **"feat: ... "** with a Markdown heading (###), or leave as plain text.

Purely cosmetic, but it will keep automated doc checks clean.

Also applies to: 219-235, 291-325

cortex/dependency_resolver.py (2)

226-246: Conflict detection can emit duplicate pairs for the same packages

conflict_patterns is symmetric for some packages (e.g., both 'mysql-server': ['mariadb-server'] and 'mariadb-server': ['mysql-server']). With the current loop, a dependency set containing both can yield both ('mysql-server', 'mariadb-server') and ('mariadb-server', 'mysql-server').

This can lead to duplicate conflict prompts in the CLI. Consider normalizing pairs (e.g., tuple(sorted((dep_name, conflicting)))) and storing them in a set before returning a list, so each conflict pair appears only once.

---

171-225: resolve_dependencies is doing several distinct jobs and is over-complex

resolve_dependencies() currently:

• Fetches apt and predefined deps.
• Merges/deduplicates them.
• Optionally traverses transitive deps.
• Detects conflicts.
• Computes installation order.
• Populates and caches DependencyGraph.

Sonar’s complexity warning here is justified; future changes (e.g., more sources, richer conflict rules) will be hard to slot in. Consider extracting helpers like _collect_direct_dependencies, _collect_transitive_dependencies, and _build_graph to keep this method focused on orchestration.

cortex/cli.py (5)

31-38: Swallowing all exceptions when loading preferences hides configuration problems

In __init__, self.prefs_manager.load() is wrapped in except Exception: pass. If the YAML is malformed or the file is unreadable, this will silently skip loading, leaving _preferences unset and deferring the real error to a later call.

Prefer at least logging the failure, or restricting the catch to known benign cases (e.g., file-not-found) while surfacing real configuration errors early.

---

73-123: Conflict-resolution UI behavior looks correct; consider minor polish

The interactive flow correctly:

• Applies saved preferences first using the min:max conflict key.
• Prompts the user with three options and loops on invalid input.
• Records packages to remove and optionally persists preferences.

Two small polish ideas:

• Tighten the type hint to List[Tuple[str, str]] instead of List[tuple].
• Extract "conflicts.saved_resolutions" into a module/class constant to avoid magic strings.

Functionality otherwise aligns with the tests and issue requirements.

---

172-188: Dependency conflict integration is defensive but may fail silently and mis-identify target package

The install flow now:

• Picks target_package = software.split()[0].
• Wraps the entire dependency resolution + conflict handling in a bare except Exception: pass.

Two implications:

• For natural-language requests ("python 3.11 with pip"), only the first token is checked for conflicts, which may not match the actual apt package the interpreter chooses.
• Any resolver failure (e.g., missing dpkg/apt-cache) quietly disables conflict handling with no user feedback.

Consider:

• Letting CommandInterpreter surface the concrete package name(s) and using that instead of software.split()[0].
• Narrowing the exception handling to expected system errors and emitting a [INFO] Skipping conflict check: ... message when it’s disabled.

---

369-483: config() mixes many concerns and is over the usual complexity budget

config() currently handles eight subcommands, I/O formatting, interactive prompts, path handling, and error reporting in a single method. Sonar’s cognitive complexity warning is expected here.

A simple refactor would be to delegate each action to a helper:

def config(self, action: str, key: Optional[str] = None, value: Optional[str] = None):
    try:
        if action == "list":
            return self._config_list()
        if action == "get":
            return self._config_get(key)
        # ...
    except ValueError as e:
        ...

This keeps the public API unchanged, but makes each subcommand easier to test and evolve.

---

585-590: main() still emits emoji-style errors, contrary to the “[LABEL] only” output style

The exception handlers in main() print messages prefixed with ❌, while the rest of the CLI intentionally uses [ERROR]/[SUCCESS] labels and the docs explicitly call out “No Emojis”.

For consistency, consider switching these lines to use the same label style, e.g.:

-    except KeyboardInterrupt:
-        print("\n❌ Operation cancelled by user", file=sys.stderr)
+    except KeyboardInterrupt:
+        print("\n[ERROR] Operation cancelled by user", file=sys.stderr)

and similarly for the generic exception case.

Configuration used: CodeRabbit UI

Review profile: CHILL

Plan: Pro

test/test_conflict_ui.py (1)

282-297: Previous review concern addressed.

The test now properly patches builtins.input to avoid blocking on the confirmation prompt. The unused mock_input parameter is required due to the @patch decorator stacking order.

cortex/user_preferences.py (4)

122-141: from_dict silently ignores unknown keys and may raise TypeError on extra keys in nested dicts.

The nested dataclass instantiations (e.g., ConfirmationSettings(**data.get("confirmations", {}))) will raise TypeError if the loaded YAML/JSON contains unexpected keys. This can happen when users manually edit config files or when migrating from older versions with different schemas.

Consider filtering keys to match dataclass fields:

+    @staticmethod
+    def _filter_dataclass_keys(data: Dict, dataclass_type) -> Dict:
+        """Filter dict to only include keys that are valid dataclass fields."""
+        valid_keys = {f.name for f in dataclass_type.__dataclass_fields__.values()}
+        return {k: v for k, v in data.items() if k in valid_keys}
+
     @classmethod
     def from_dict(cls, data: Dict[str, Any]) -> 'UserPreferences':
         """Create UserPreferences from dictionary"""
-        confirmations = ConfirmationSettings(**data.get("confirmations", {}))
+        confirmations = ConfirmationSettings(**cls._filter_dataclass_keys(
+            data.get("confirmations", {}), ConfirmationSettings))

This improves forward/backward compatibility and prevents crashes on schema mismatches.

---

193-198: Add exception chaining for better traceability.

Multiple except blocks catch Exception and re-raise without chaining (also flagged at lines 223-225, 255-256, 354). This loses the original traceback and makes debugging harder.

         try:
             import shutil
             shutil.copy2(self.config_path, backup_path)
             return backup_path
-        except Exception as e:
-            raise IOError(f"Failed to create backup: {str(e)}")
+        except Exception as e:
+            raise IOError(f"Failed to create backup: {e}") from e

Apply the same pattern (raise ... from e) to the other locations for consistent error handling.

---

327-329: Consider adding range validation for max_suggestions in set() to match validate() logic.

set() only checks that max_suggestions is an integer, but validate() (line 407-408) also requires it to be at least 1. This allows invalid values to be set and persisted before validation catches them.

             elif parts[1] == "max_suggestions" and not isinstance(value, int):
                 raise ValueError("max_suggestions must be an integer")
+            elif parts[1] == "max_suggestions" and value < 1:
+                raise ValueError("max_suggestions must be at least 1")

---

403-405: Hardcoded model list may become stale.

The valid_models list is hardcoded in validate(). As new models are released and old ones deprecated, this list will require manual updates.

Consider extracting this to a module-level constant or making it configurable to simplify future maintenance.

test/test_conflict_ui.py (1)

248-251: Assertion at line 250 may be fragile due to YAML output format.

The test asserts 'ai.model' in output, but yaml.dump() produces nested YAML with ai: and model: on separate lines, not the dot-notation key. The current assertion might pass if ai.model or gpt-4 appears elsewhere, but it doesn't precisely validate the intended behavior.

Consider asserting on the actual YAML structure or just the value:

         output = mock_stdout.getvalue()
-        self.assertIn('ai.model', output)
-        self.assertIn('gpt-4', output)
+        self.assertIn('model: gpt-4', output)

Configuration used: CodeRabbit UI

Review profile: CHILL

Plan: Pro

test/test_conflict_ui.py (2)

282-297: Past review addressed: input is now patched for reset test.

The test correctly patches builtins.input to return 'y', preventing the test from blocking on interactive input. The unused mock_stdout and mock_input arguments are intentional for stdout capture and mock ordering.

---

385-399: Weak assertion already flagged in past review.

The assertion at line 399 (len(graph.conflicts) > 0 or mock_run.called) is too permissive and was previously flagged. Consider testing _detect_conflicts directly with controlled inputs for reliable coverage.

test/test_conflict_ui.py (2)

60-68: Remove unused result variable assignment.

The result variable is assigned but never used since the test expects SystemExit. Static analysis correctly flags this.

         # Should exit on choice 3
         with self.assertRaises(SystemExit):
-            result = self.cli._resolve_conflicts_interactive(conflicts)
+            self.cli._resolve_conflicts_interactive(conflicts)

---

362-364: Remove unused result variable assignment.

Same issue as line 62 - the result variable is never used.

         # Should exit on choice 3
         with self.assertRaises(SystemExit):
-            result = self.cli._resolve_conflicts_interactive(conflicts)
+            self.cli._resolve_conflicts_interactive(conflicts)

cortex/user_preferences.py (4)

127-146: Consider handling unknown keys in from_dict() for forward compatibility.

If a config file contains keys not defined in the dataclass (e.g., from a newer version), the **data.get("ai", {}) unpacking will raise TypeError. Consider filtering to known fields:

     @classmethod
     def from_dict(cls, data: Dict[str, Any]) -> 'UserPreferences':
         """Create UserPreferences from dictionary"""
-        confirmations = ConfirmationSettings(**data.get("confirmations", {}))
-        auto_update = AutoUpdateSettings(**data.get("auto_update", {}))
-        ai = AISettings(**data.get("ai", {}))
-        packages = PackageSettings(**data.get("packages", {}))
-        conflicts = ConflictSettings(**data.get("conflicts", {}))
+        def filter_fields(cls, d):
+            from dataclasses import fields
+            valid = {f.name for f in fields(cls)}
+            return {k: v for k, v in d.items() if k in valid}
+        
+        confirmations = ConfirmationSettings(**filter_fields(ConfirmationSettings, data.get("confirmations", {})))
+        auto_update = AutoUpdateSettings(**filter_fields(AutoUpdateSettings, data.get("auto_update", {})))
+        ai = AISettings(**filter_fields(AISettings, data.get("ai", {})))
+        packages = PackageSettings(**filter_fields(PackageSettings, data.get("packages", {})))
+        conflicts = ConflictSettings(**filter_fields(ConflictSettings, data.get("conflicts", {})))

---

288-359: High cognitive complexity in set() method.

SonarCloud flags cognitive complexity of 42 (limit: 15). The method works correctly but could benefit from refactoring using a dispatch table pattern. This is a recommended improvement for maintainability but not blocking for this PR.

Consider extracting validators/setters into a dispatch table:

# Example refactor approach
_SETTERS = {
    "verbosity": _set_verbosity,
    "confirmations": _set_confirmations,
    "ai": _set_ai,
    # ...
}

def set(self, key: str, value: Any) -> bool:
    parts = key.split(".")
    setter = self._SETTERS.get(parts[0])
    if setter:
        return setter(self, parts, value)
    raise ValueError(f"Unknown preference key: {key}")

---

226-230: Add exception chaining for better debugging.

When re-raising exceptions, use from e to preserve the original stack trace. This applies to multiple locations in the file.

         except yaml.YAMLError as e:
-            raise ValueError(f"Invalid YAML in config file: {str(e)}")
+            raise ValueError(f"Invalid YAML in config file: {e}") from e
         except Exception as e:
-            raise IOError(f"Failed to load config file: {str(e)}")
+            raise IOError(f"Failed to load config file: {e}") from e

---

361-388: Method always returns True - consider simplifying.

SonarCloud notes that reset() always returns True since errors raise exceptions. Consider returning None or making it a void method, though this is a minor stylistic preference.

cortex/cli.py (3)

35-38: Silent exception handling on preferences load.

The bare except Exception: pass silently ignores all errors when loading preferences. Consider logging a warning so users know if their config failed to load.

         try:
             self.prefs_manager.load()
-        except Exception:
-            pass
+        except Exception as e:
+            # Preferences load failed - continue with defaults
+            import logging
+            logging.warning(f"Failed to load preferences, using defaults: {e}")

---

83-84: Extract repeated literals to constants.

The string "conflicts.saved_resolutions" is used 3 times. Consider defining it as a class constant for maintainability.

 class CortexCLI:
+    CONFLICTS_SAVED_RESOLUTIONS_KEY = "conflicts.saved_resolutions"
+    
     def __init__(self):
         # ...
     
     def _resolve_conflicts_interactive(self, conflicts: List[tuple]) -> Dict[str, List[str]]:
         resolutions = {'remove': []}
-        saved_resolutions = self.prefs_manager.get("conflicts.saved_resolutions") or {}
+        saved_resolutions = self.prefs_manager.get(self.CONFLICTS_SAVED_RESOLUTIONS_KEY) or {}

---

369-482: High cognitive complexity in config() method.

SonarCloud flags cognitive complexity of 37 (limit: 15). Consider extracting each action into a separate method (e.g., _config_list(), _config_get(), etc.) using a dispatch table pattern.

docs/IMPLEMENTATION_SUMMARY.md (2)

73-84: Add language specifier to fenced code block.

The code block showing example output should have a language specifier for proper rendering.

 **Example Output:**
-```
+```text
 ====================================================================
 Package Conflicts Detected
 ====================================================================

---

219-234: Add language specifier to workflow diagram.

The workflow diagram code block should have a language specifier.

 **Workflow:**
-```
+```text
 User runs: cortex install nginx
     ↓

Configuration used: CodeRabbit UI

Review profile: CHILL

Plan: Pro

test/test_conflict_ui.py (1)

385-399: Strengthen assertion in test_dependency_resolver_detects_conflicts.

The final assertion:

self.assertTrue(len(graph.conflicts) > 0 or mock_run.called)

passes whenever the subprocess mock is called, even if no conflicts are detected, so it doesn’t really validate conflict detection logic (as previously noted). Prefer asserting on the actual conflicts, e.g.:

-        self.assertTrue(len(graph.conflicts) > 0 or mock_run.called)
+        self.assertTrue(mock_run.called)
+        self.assertIn(('nginx', 'apache2'), graph.conflicts)

or directly unit‑test _detect_conflicts with a controlled dependency list.

cortex/cli.py (2)

172-189: Avoid swallowing dependency resolver failures; report them instead.

This block:

try:
    graph = resolver.resolve_dependencies(target_package)
    ...
except Exception:
    pass

means any resolver error (e.g., missing apt-cache, permissions, bugs) will be completely silent and conflicts won’t be checked. That undermines the feature and was already flagged in a prior review.

You should at least surface a warning and keep installing, e.g.:

-            try:
-                graph = resolver.resolve_dependencies(target_package)
-                if graph.conflicts:
-                    resolutions = self._resolve_conflicts_interactive(graph.conflicts)
-                    
-                    if resolutions['remove']:
-                        for pkg_to_remove in resolutions['remove']:
-                            if not any(f"remove {pkg_to_remove}" in cmd for cmd in commands):
-                                commands.insert(0, f"sudo apt-get remove -y {pkg_to_remove}")
-                                self._print_status("[INFO]", f"Added command to remove conflicting package: {pkg_to_remove}")
-            except Exception:
-                pass
+            try:
+                graph = resolver.resolve_dependencies(target_package)
+                if graph.conflicts:
+                    resolutions = self._resolve_conflicts_interactive(graph.conflicts)
+                    if resolutions['remove']:
+                        for pkg_to_remove in resolutions['remove']:
+                            if not any(f"remove {pkg_to_remove}" in cmd for cmd in commands):
+                                commands.insert(0, f"sudo apt-get remove -y {pkg_to_remove}")
+                                self._print_status("[INFO]", f"Added command to remove conflicting package: {pkg_to_remove}")
+            except Exception as e:
+                self._print_status("[INFO]", f"Could not check for conflicts for {target_package}: {e}")

Optionally narrow the exception type if DependencyResolver exposes its own error class.

Also, target_package = software.split()[0] is a coarse heuristic for natural‑language requests; consider deriving the primary package name from the parsed commands instead for better accuracy.

---

369-482: Config command works but is brittle around yaml and a bit monolithic.

• The inline import yaml in the "list" branch will raise ImportError if PyYAML isn’t installed. Given previous feedback, consider moving the import to module level with a guarded fallback (e.g., to JSON) so cortex config list doesn’t crash outright.

• The config() method’s long if/elif ladder plus embedded input prompts gives it high cognitive complexity (also flagged by Sonar). Splitting each action into a small helper (e.g., _config_list(), _config_get(), …) would simplify reasoning and testing.

• For action == "reset" without key, you always prompt via input("Continue? (y/n): "). That’s fine for interactive CLI use, but it complicates non‑interactive callers; a future force flag (plumbed from argparse) would make scripting easier while preserving safety for humans.

Check current PyYAML installation recommendations for CLI tools that optionally render YAML, and whether a JSON fallback is considered a best practice when PyYAML is missing.

cortex/cli.py (1)

54-61: Consider central constants for status labels.

"[INFO]" and other status labels are duplicated; Sonar already flagged this. A small module-level constant (e.g., INFO = "[INFO]", ERROR = "[ERROR]", etc.) keeps the labels consistent and makes future changes easier.

test/test_conflict_ui.py (2)

235-284: Tidy unused mock arguments in config tests.

mock_stdout / mock_input are injected by @patch but not used in test_config_list_command and test_config_reset_command, which Ruff flags. Either use them (e.g., inspect output) or rename to _stdout / _input to make the intentional discard explicit and silence the warnings.

---

366-384: test_saved_preference_bypasses_ui doesn’t actually exercise the UI path.

This test currently just inspects the stored dict and re‑implements the “if conflict_key in saved” logic inline, without calling _resolve_conflicts_interactive or asserting that input() isn’t called.

To truly verify auto‑apply behavior, consider something like:

+    @patch('builtins.input')
+    def test_saved_preference_bypasses_ui(self, mock_input):
+        conflict_key = 'mariadb-server:mysql-server'
+        self.cli.prefs_manager.set('conflicts.saved_resolutions', {
+            conflict_key: 'mysql-server'
+        })
+        self.cli.prefs_manager.save()
+
+        conflicts = [('mysql-server', 'mariadb-server')]
+        result = self.cli._resolve_conflicts_interactive(conflicts)
+
+        mock_input.assert_not_called()
+        self.assertIn('remove', result)
+        self.assertIn('mariadb-server', result['remove'])

This would explicitly confirm that saved preferences bypass prompts and still yield the expected removal list.

Configuration used: CodeRabbit UI

Review profile: CHILL

Plan: Pro

cortex/cli.py (3)

223-241: Fix import path and avoid silently swallowing exceptions.

Two issues:

1. Incorrect import path: Line 225 imports from dependency_resolver but the module is at cortex/dependency_resolver.py based on the project structure.

2. Silent exception handling (noted in previous review): The bare except Exception: pass hides failures like missing apt-cache, permission errors, or import failures.

             # Check for package conflicts using DependencyResolver
-            from dependency_resolver import DependencyResolver
+            from cortex.dependency_resolver import DependencyResolver
             resolver = DependencyResolver()
             
             target_package = software.split()[0]
             
             try:
                 graph = resolver.resolve_dependencies(target_package)
                 if graph.conflicts:
                     resolutions = self._resolve_conflicts_interactive(graph.conflicts)
                     
                     if resolutions['remove']:
                         for pkg_to_remove in resolutions['remove']:
                             if not any(f"remove {pkg_to_remove}" in cmd for cmd in commands):
                                 commands.insert(0, f"sudo apt-get remove -y {pkg_to_remove}")
                                 self._print_status("[INFO]", f"Added command to remove conflicting package: {pkg_to_remove}")
-            except Exception:
-                pass
+            except ImportError:
+                self._print_status("[INFO]", "Dependency resolver not available, skipping conflict check")
+            except Exception as e:
+                self._print_status("[INFO]", f"Could not check for conflicts: {e}")

This repeats feedback from the previous review regarding silent exception handling.

---

437-444: Handle missing PyYAML dependency gracefully.

The import yaml at line 439 will raise ImportError if PyYAML is not installed, crashing the CLI. This was noted in a previous review.

+# At module level or with fallback:
+try:
+    import yaml
+    HAS_YAML = True
+except ImportError:
+    HAS_YAML = False
+
 # In config() method, action == "list":
             if action == "list":
                 prefs = self.prefs_manager.list_all()
                 
                 print("\n[INFO] Current Configuration:")
                 print("=" * 60)
-                import yaml
-                print(yaml.dump(prefs, default_flow_style=False, sort_keys=False))
+                if HAS_YAML:
+                    print(yaml.dump(prefs, default_flow_style=False, sort_keys=False))
+                else:
+                    print(json.dumps(prefs, indent=2))

---

472-484: Interactive input() in config('reset') blocks non-interactive use.

When action == "reset" and key is None, the method calls input() which will block or crash in automated/test environments. Consider adding a --force flag or ensuring tests mock input.

This was noted in a previous review. Options:

• Add a force parameter to skip confirmation
• Document that tests must patch input

cortex/cli.py (2)

169-186: Extract duplicated literal and add null guard.

The literal "conflicts.saved_resolutions" is duplicated 3 times (SonarCloud flagged). Also, prefs_manager may be None.

Define a constant at module or class level:

CONFLICTS_SAVED_RESOLUTIONS_KEY = "conflicts.saved_resolutions"

Then use it consistently:

+CONFLICTS_SAVED_RESOLUTIONS_KEY = "conflicts.saved_resolutions"
+
 def _ask_save_preference(self, pkg1: str, pkg2: str, preferred: str):
     ...
     save = input("Save this preference for future conflicts? (y/N): ").strip().lower()
-    if save == 'y':
+    if save == 'y' and self.prefs_manager is not None:
         conflict_key = f"{min(pkg1, pkg2)}:{max(pkg1, pkg2)}"
-        saved_resolutions = self.prefs_manager.get("conflicts.saved_resolutions") or {}
+        saved_resolutions = self.prefs_manager.get(CONFLICTS_SAVED_RESOLUTIONS_KEY) or {}
         saved_resolutions[conflict_key] = preferred
-        self.prefs_manager.set("conflicts.saved_resolutions", saved_resolutions)
+        self.prefs_manager.set(CONFLICTS_SAVED_RESOLUTIONS_KEY, saved_resolutions)
         self.prefs_manager.save()
         print("Preference saved.")

---

421-534: Consider refactoring config() to reduce cognitive complexity.

SonarCloud reports cognitive complexity of 37 (allowed: 15). The method handles 8 different actions with nested conditionals. Consider extracting each action into a private method.

def config(self, action: str, key: Optional[str] = None, value: Optional[str] = None):
    """Manage user preferences and configuration."""
    handlers = {
        "list": self._config_list,
        "get": self._config_get,
        "set": self._config_set,
        "reset": self._config_reset,
        "validate": self._config_validate,
        "info": self._config_info,
        "export": self._config_export,
        "import": self._config_import,
    }
    
    handler = handlers.get(action)
    if not handler:
        self._print_error(f"Unknown config action: {action}")
        return 1
    
    try:
        return handler(key, value)
    except ValueError as e:
        self._print_error(str(e))
        return 1
    except Exception as e:
        self._print_error(f"Configuration error: {e}")
        return 1

docs/IMPLEMENTATION_SUMMARY.md (2)

9-9: Add language specifier to fenced code block.

The code block at line 9 lacks a language specifier (markdownlint MD040).

 Select action for Conflict 1 [1-3]: 
-```
+```text

---

144-159: Add language specifier to workflow diagram.

The workflow diagram code block lacks a language specifier.

 ### Workflow:
-```
+```text
 User runs: cortex install nginx
     ↓
 DependencyResolver detects conflict with apache2

Configuration used: CodeRabbit UI

Review profile: CHILL

Plan: Pro