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Update review-ready changes#27

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syntaxwanderer wants to merge 3 commits intomasterfrom
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Update review-ready changes#27
syntaxwanderer wants to merge 3 commits intomasterfrom
develop

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@syntaxwanderer syntaxwanderer commented Apr 30, 2026

Summary

  • Review-ready branch develop targeting master
  • 8 commit(s) ahead, 137 changed file(s)

Changes

  • Refactor configuration, Ai, and related areas
  • Fix phpunit no-tests review findings
  • Fix Ai and tests
  • Harden review ownership boundary guards
  • Fix README.md, resources, and related areas
  • Reject empty make module target
  • Tighten make module target guidance
  • Fix Capability, Console, and related areas

Checks

  • No repo-defined automated checks were found

What to Review

  • README.md
  • config/module-structure.php
  • config/phpstan-ai-verify.neon
  • resources/auto-deploy
  • resources/remote-deploy
  • src/Ai
  • src/Application
  • src/Capability

What to Verify

  • Smoke-check the main behavior changed by this branch
  • Watch logs or console output for regressions in touched paths

Summary by CodeRabbit

  • New Features

    • Added module structure validation to ai:verify command with new --all option for repo-wide verification across packages and modules.
    • Added PHPStan DI verification support to detect dependency injection issues.
    • Enhanced test fixture classification to distinguish fixtures from actual test cases.
  • Improvements

    • Simplified lint command names from semitexa:lint:* to lint:* format.

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coderabbitai Bot commented Apr 30, 2026

Important

Review skipped

Too many files!

This PR contains 157 files, which is 7 over the limit of 150.

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: ac398336-b0df-41b2-94d3-416920244158

📥 Commits

Reviewing files that changed from the base of the PR and between 71417a3 and 706be85.

📒 Files selected for processing (157)
  • config/module-structure.php
  • resources/templates/payload.php.tpl
  • src/Application/Console/Command/AiAskCommand.php
  • src/Application/Console/Command/AiBacklogCommand.php
  • src/Application/Console/Command/AiContextCommand.php
  • src/Application/Console/Command/AiEpicCommand.php
  • src/Application/Console/Command/AiOrientCommand.php
  • src/Application/Console/Command/AiPlanCommand.php
  • src/Application/Console/Command/AiTaskCommand.php
  • src/Application/Console/Command/AiTraceCommand.php
  • src/Application/Console/Command/AiVerifyCommand.php
  • src/Application/Console/Command/AiWorkCommand.php
  • src/Application/Console/Command/DevGraph/DevGraphCapabilitiesCommand.php
  • src/Application/Console/Command/DevGraph/DevGraphMineConventionsCommand.php
  • src/Application/Console/Command/DevGraph/DevGraphPathCommand.php
  • src/Application/Console/Command/MakeCommand.php
  • src/Application/Console/Command/MakeCommandCommand.php
  • src/Application/Console/Command/MakeContractCommand.php
  • src/Application/Console/Command/MakeEventListenerCommand.php
  • src/Application/Console/Command/MakeHandlerCommand.php
  • src/Application/Console/Command/MakeModuleCommand.php
  • src/Application/Console/Command/MakePageCommand.php
  • src/Application/Console/Command/MakePayloadCommand.php
  • src/Application/Console/Command/MakeResourceCommand.php
  • src/Application/Console/Command/MakeServiceCommand.php
  • src/Application/Service/Ai/Classifier/ClassificationResult.php
  • src/Application/Service/Ai/Classifier/TaskClassifier.php
  • src/Application/Service/Ai/Context/ContextPacker.php
  • src/Application/Service/Ai/Context/PriorArtItem.php
  • src/Application/Service/Ai/Convention/ConventionMiner.php
  • src/Application/Service/Ai/Convention/ConventionStore.php
  • src/Application/Service/Ai/Convention/HandlerInjection.php
  • src/Application/Service/Ai/Convention/ModuleConventions.php
  • src/Application/Service/Ai/Plan/RiskAssessment.php
  • src/Application/Service/Ai/Plan/RiskScorer.php
  • src/Application/Service/Ai/Recipe/Recipe.php
  • src/Application/Service/Ai/Recipe/RecipeRegistry.php
  • src/Application/Service/Ai/Similarity/DuplicateDetector.php
  • src/Application/Service/Ai/Similarity/DuplicateGate.php
  • src/Application/Service/Ai/Similarity/DuplicateQuery.php
  • src/Application/Service/Ai/Similarity/IndexedArtifact.php
  • src/Application/Service/Ai/Similarity/SimilarityFinding.php
  • src/Application/Service/Ai/Similarity/SimilarityIndex.php
  • src/Application/Service/Ai/Similarity/SimilarityIndexBuilder.php
  • src/Application/Service/Ai/Trace/Trace.php
  • src/Application/Service/Ai/Trace/TraceAutoAppender.php
  • src/Application/Service/Ai/Trace/TraceEvent.php
  • src/Application/Service/Ai/Trace/TraceEventKind.php
  • src/Application/Service/Ai/Trace/TraceHeader.php
  • src/Application/Service/Ai/Trace/TraceStore.php
  • src/Application/Service/Ai/Verify/ChangedFile.php
  • src/Application/Service/Ai/Verify/ChangedFileClassifier.php
  • src/Application/Service/Ai/Verify/Phpstan/PhpstanRunResult.php
  • src/Application/Service/Ai/Verify/Phpstan/PhpstanRunner.php
  • src/Application/Service/Ai/Verify/ProcessRunner.php
  • src/Application/Service/Ai/Verify/ShellProcessRunner.php
  • src/Application/Service/Ai/Verify/Structure/DetectedModule.php
  • src/Application/Service/Ai/Verify/Structure/FilePlacementRule.php
  • src/Application/Service/Ai/Verify/Structure/LocalModuleStructureExtension.php
  • src/Application/Service/Ai/Verify/Structure/ModuleStructureRule.php
  • src/Application/Service/Ai/Verify/Structure/ModuleStructureSpec.php
  • src/Application/Service/Ai/Verify/Structure/ModuleStructureSpecLoader.php
  • src/Application/Service/Ai/Verify/Structure/ModuleStructureTargetResolver.php
  • src/Application/Service/Ai/Verify/Structure/ModuleStructureValidator.php
  • src/Application/Service/Ai/Verify/Structure/ModuleStructureViolation.php
  • src/Application/Service/Ai/Verify/VerificationExecutor.php
  • src/Application/Service/Ai/Verify/VerificationPlan.php
  • src/Application/Service/Ai/Verify/VerificationPlanner.php
  • src/Application/Service/Ai/Verify/VerificationResult.php
  • src/Application/Service/Ai/Verify/VerificationTarget.php
  • src/Application/Service/Ai/Work/BacklogHygiene.php
  • src/Application/Service/Ai/Work/BacklogQuality.php
  • src/Application/Service/Ai/Work/BacklogScope.php
  • src/Application/Service/Ai/Work/Epic.php
  • src/Application/Service/Ai/Work/EpicStatus.php
  • src/Application/Service/Ai/Work/EpicStore.php
  • src/Application/Service/Ai/Work/HygieneAssessment.php
  • src/Application/Service/Ai/Work/JsonFile.php
  • src/Application/Service/Ai/Work/ResumeService.php
  • src/Application/Service/Ai/Work/ResumeSnapshot.php
  • src/Application/Service/Ai/Work/Task.php
  • src/Application/Service/Ai/Work/TaskStatus.php
  • src/Application/Service/Ai/Work/TaskStore.php
  • src/Application/Service/Ai/Work/WorkId.php
  • src/Application/Service/Capability/CapabilityRegistry.php
  • src/Application/Service/Console/CommandDelegator.php
  • src/Application/Service/Generation/Builder/CommandPlanBuilder.php
  • src/Application/Service/Generation/Builder/ContractPlanBuilder.php
  • src/Application/Service/Generation/Builder/EventListenerPlanBuilder.php
  • src/Application/Service/Generation/Builder/HandlerPlanBuilder.php
  • src/Application/Service/Generation/Builder/ModulePlanBuilder.php
  • src/Application/Service/Generation/Builder/PagePlanBuilder.php
  • src/Application/Service/Generation/Builder/PayloadPlanBuilder.php
  • src/Application/Service/Generation/Builder/ResourcePlanBuilder.php
  • src/Application/Service/Generation/Builder/ServicePlanBuilder.php
  • src/Application/Service/Generation/Contract/FileWriterInterface.php
  • src/Application/Service/Generation/Contract/NameInflectorInterface.php
  • src/Application/Service/Generation/Contract/TemplateResolverInterface.php
  • src/Application/Service/Generation/Data/CapabilityManifest.php
  • src/Application/Service/Generation/Data/CommandCapability.php
  • src/Application/Service/Generation/Data/FileType.php
  • src/Application/Service/Generation/Data/GenerationPlan.php
  • src/Application/Service/Generation/Data/GenerationResult.php
  • src/Application/Service/Generation/Data/PlannedFile.php
  • src/Application/Service/Generation/Support/CapabilityManifestFormatter.php
  • src/Application/Service/Generation/Support/JsonResultFormatter.php
  • src/Application/Service/Generation/Support/LlmHintsFormatter.php
  • src/Application/Service/Generation/Support/NameInflector.php
  • src/Application/Service/Generation/Support/ReplayArgBuilder.php
  • src/Application/Service/Generation/Support/TemplateRenderer.php
  • src/Application/Service/Generation/Support/TemplateResolver.php
  • src/Application/Service/Generation/Verifier/PostWriteLinter.php
  • src/Application/Service/Generation/Writer/SafeFileWriter.php
  • tests/Fixtures/Expected/non-public-post-payload.php
  • tests/Fixtures/Expected/public-get-payload.php
  • tests/Integration/AiAskCommandTest.php
  • tests/Integration/AiTraceCommandTest.php
  • tests/Integration/AiVerifyCommandTest.php
  • tests/Integration/DevGraphPathCommandTest.php
  • tests/Integration/DryRunTest.php
  • tests/Integration/ForceOverwriteTest.php
  • tests/Integration/MakeDispatcherTest.php
  • tests/Integration/MakeHandlerCommandTest.php
  • tests/Integration/MakePageCommandTest.php
  • tests/Integration/MakePayloadCommandTest.php
  • tests/Integration/MakeResourceCommandTest.php
  • tests/Integration/WorkflowTraceTest.php
  • tests/Unit/Ai/Convention/ConventionMinerTest.php
  • tests/Unit/Ai/Plan/RiskScorerTest.php
  • tests/Unit/Ai/Similarity/DuplicateDetectorTest.php
  • tests/Unit/Ai/Similarity/DuplicateGateTest.php
  • tests/Unit/Ai/Similarity/SimilarityIndexBuilderTest.php
  • tests/Unit/Ai/Trace/TraceStoreTest.php
  • tests/Unit/Ai/Verify/ChangedFileClassifierTest.php
  • tests/Unit/Ai/Verify/Phpstan/PhpstanRunnerTest.php
  • tests/Unit/Ai/Verify/Structure/LocalModuleStructureExtensionTest.php
  • tests/Unit/Ai/Verify/Structure/ModuleStructureCrashTestTest.php
  • tests/Unit/Ai/Verify/Structure/ModuleStructureSpecLoaderTest.php
  • tests/Unit/Ai/Verify/Structure/ModuleStructureTargetResolverTest.php
  • tests/Unit/Ai/Verify/Structure/ModuleStructureValidatorTest.php
  • tests/Unit/Ai/Verify/VerificationExecutorTest.php
  • tests/Unit/Ai/Verify/VerificationPlannerTest.php
  • tests/Unit/Ai/Work/EpicStoreTest.php
  • tests/Unit/Ai/Work/ResumeServiceTest.php
  • tests/Unit/Ai/Work/TaskStoreTest.php
  • tests/Unit/Ai/Work/WorkIdTest.php
  • tests/Unit/CapabilityManifestFormatterTest.php
  • tests/Unit/Console/Command/AiEpicCommandTest.php
  • tests/Unit/Console/Command/AiWorkCommandTest.php
  • tests/Unit/Generation/Builder/HandlerPlanBuilderTest.php
  • tests/Unit/Generation/Builder/ModulePlanBuilderTest.php
  • tests/Unit/JsonResultFormatterTest.php
  • tests/Unit/LlmHintsFormatterTest.php
  • tests/Unit/NameInflectorTest.php
  • tests/Unit/OwnershipBoundaryTest.php
  • tests/Unit/SafeFileWriterTest.php
  • tests/Unit/TemplateRendererTest.php

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📝 Walkthrough

Walkthrough

This pull request introduces a comprehensive module structure validation framework for Semitexa, migrates console commands to the Application layer, and extends the ai:verify command with structure and dependency-injection validation capabilities. The changes include a new authoritative module-structure specification, a strict validator for directory/file placement, enhanced file classification distinguishing tests from test fixtures, and PHPStan-DI verification infrastructure.

Changes

Cohort / File(s) Summary
Module Structure Specification & Validation Framework
config/module-structure.php, src/Ai/Verify/Structure/ModuleStructureSpec.php, src/Ai/Verify/Structure/ModuleStructureRule.php, src/Ai/Verify/Structure/FilePlacementRule.php, src/Ai/Verify/Structure/ModuleStructureSpecLoader.php, src/Ai/Verify/Structure/ModuleStructureValidator.php, src/Ai/Verify/Structure/ModuleStructureViolation.php
Introduces authoritative module/package structure specification with strict allowlists for Application, Domain, and package layers; defines file placement rules with exemption and content-revocation mechanisms; provides spec loading, validation, and violation reporting infrastructure.
Module Detection & Verification Planning
src/Ai/Verify/Structure/DetectedModule.php, src/Ai/Verify/Structure/ModuleStructureTargetResolver.php, src/Ai/Verify/VerificationPlanner.php, src/Ai/Verify/VerificationTarget.php
Adds module detection logic for application and package modules, resolver to map changed files to affected modules, and extends verification planner to schedule module-structure and phpstan-DI targets alongside existing lint/phpunit targets.
File Classification Enhancement
src/Ai/Verify/ChangedFile.php, src/Ai/Verify/ChangedFileClassifier.php
Introduces KIND_TEST_FIXTURE constant and refines classifier to distinguish test-fixture helpers/stubs in tests/ tree from actual *Test.php test classes using directory-name heuristics.
PHPStan DI Verification Infrastructure
config/phpstan-ai-verify.neon, src/Ai/Verify/Phpstan/PhpstanRunResult.php, src/Ai/Verify/Phpstan/PhpstanRunner.php
Adds dedicated PHPStan configuration for DI rule validation, result value object capturing status/diagnostics/signal, and runner orchestrator that executes PHPStan and translates JSON results into structured diagnostics with rule identifiers preserved.
Verification Executor Extensions
src/Ai/Verify/VerificationExecutor.php, src/Ai/Verify/VerificationResult.php
Extends executor to route module_structure and phpstan_di verification types, adds diagnostics array to results, and expands phpunit handling to support directory-scoped test suite execution via filePath.
Console Command Namespace Migration
src/Application/Console/Command/Ai*Command.php, src/Application/Console/Command/DevGraph/*Command.php, src/Application/Console/Command/Make*Command.php, src/Application/Console/Command/Logs*Command.php, src/Application/Console/Command/Scaffold*Command.php, src/Application/Console/Command/Support/CommandDelegator.php
Migrates all console commands from Semitexa\Dev\Console\Command namespace to Semitexa\Dev\Application\Console\Command, updates BaseCommand import paths, and adjusts command registration in lint tooling.
Extended Verification Integration Tests
tests/Integration/AiVerifyCommandTest.php, tests/Integration/AiAskCommandTest.php, tests/Integration/AiTraceCommandTest.php, tests/Integration/WorkflowTraceTest.php, tests/Integration/DevGraphCommandTest.php, tests/Integration/DuplicateRefusalTest.php, tests/Integration/MakeModuleCommandTest.php, tests/Integration/MakeDispatcherTest.php
Updates command imports to new namespace, switches lint command identifiers from semitexa:lint:* to lint:*, and adds comprehensive module-structure validation scenarios including violation detection and passing canonical layouts.
New Unit Test Coverage
tests/Unit/Ai/Verify/ChangedFileClassifierTest.php, tests/Unit/Ai/Verify/Phpstan/PhpstanRunnerTest.php, tests/Unit/Ai/Verify/Structure/ModuleStructureCrashTestTest.php, tests/Unit/Ai/Verify/Structure/ModuleStructureSpecLoaderTest.php, tests/Unit/Ai/Verify/Structure/ModuleStructureTargetResolverTest.php, tests/Unit/Ai/Verify/VerificationExecutorTest.php, tests/Unit/Ai/Verify/VerificationPlannerTest.php, tests/Unit/Console/Command/Ai*.php, tests/Unit/Console/Command/AiWorkCommandTest.php, tests/Unit/OwnershipBoundaryTest.php
Adds extensive test coverage for file classification fixture detection, PHPStan result parsing, module structure validation against canonical and violation scenarios, resolver behavior, verification planning with fixture/phpstan-DI scheduling, and command namespace alignment.
Recipe & Post-Write Updates
src/Ai/Recipe/RecipeRegistry.php, src/Generation/Verifier/PostWriteLinter.php
Updates CLI command example hints in recipe registry and switches post-write lint checks from semitexa:lint:* to lint:* command names.

Sequence Diagram(s)

sequenceDiagram
    participant Client as ai:verify Command
    participant Planner as VerificationPlanner
    participant Resolver as ModuleStructureTargetResolver
    participant Executor as VerificationExecutor
    participant Validator as ModuleStructureValidator
    participant Loader as ModuleStructureSpecLoader
    participant PhpstanRunner as PhpstanRunner

    Client->>Planner: plan(changedFiles)
    Planner->>Resolver: resolve(changedFiles)
    Resolver-->>Planner: DetectedModule[] (app & package modules)
    Planner->>Planner: schedule targets for each module<br/>(module_structure, phpunit, lint, phpstan_di)
    Planner-->>Client: VerificationTarget[]

    Client->>Executor: execute(targets)
    
    par For each module_structure target
        Executor->>Loader: load()
        Loader-->>Executor: ModuleStructureSpec
        Executor->>Validator: validate(DetectedModule)
        Validator->>Validator: recursively walk module tree<br/>verify directories/files against spec
        Validator-->>Executor: ModuleStructureViolation[]
        Executor-->>Client: VerificationResult (pass/fail + diagnostics)
    and For each phpstan_di target
        Executor->>PhpstanRunner: run(filePaths)
        PhpstanRunner->>PhpstanRunner: execute phpstan with<br/>phpstan-ai-verify.neon config
        PhpstanRunner->>PhpstanRunner: parse JSON results<br/>extract diagnostics by identifier
        PhpstanRunner-->>Executor: PhpstanRunResult
        Executor-->>Client: VerificationResult (pass/fail + diagnostics)
    and For other targets (lint, phpunit, syntax)
        Executor->>Executor: execute existing verification flow
        Executor-->>Client: VerificationResult
    end
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Estimated code review effort

🎯 4 (Complex) | ⏱️ ~70 minutes

Possibly related PRs

Poem

🐰 A hop through the structure, so neat and aligned,
With modules and layers all carefully defined,
Commands march Application-ward in formation,
While fixtures meet tests without confusion,
And PHPStan joins in—no more intrusion!

🚥 Pre-merge checks | ✅ 3 | ❌ 2

❌ Failed checks (1 warning, 1 inconclusive)

Check name Status Explanation Resolution
Docstring Coverage ⚠️ Warning Docstring coverage is 50.54% which is insufficient. The required threshold is 80.00%. Write docstrings for the functions missing them to satisfy the coverage threshold.
Title check ❓ Inconclusive The title 'Update review-ready changes' is vague and generic, using non-descriptive language that does not convey meaningful information about the specific changeset. Replace with a more specific title that describes the main change, such as 'Add module structure validation and refactor console commands' or 'Introduce strict module structure spec and PHPStan DI verification'.
✅ Passed checks (3 passed)
Check name Status Explanation
Description Check ✅ Passed Check skipped - CodeRabbit’s high-level summary is enabled.
Linked Issues check ✅ Passed Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check ✅ Passed Check skipped because no linked issues were found for this pull request.

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Actionable comments posted: 18

Note

Due to the large number of review comments, Critical, Major severity comments were prioritized as inline comments.

Caution

Some comments are outside the diff and can’t be posted inline due to platform limitations.

⚠️ Outside diff range comments (2)
src/Application/Console/Command/MakeCommandCommand.php (1)

84-98: ⚠️ Potential issue | 🟡 Minor | ⚡ Quick win

Align the scaffold hint path with the validator.

The generated LLM hint still points to src/modules/<Module>/Application/Command/..., but config/module-structure.php now requires command classes under Application/Console/Command/. That mismatch will send users to a path the verifier rejects.

Proposed fix
-                        "src/modules/{$module}/Application/Command/{$className}.php" => [
+                        "src/modules/{$module}/Application/Console/Command/{$className}.php" => [
🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed.

In `@src/Application/Console/Command/MakeCommandCommand.php` around lines 84 - 98,
The scaffold hint path emitted by MakeCommandCommand (in the
formatter->format('command_scaffold', ...) call) points to
"src/modules/{$module}/Application/Command/{$className}.php" which no longer
matches the project's validator/config/module-structure.php; update that hint to
"src/modules/{$module}/Application/Console/Command/{$className}.php" so the
generated guidance aligns with the expected directory and the verifier accepts
the path.
src/Application/Console/Command/DevGraph/DevGraphMineConventionsCommand.php (1)

36-73: ⚠️ Potential issue | 🟡 Minor | ⚡ Quick win

Filter the summary before counting modules.

When --module is supplied, the NDJSON loop is filtered, but modules_mined and injections_total are still computed from every module. That makes the first summary record misleading for filtered runs.

♻️ Suggested fix
-        $totalInjections = 0;
-        foreach ($byModule as $conv) {
-            $totalInjections += count($conv->handler_injections);
-        }
+        $filtered = [];
+        foreach ($byModule as $module => $conv) {
+            if ($moduleFilter !== null && $module !== $moduleFilter) {
+                continue;
+            }
+            $filtered[$module] = $conv;
+        }
+
+        $totalInjections = 0;
+        foreach ($filtered as $conv) {
+            $totalInjections += count($conv->handler_injections);
+        }
🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed.

In `@src/Application/Console/Command/DevGraph/DevGraphMineConventionsCommand.php`
around lines 36 - 73, The summary is computed from $byModule without applying
the $moduleFilter, so modules_mined and injections_total become misleading when
--module is used; fix by filtering $byModule using $moduleFilter first (e.g.
build $filtered = array_filter($byModule, fn($k,$v) => $moduleFilter === null ||
$k === $moduleFilter, ARRAY_FILTER_USE_BOTH) or equivalent), then compute
modules_mined as count($filtered) and injections_total by summing
count($conv->handler_injections) over $filtered; keep the existing loop but
iterate over $filtered (or keep the loop with the same filter) so the summary
(using $store, dry-run via $input->getOption('dry-run')) matches the per-module
output and recurringHandlerInjections()/handler_injections counts.
🟡 Minor comments (3)
src/Ai/Verify/Structure/ModuleStructureSpecLoader.php-61-74 (1)

61-74: ⚠️ Potential issue | 🟡 Minor | ⚡ Quick win

mtime-only caching can return a stale spec after quick edits.

filemtime() is second-granularity on common filesystems, so two writes to the spec within the same second will reuse the previous cached ModuleStructureSpec. That is exactly the stale-config case this long-running-worker cache is supposed to avoid. Include filesize/content hash in the cache key, or skip caching for override paths.

🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed.

In `@src/Ai/Verify/Structure/ModuleStructureSpecLoader.php` around lines 61 - 74,
The current caching in ModuleStructureSpecLoader uses only filemtime (the $mtime
variable) so rapid rewrites within the same second can return a stale
ModuleStructureSpec from $this->cache[$abs]; change the cache key/validation to
also consider file contents (e.g., filesize or a hash of the required file) or
bypass caching for override paths: when loading in load/require ($abs) compute
an additional fingerprint (filesize or sha1 of file_get_contents($abs)) and
store/compare it alongside 'mtime' in $this->cache[$abs] before returning
$this->cache[$abs]['spec'], or skip storing/reading from $this->cache for known
override files. Ensure you update the comparison that currently uses
$this->cache[$abs]['mtime'] === $mtime to validate both mtime and the new
fingerprint.
src/Ai/Verify/Structure/ModuleStructureValidator.php-102-116 (1)

102-116: ⚠️ Potential issue | 🟡 Minor | ⚡ Quick win

Avoid directory-only wording for required root entries.

requiredPackageRootEntries includes both files and directories, but the message at Line 110 always renders the missing entry as .../'. That makes missing composer.json diagnostics inaccurate and harder for NDJSON consumers to act on.

🩹 Proposed fix
-                    message: sprintf(
-                        "Package '%s' is missing required entry '%s/'.",
-                        $module->relativePath,
-                        $required,
-                    ),
+                    message: sprintf(
+                        "Package '%s' is missing required entry '%s'.",
+                        $module->relativePath,
+                        $required,
+                    ),
🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed.

In `@src/Ai/Verify/Structure/ModuleStructureValidator.php` around lines 102 - 116,
The diagnostic always appends a trailing '/' when reporting missing required
root entries, but requiredPackageRootEntries can be files (e.g., composer.json),
so update the ModuleStructureValidator loop that builds the
ModuleStructureViolation (inside the foreach over
$this->spec->requiredPackageRootEntries) to stop rendering the missing entry as
'%s/' — change the sprintf to "Package '%s' is missing required entry '%s'."
(i.e., remove the '/' suffix) so the message correctly reports files and
directories; leave path, expected, and suggestedFix as they are.
config/module-structure.php-853-860 (1)

853-860: ⚠️ Potential issue | 🟡 Minor | ⚡ Quick win

Opaque-mode status comments are out of sync with the active rules.

Lines 854-860 and 927-930 state that no directory currently uses MODE_OPAQUE_INTERNAL, but opaque rules still exist earlier (e.g., Line 440, Line 453, Line 475). Please align the comments with actual behavior (or finish the migration).

Also applies to: 927-930

🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed.

In `@config/module-structure.php` around lines 853 - 860, The header comment
claiming no directory uses MODE_OPAQUE_INTERNAL is incorrect because opaque
rules remain; either update the comment to state that MODE_OPAQUE_INTERNAL is
still in use for specific entries or finish the migration by removing all opaque
rules and clearing $coreOpaqueDirs. Locate and reconcile occurrences of
MODE_OPAQUE_INTERNAL and any opaque entries earlier in the file (e.g., the
opaque rule array entries and $coreOpaqueDirs usages) so the comment and the
active rule set are consistent: if you keep opaque rules, list or note that some
directories still use MODE_OPAQUE_INTERNAL; if you finish the migration, remove
those opaque entries and any references to MODE_OPAQUE_INTERNAL and ensure
$coreOpaqueDirs is empty.
🧹 Nitpick comments (2)
config/module-structure.php (1)

942-945: ⚡ Quick win

Guard against duplicate rule paths when building $codeRootMap.

Line 944 silently overwrites earlier rules for the same path. In a spec this large, duplicate keys can accidentally weaken validation with no signal.

Suggested hard-fail on duplicates
 $codeRootMap = [];
 foreach ($codeRoot as $r) {
+    if (isset($codeRootMap[$r->path])) {
+        throw new \LogicException('Duplicate module structure rule path: ' . $r->path);
+    }
     $codeRootMap[$r->path] = $r;
 }
🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed.

In `@config/module-structure.php` around lines 942 - 945, When building
$codeRootMap from $codeRoot, currently duplicate $r->path entries silently
overwrite earlier ones; update the loop that iterates $codeRoot (the block
creating $codeRootMap using $r and $r->path) to detect duplicates (e.g. check
isset($codeRootMap[$r->path]) or array_key_exists) and hard-fail (throw an
exception or trigger a fatal error) including the duplicate path and any
identifying info from $r so duplicates are surfaced rather than overwritten.
tests/Unit/Ai/Verify/Structure/ModuleStructureCrashTestTest.php (1)

30-31: ⚡ Quick win

Use a stronger unique suffix for temp test roots to reduce CI flakiness.

uniqid() is time-based and can collide under parallel execution. Prefer cryptographic randomness for directory suffixes.

Suggested update
-        $this->root = sys_get_temp_dir() . '/semitexa-crash-test-' . uniqid();
+        $this->root = sys_get_temp_dir() . '/semitexa-crash-test-' . bin2hex(random_bytes(8));
🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed.

In `@tests/Unit/Ai/Verify/Structure/ModuleStructureCrashTestTest.php` around lines
30 - 31, Replace the time-based uniqid() suffix used when building the temp test
root with a cryptographically strong random suffix to avoid collisions in
parallel CI; specifically update the assignment that sets $this->root (which
currently uses sys_get_temp_dir() . '/semitexa-crash-test-' . uniqid()) to use a
secure generator such as bin2hex(random_bytes(...)) or random_bytes converted to
hex, then continue to call mkdir($this->root, 0755, true) as before; ensure you
handle potential exceptions from random_bytes if your PHP version requires it.
🤖 Prompt for all review comments with AI agents
Verify each finding against the current code and only fix it if needed.

Inline comments:
In `@src/Ai/Verify/Phpstan/PhpstanRunner.php`:
- Around line 120-123: The current early return when $files is not an array in
PhpstanRunner (method in src/Ai/Verify/Phpstan/PhpstanRunner.php) drops
top-level PHPStan "errors" and causes config-level failures to be ignored;
instead of returning [], ensure $files is set to an empty array (or left as-is)
and continue processing so the later handling of $payload['errors'] (the
top-level non-file-specific errors) still runs; update the branch around $files
= $payload['files'] ?? []; / if (!is_array($files)) to avoid an early return and
let the code that inspects $payload['errors'] (lines handling top-level errors)
execute.

In `@src/Ai/Verify/Structure/ModuleStructureTargetResolver.php`:
- Around line 55-65: Module detection currently treats paths like
src/modules/Foo.php as a module because the check uses count($parts) >= 3;
update the ModuleStructureTargetResolver logic to require at least one path
segment after the module folder (i.e. change the guard to require count($parts)
>= 4) so only paths matching src/modules/{Name}/... are considered; keep using
$parts[2] for the module name and return the DetectedModule (name, relativePath
'src/modules/'.$name, kind DetectedModule::KIND_APPLICATION) only when that
stricter condition is met.

In `@src/Ai/Verify/VerificationPlanner.php`:
- Around line 115-123: The minimal-scope guard in VerificationPlanner prevents
scheduling module_structure and phpstan_di targets causing ai:verify --all
--scope=minimal to produce no targets; update VerificationPlanner logic so that
when AiVerifyCommand::repoWidePaths() indicates a repo-wide run (i.e., the
command was invoked with --all) you still call
moduleStructureTargets($changedFiles) and include the
phpstanDiTarget($changedFiles) even if $effectiveScope ===
VerificationPlan::SCOPE_MINIMAL (or alternatively throw a validation error for
the invalid flag combo); locate the block using VerificationPlanner,
moduleStructureTargets, and phpstanDiTarget and either force-add those targets
when repo-wide is true or validate/reject the --all + --scope=minimal
combination.

In `@src/Application/Console/Command/AiBacklogCommand.php`:
- Line 9: The import for BaseCommand in AiBacklogCommand is pointing to the
wrong namespace; update the use statement to import
Semitexa\Core\Console\Command\BaseCommand (so the class resolves to the actual
BaseCommand class) and keep the class declaration that extends BaseCommand
unchanged; locate the use line referencing BaseCommand and replace the namespace
segment to include the Command sub-namespace.

In `@src/Application/Console/Command/AiEpicCommand.php`:
- Line 9: The import for BaseCommand is incorrect; update the use statement that
currently references Semitexa\Core\Console\BaseCommand to import
Semitexa\Core\Console\Command\BaseCommand so the class resolves correctly
(locate the use statement near the top of AiEpicCommand.php and replace the
incorrect namespace import for BaseCommand).

In `@src/Application/Console/Command/AiInvokeCommand.php`:
- Line 10: The import for BaseCommand in AiInvokeCommand is incorrect and will
cause a fatal error; update the use statement that references
Semitexa\Core\Console\BaseCommand to the correct namespace
Semitexa\Core\Console\Command\BaseCommand so the AiInvokeCommand class extends
the actual BaseCommand implementation (look for the use line and any "class
AiInvokeCommand extends BaseCommand" declaration).

In `@src/Application/Console/Command/AiPlanCommand.php`:
- Line 9: Update the incorrect import for BaseCommand in AiPlanCommand: replace
the current use statement that imports Semitexa\Core\Console\BaseCommand with
the correct namespace Semitexa\Core\Console\Command\BaseCommand so the
AiPlanCommand class extends the actual BaseCommand implementation and resolves
correctly under strict autoloading.

In `@src/Application/Console/Command/AiTaskCommand.php`:
- Line 9: Update the import for BaseCommand in AiTaskCommand.php to the correct
fully-qualified class name: replace the incorrect use statement referencing
Semitexa\Core\Console\BaseCommand with the correct namespace
Semitexa\Core\Console\Command\BaseCommand so the class (e.g., AiTaskCommand)
extends the actual BaseCommand implementation from vendor; locate the use
statement at the top of the file and update it to the Command namespace segment.

In `@src/Application/Console/Command/AiWorkCommand.php`:
- Line 9: The import for BaseCommand is incorrect; update the use statement to
reference the correct namespace segment so the class resolves at runtime —
change the import from Semitexa\Core\Console\BaseCommand to
Semitexa\Core\Console\Command\BaseCommand where AiWorkCommand references/extends
BaseCommand (class AiWorkCommand) so the correct BaseCommand class is imported.

In `@src/Application/Console/Command/DevGraph/DevGraphEventCommand.php`:
- Line 8: The import for BaseCommand is using the wrong namespace; update the
use statement to reference Semitexa\Core\Console\Command\BaseCommand so the
DevGraphEventCommand class resolves BaseCommand correctly (locate the use line
importing BaseCommand in DevGraphEventCommand and change the namespace to
include the Command segment).

In `@src/Application/Console/Command/LogsAppCommand.php`:
- Line 8: Update the import for BaseCommand in LogsAppCommand so it points to
the actual class location; replace the incorrect use
Semitexa\Core\Console\BaseCommand with use
Semitexa\Core\Console\Command\BaseCommand so the LogsAppCommand class (which
extends BaseCommand) will autoload correctly.

In `@src/Application/Console/Command/MakeCommandCommand.php`:
- Line 8: The import for BaseCommand in MakeCommandCommand.php is incorrect;
update the use statement to import the actual class location
Semitexa\Core\Console\Command\BaseCommand so the MakeCommandCommand class can
extend/resolve BaseCommand correctly—locate the current use
Semitexa\Core\Console\BaseCommand and replace it with use
Semitexa\Core\Console\Command\BaseCommand.

In `@src/Application/Console/Command/MakeContractCommand.php`:
- Line 8: The import statement for BaseCommand in MakeContractCommand.php is
wrong — replace the nonexistent Semitexa\Core\Console\BaseCommand import with
the correct fully-qualified class Semitexa\Core\Console\Command\BaseCommand so
the MakeContractCommand class references the real BaseCommand class (update the
use line that currently imports BaseCommand).

In `@src/Application/Console/Command/MakeEventListenerCommand.php`:
- Line 8: The import for BaseCommand in MakeEventListenerCommand.php is wrong
and will break autoloading; update the use statement that currently references
Semitexa\Core\Console\BaseCommand to the correct namespace
Semitexa\Core\Console\Command\BaseCommand so the MakeEventListenerCommand class
imports the actual BaseCommand class used by the console command subsystem.

In `@src/Application/Console/Command/MakePageCommand.php`:
- Line 8: The import for BaseCommand in MakePageCommand is incorrect; replace
the current use statement referencing Semitexa\Core\Console\BaseCommand with the
correct fully qualified import Semitexa\Core\Console\Command\BaseCommand so that
the MakePageCommand class extends the actual BaseCommand class (update the use
line in MakePageCommand.php to reference BaseCommand in the Command namespace).

In `@src/Application/Console/Command/MakeResourceCommand.php`:
- Line 8: The import for BaseCommand is incorrect and causes autoloading to
fail; update the use statement in MakeResourceCommand (the class referencing
BaseCommand) to import Semitexa\Core\Console\Command\BaseCommand instead of
Semitexa\Core\Console\BaseCommand so the class symbol BaseCommand resolves
correctly; confirm the MakeResourceCommand class extends BaseCommand and run a
quick autoload/classmap check to verify resolution.

In `@src/Generation/Verifier/PostWriteLinter.php`:
- Around line 24-27: The CHECKS mapping in PostWriteLinter.php uses unregistered
command IDs ('lint:handlers' and 'lint:di') so Application::find() cannot
resolve them and they get skipped; update the CHECKS constant to use the actual
registered command IDs ('semitexa:lint:handlers' and 'semitexa:lint:di') so the
code in PostWriteLinter (which looks up these keys to call Application::find and
execute the commands) finds and runs the real lint commands.

---

Outside diff comments:
In `@src/Application/Console/Command/DevGraph/DevGraphMineConventionsCommand.php`:
- Around line 36-73: The summary is computed from $byModule without applying the
$moduleFilter, so modules_mined and injections_total become misleading when
--module is used; fix by filtering $byModule using $moduleFilter first (e.g.
build $filtered = array_filter($byModule, fn($k,$v) => $moduleFilter === null ||
$k === $moduleFilter, ARRAY_FILTER_USE_BOTH) or equivalent), then compute
modules_mined as count($filtered) and injections_total by summing
count($conv->handler_injections) over $filtered; keep the existing loop but
iterate over $filtered (or keep the loop with the same filter) so the summary
(using $store, dry-run via $input->getOption('dry-run')) matches the per-module
output and recurringHandlerInjections()/handler_injections counts.

In `@src/Application/Console/Command/MakeCommandCommand.php`:
- Around line 84-98: The scaffold hint path emitted by MakeCommandCommand (in
the formatter->format('command_scaffold', ...) call) points to
"src/modules/{$module}/Application/Command/{$className}.php" which no longer
matches the project's validator/config/module-structure.php; update that hint to
"src/modules/{$module}/Application/Console/Command/{$className}.php" so the
generated guidance aligns with the expected directory and the verifier accepts
the path.

---

Minor comments:
In `@config/module-structure.php`:
- Around line 853-860: The header comment claiming no directory uses
MODE_OPAQUE_INTERNAL is incorrect because opaque rules remain; either update the
comment to state that MODE_OPAQUE_INTERNAL is still in use for specific entries
or finish the migration by removing all opaque rules and clearing
$coreOpaqueDirs. Locate and reconcile occurrences of MODE_OPAQUE_INTERNAL and
any opaque entries earlier in the file (e.g., the opaque rule array entries and
$coreOpaqueDirs usages) so the comment and the active rule set are consistent:
if you keep opaque rules, list or note that some directories still use
MODE_OPAQUE_INTERNAL; if you finish the migration, remove those opaque entries
and any references to MODE_OPAQUE_INTERNAL and ensure $coreOpaqueDirs is empty.

In `@src/Ai/Verify/Structure/ModuleStructureSpecLoader.php`:
- Around line 61-74: The current caching in ModuleStructureSpecLoader uses only
filemtime (the $mtime variable) so rapid rewrites within the same second can
return a stale ModuleStructureSpec from $this->cache[$abs]; change the cache
key/validation to also consider file contents (e.g., filesize or a hash of the
required file) or bypass caching for override paths: when loading in
load/require ($abs) compute an additional fingerprint (filesize or sha1 of
file_get_contents($abs)) and store/compare it alongside 'mtime' in
$this->cache[$abs] before returning $this->cache[$abs]['spec'], or skip
storing/reading from $this->cache for known override files. Ensure you update
the comparison that currently uses $this->cache[$abs]['mtime'] === $mtime to
validate both mtime and the new fingerprint.

In `@src/Ai/Verify/Structure/ModuleStructureValidator.php`:
- Around line 102-116: The diagnostic always appends a trailing '/' when
reporting missing required root entries, but requiredPackageRootEntries can be
files (e.g., composer.json), so update the ModuleStructureValidator loop that
builds the ModuleStructureViolation (inside the foreach over
$this->spec->requiredPackageRootEntries) to stop rendering the missing entry as
'%s/' — change the sprintf to "Package '%s' is missing required entry '%s'."
(i.e., remove the '/' suffix) so the message correctly reports files and
directories; leave path, expected, and suggestedFix as they are.

---

Nitpick comments:
In `@config/module-structure.php`:
- Around line 942-945: When building $codeRootMap from $codeRoot, currently
duplicate $r->path entries silently overwrite earlier ones; update the loop that
iterates $codeRoot (the block creating $codeRootMap using $r and $r->path) to
detect duplicates (e.g. check isset($codeRootMap[$r->path]) or array_key_exists)
and hard-fail (throw an exception or trigger a fatal error) including the
duplicate path and any identifying info from $r so duplicates are surfaced
rather than overwritten.

In `@tests/Unit/Ai/Verify/Structure/ModuleStructureCrashTestTest.php`:
- Around line 30-31: Replace the time-based uniqid() suffix used when building
the temp test root with a cryptographically strong random suffix to avoid
collisions in parallel CI; specifically update the assignment that sets
$this->root (which currently uses sys_get_temp_dir() . '/semitexa-crash-test-' .
uniqid()) to use a secure generator such as bin2hex(random_bytes(...)) or
random_bytes converted to hex, then continue to call mkdir($this->root, 0755,
true) as before; ensure you handle potential exceptions from random_bytes if
your PHP version requires it.
🪄 Autofix (Beta)

Fix all unresolved CodeRabbit comments on this PR:

  • Push a commit to this branch (recommended)
  • Create a new PR with the fixes

ℹ️ Review info
⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro

Run ID: d9857ed1-6df7-423d-9ac5-ccc52af14f84

📥 Commits

Reviewing files that changed from the base of the PR and between 8e27404 and 71417a3.

📒 Files selected for processing (69)
  • config/module-structure.php
  • config/phpstan-ai-verify.neon
  • src/Ai/Recipe/RecipeRegistry.php
  • src/Ai/Verify/ChangedFile.php
  • src/Ai/Verify/ChangedFileClassifier.php
  • src/Ai/Verify/Phpstan/PhpstanRunResult.php
  • src/Ai/Verify/Phpstan/PhpstanRunner.php
  • src/Ai/Verify/Structure/DetectedModule.php
  • src/Ai/Verify/Structure/FilePlacementRule.php
  • src/Ai/Verify/Structure/ModuleStructureRule.php
  • src/Ai/Verify/Structure/ModuleStructureSpec.php
  • src/Ai/Verify/Structure/ModuleStructureSpecLoader.php
  • src/Ai/Verify/Structure/ModuleStructureTargetResolver.php
  • src/Ai/Verify/Structure/ModuleStructureValidator.php
  • src/Ai/Verify/Structure/ModuleStructureViolation.php
  • src/Ai/Verify/VerificationExecutor.php
  • src/Ai/Verify/VerificationPlanner.php
  • src/Ai/Verify/VerificationResult.php
  • src/Ai/Verify/VerificationTarget.php
  • src/Application/Console/Command/AiAskCommand.php
  • src/Application/Console/Command/AiBacklogCommand.php
  • src/Application/Console/Command/AiContextCommand.php
  • src/Application/Console/Command/AiEpicCommand.php
  • src/Application/Console/Command/AiInvokeCommand.php
  • src/Application/Console/Command/AiOrientCommand.php
  • src/Application/Console/Command/AiPlanCommand.php
  • src/Application/Console/Command/AiTaskCommand.php
  • src/Application/Console/Command/AiTraceCommand.php
  • src/Application/Console/Command/AiVerifyCommand.php
  • src/Application/Console/Command/AiWorkCommand.php
  • src/Application/Console/Command/DevGraph/DevGraphCapabilitiesCommand.php
  • src/Application/Console/Command/DevGraph/DevGraphEventCommand.php
  • src/Application/Console/Command/DevGraph/DevGraphMineConventionsCommand.php
  • src/Application/Console/Command/DevGraph/DevGraphModuleCommand.php
  • src/Application/Console/Command/DevGraph/DevGraphProjectCommand.php
  • src/Application/Console/Command/DevGraph/DevGraphRouteCommand.php
  • src/Application/Console/Command/LogsAppCommand.php
  • src/Application/Console/Command/MakeCommand.php
  • src/Application/Console/Command/MakeCommandCommand.php
  • src/Application/Console/Command/MakeContractCommand.php
  • src/Application/Console/Command/MakeEventListenerCommand.php
  • src/Application/Console/Command/MakeHandlerCommand.php
  • src/Application/Console/Command/MakeModuleCommand.php
  • src/Application/Console/Command/MakePageCommand.php
  • src/Application/Console/Command/MakePayloadCommand.php
  • src/Application/Console/Command/MakeResourceCommand.php
  • src/Application/Console/Command/MakeServiceCommand.php
  • src/Application/Console/Command/ScaffoldSyncDocsCommand.php
  • src/Application/Console/Command/Support/CommandDelegator.php
  • src/Generation/Verifier/PostWriteLinter.php
  • tests/Integration/AiAskCommandTest.php
  • tests/Integration/AiTraceCommandTest.php
  • tests/Integration/AiVerifyCommandTest.php
  • tests/Integration/DevGraphCommandTest.php
  • tests/Integration/DuplicateRefusalTest.php
  • tests/Integration/MakeDispatcherTest.php
  • tests/Integration/MakeModuleCommandTest.php
  • tests/Integration/WorkflowTraceTest.php
  • tests/Unit/Ai/Verify/ChangedFileClassifierTest.php
  • tests/Unit/Ai/Verify/Phpstan/PhpstanRunnerTest.php
  • tests/Unit/Ai/Verify/Structure/ModuleStructureCrashTestTest.php
  • tests/Unit/Ai/Verify/Structure/ModuleStructureSpecLoaderTest.php
  • tests/Unit/Ai/Verify/Structure/ModuleStructureTargetResolverTest.php
  • tests/Unit/Ai/Verify/Structure/ModuleStructureValidatorTest.php
  • tests/Unit/Ai/Verify/VerificationExecutorTest.php
  • tests/Unit/Ai/Verify/VerificationPlannerTest.php
  • tests/Unit/Console/Command/AiEpicCommandTest.php
  • tests/Unit/Console/Command/AiWorkCommandTest.php
  • tests/Unit/OwnershipBoundaryTest.php

Comment on lines +120 to +123
$files = $payload['files'] ?? [];
if (!is_array($files)) {
return [];
}
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⚠️ Potential issue | 🟠 Major

🧩 Analysis chain

🌐 Web query:

Official PHPStan JSON output format: can a run emit top-level "errors" while the "files" section is empty, null, or absent?

💡 Result:

No, a PHPStan JSON output run cannot emit a top-level "errors" array containing file-specific errors while the "files" section is empty, null, or absent. The "files" object is always present and populated with file-specific errors grouped by filename from AnalysisResult::getFileSpecificErrors. The top-level "errors" array is reserved for non-file-specific errors (e.g., configuration issues like malformed ignoreErrors patterns), which are added separately via AnalysisResult::getNonFileSpecificErrors or similar. If there are no file-specific errors, "files" is an empty object {}. If there are no generic errors, top-level "errors" is an empty array []. Examples from sources confirm this structure, with "errors": [] when all issues are file-specific.

Citations:


Don't drop top-level PHPStan errors here.

Line 121 returns immediately when files is not an array, preventing processing of top-level "errors" at lines 154–174. Since PHPStan's JSON output reserves the top-level "errors" array for non-file-specific errors (configuration failures, discovery issues), this early return converts config-level failures into false passes.

🩹 Proposed fix
-        $files = $payload['files'] ?? [];
-        if (!is_array($files)) {
-            return [];
-        }
+        $files = $payload['files'] ?? [];
+        if (!is_array($files)) {
+            $files = [];
+        }
🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed.

In `@src/Ai/Verify/Phpstan/PhpstanRunner.php` around lines 120 - 123, The current
early return when $files is not an array in PhpstanRunner (method in
src/Ai/Verify/Phpstan/PhpstanRunner.php) drops top-level PHPStan "errors" and
causes config-level failures to be ignored; instead of returning [], ensure
$files is set to an empty array (or left as-is) and continue processing so the
later handling of $payload['errors'] (the top-level non-file-specific errors)
still runs; update the branch around $files = $payload['files'] ?? []; / if
(!is_array($files)) to avoid an early return and let the code that inspects
$payload['errors'] (lines handling top-level errors) execute.

Comment on lines +55 to +65
if (count($parts) >= 3 && $parts[0] === 'src' && $parts[1] === 'modules') {
$name = $parts[2];
if ($name === '' || $name === '.' || $name === '..') {
return null;
}
return new DetectedModule(
name: $name,
relativePath: 'src/modules/' . $name,
kind: DetectedModule::KIND_APPLICATION,
);
}
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⚠️ Potential issue | 🟠 Major | ⚡ Quick win

Tighten application-module detection.

A path like src/modules/Foo.php currently resolves to module Foo.php, which creates a bogus target instead of ignoring the file. Requiring at least one segment after the module name keeps the resolver aligned with the documented src/modules/{Name}/... shape.

🔧 Suggested fix
-        if (count($parts) >= 3 && $parts[0] === 'src' && $parts[1] === 'modules') {
+        if (count($parts) >= 4 && $parts[0] === 'src' && $parts[1] === 'modules') {
             $name = $parts[2];
             if ($name === '' || $name === '.' || $name === '..') {
                 return null;
             }
🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed.

In `@src/Ai/Verify/Structure/ModuleStructureTargetResolver.php` around lines 55 -
65, Module detection currently treats paths like src/modules/Foo.php as a module
because the check uses count($parts) >= 3; update the
ModuleStructureTargetResolver logic to require at least one path segment after
the module folder (i.e. change the guard to require count($parts) >= 4) so only
paths matching src/modules/{Name}/... are considered; keep using $parts[2] for
the module name and return the DetectedModule (name, relativePath
'src/modules/'.$name, kind DetectedModule::KIND_APPLICATION) only when that
stricter condition is met.

Comment on lines +115 to +123
if ($effectiveScope !== VerificationPlan::SCOPE_MINIMAL) {
foreach ($this->moduleStructureTargets($changedFiles) as $target) {
$targets[] = $target;
}
$phpstanTarget = $this->phpstanDiTarget($changedFiles);
if ($phpstanTarget !== null) {
$targets[] = $phpstanTarget;
}
}
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⚠️ Potential issue | 🟠 Major | ⚡ Quick win

--all --scope=minimal currently produces a false clean pass.

AiVerifyCommand::repoWidePaths() feeds directory roots, but this guard suppresses module_structure and phpstan_di in minimal scope, and the earlier loop only schedules syntax targets for changed .php files. For ai:verify --all --scope=minimal, that means zero targets and a passing verdict even though the CLI help advertises a repo-wide module-structure check. Either force module_structure scheduling for --all, reject that flag combination, or narrow the help text.

🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed.

In `@src/Ai/Verify/VerificationPlanner.php` around lines 115 - 123, The
minimal-scope guard in VerificationPlanner prevents scheduling module_structure
and phpstan_di targets causing ai:verify --all --scope=minimal to produce no
targets; update VerificationPlanner logic so that when
AiVerifyCommand::repoWidePaths() indicates a repo-wide run (i.e., the command
was invoked with --all) you still call moduleStructureTargets($changedFiles) and
include the phpstanDiTarget($changedFiles) even if $effectiveScope ===
VerificationPlan::SCOPE_MINIMAL (or alternatively throw a validation error for
the invalid flag combo); locate the block using VerificationPlanner,
moduleStructureTargets, and phpstanDiTarget and either force-add those targets
when repo-wide is true or validate/reject the --all + --scope=minimal
combination.

use Semitexa\Core\Attribute\AsCommand;
use Semitexa\Core\Attribute\InjectAsReadonly;
use Semitexa\Core\Console\Command\BaseCommand;
use Semitexa\Core\Console\BaseCommand;
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⚠️ Potential issue | 🔴 Critical

🧩 Analysis chain

🏁 Script executed:

# First, let's look at the file in question
cat -n src/Application/Console/Command/AiBacklogCommand.php | head -20

Repository: semitexa/semitexa-dev

Length of output: 847


🏁 Script executed:

# Search for BaseCommand class definition in the codebase
rg "class BaseCommand" -A 2

Repository: semitexa/semitexa-dev

Length of output: 352


🏁 Script executed:

# Check if there's a vendor directory or composer.json to understand dependencies
fd "BaseCommand" --type f

Repository: semitexa/semitexa-dev

Length of output: 122


🏁 Script executed:

# Look for any use statements of BaseCommand to see the pattern
rg "use.*BaseCommand" -B 2 -A 2

Repository: semitexa/semitexa-dev

Length of output: 18591


Restore the BaseCommand import path.

The import uses Semitexa\Core\Console\BaseCommand, but the class is defined at Semitexa\Core\Console\Command\BaseCommand. This will cause an autoload failure when the file is loaded.

🔧 Suggested fix
-use Semitexa\Core\Console\BaseCommand;
+use Semitexa\Core\Console\Command\BaseCommand;
📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
use Semitexa\Core\Console\BaseCommand;
use Semitexa\Core\Console\Command\BaseCommand;
🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed.

In `@src/Application/Console/Command/AiBacklogCommand.php` at line 9, The import
for BaseCommand in AiBacklogCommand is pointing to the wrong namespace; update
the use statement to import Semitexa\Core\Console\Command\BaseCommand (so the
class resolves to the actual BaseCommand class) and keep the class declaration
that extends BaseCommand unchanged; locate the use line referencing BaseCommand
and replace the namespace segment to include the Command sub-namespace.

use Semitexa\Core\Attribute\AsCommand;
use Semitexa\Core\Attribute\InjectAsReadonly;
use Semitexa\Core\Console\Command\BaseCommand;
use Semitexa\Core\Console\BaseCommand;
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⚠️ Potential issue | 🔴 Critical

🧩 Analysis chain

🏁 Script executed:

# First, find the file and check its actual import
cat src/Application/Console/Command/AiEpicCommand.php | head -20

Repository: semitexa/semitexa-dev

Length of output: 731


🏁 Script executed:

# Search for BaseCommand class definition
rg "class BaseCommand" --type php

Repository: semitexa/semitexa-dev

Length of output: 165


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# Search for any namespace declarations related to BaseCommand
rg "namespace.*BaseCommand|class BaseCommand" --type php -B 2

Repository: semitexa/semitexa-dev

Length of output: 1298


🏁 Script executed:

# Check the namespace declaration in BaseCommand.php
head -10 vendor/semitexa/core/src/Console/Command/BaseCommand.php

Repository: semitexa/semitexa-dev

Length of output: 277


Fix the BaseCommand import.

The import use Semitexa\Core\Console\BaseCommand; is incorrect. The BaseCommand class is declared in namespace Semitexa\Core\Console\Command (in vendor/semitexa/core/src/Console/Command/BaseCommand.php), so the correct import is Semitexa\Core\Console\Command\BaseCommand. This will cause a class resolution failure at runtime.

Proposed fix
-use Semitexa\Core\Console\BaseCommand;
+use Semitexa\Core\Console\Command\BaseCommand;
📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
use Semitexa\Core\Console\BaseCommand;
use Semitexa\Core\Console\Command\BaseCommand;
🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed.

In `@src/Application/Console/Command/AiEpicCommand.php` at line 9, The import for
BaseCommand is incorrect; update the use statement that currently references
Semitexa\Core\Console\BaseCommand to import
Semitexa\Core\Console\Command\BaseCommand so the class resolves correctly
(locate the use statement near the top of AiEpicCommand.php and replace the
incorrect namespace import for BaseCommand).


use Semitexa\Core\Attribute\AsCommand;
use Semitexa\Core\Console\Command\BaseCommand;
use Semitexa\Core\Console\BaseCommand;
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⚠️ Potential issue | 🔴 Critical

🧩 Analysis chain

🏁 Script executed:

# Search for BaseCommand class definition
rg "class BaseCommand" --type php

Repository: semitexa/semitexa-dev

Length of output: 165


🏁 Script executed:

# Find all files containing BaseCommand
find . -name "*.php" -type f | xargs grep -l "class BaseCommand" 2>/dev/null | head -20

Repository: semitexa/semitexa-dev

Length of output: 124


🏁 Script executed:

# Check if there's a vendor directory and its structure
ls -la vendor/semitexa/ 2>/dev/null || echo "Vendor dir not found or Semitexa not installed"

Repository: semitexa/semitexa-dev

Length of output: 341


🏁 Script executed:

# Check the actual file and its imports
head -20 src/Application/Console/Command/MakeEventListenerCommand.php

Repository: semitexa/semitexa-dev

Length of output: 868


Restore the BaseCommand import path.

The current import Semitexa\Core\Console\BaseCommand is incorrect. The class is located at Semitexa\Core\Console\Command\BaseCommand, and this file will fail to autoload without the corrected namespace.

🔧 Suggested fix
-use Semitexa\Core\Console\BaseCommand;
+use Semitexa\Core\Console\Command\BaseCommand;
📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
use Semitexa\Core\Console\BaseCommand;
use Semitexa\Core\Console\Command\BaseCommand;
🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed.

In `@src/Application/Console/Command/MakeEventListenerCommand.php` at line 8, The
import for BaseCommand in MakeEventListenerCommand.php is wrong and will break
autoloading; update the use statement that currently references
Semitexa\Core\Console\BaseCommand to the correct namespace
Semitexa\Core\Console\Command\BaseCommand so the MakeEventListenerCommand class
imports the actual BaseCommand class used by the console command subsystem.


use Semitexa\Core\Attribute\AsCommand;
use Semitexa\Core\Console\Command\BaseCommand;
use Semitexa\Core\Console\BaseCommand;
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⚠️ Potential issue | 🔴 Critical

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🏁 Script executed:

#!/bin/bash
# Check if the file exists and view its imports
if [ -f "src/Application/Console/Command/MakePageCommand.php" ]; then
  echo "=== File found, showing imports (lines 1-20) ==="
  head -20 "src/Application/Console/Command/MakePageCommand.php"
else
  echo "File not found at src/Application/Console/Command/MakePageCommand.php"
fi

Repository: semitexa/semitexa-dev

Length of output: 916


🏁 Script executed:

#!/bin/bash
# Search for BaseCommand class definition in the codebase
echo "=== Searching for BaseCommand class definition ==="
rg "class BaseCommand" --type php -B 2 -A 5

Repository: semitexa/semitexa-dev

Length of output: 783


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#!/bin/bash
# Search for any namespace declarations related to BaseCommand
echo "=== Searching for BaseCommand in namespace contexts ==="
rg "namespace.*Console.*BaseCommand|BaseCommand" --type php | grep -E "(namespace|class.*BaseCommand)" | head -20

Repository: semitexa/semitexa-dev

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#!/bin/bash
# Check composer.json for autoloading or aliases
if [ -f "composer.json" ]; then
  echo "=== composer.json autoload section ==="
  cat composer.json | jq '.autoload // .autoload-dev // .extra'
fi

Repository: semitexa/semitexa-dev

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#!/bin/bash
# Check if BaseCommand is re-exported in the Console namespace
echo "=== Checking for alias/re-export in Console.php or Console/BaseCommand.php ==="
find vendor/semitexa/core/src/Console -type f -name "*.php" | head -10

Repository: semitexa/semitexa-dev

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#!/bin/bash
# Check the Console directory structure
echo "=== Console directory structure ==="
ls -la vendor/semitexa/core/src/Console/ 2>/dev/null || echo "Directory structure:"
find vendor/semitexa/core/src/Console -type f -name "*.php" -exec echo {} \;

Repository: semitexa/semitexa-dev

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#!/bin/bash
# Check if there's any file in Console that might re-export BaseCommand
rg "BaseCommand" vendor/semitexa/core/src/Console --type php -B 2 -A 2

Repository: semitexa/semitexa-dev

Length of output: 7322


Fix the BaseCommand import.

Semitexa\Core\Console\BaseCommand does not exist. The class is located at Semitexa\Core\Console\Command\BaseCommand.

Proposed fix
-use Semitexa\Core\Console\BaseCommand;
+use Semitexa\Core\Console\Command\BaseCommand;
📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
use Semitexa\Core\Console\BaseCommand;
use Semitexa\Core\Console\Command\BaseCommand;
🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed.

In `@src/Application/Console/Command/MakePageCommand.php` at line 8, The import
for BaseCommand in MakePageCommand is incorrect; replace the current use
statement referencing Semitexa\Core\Console\BaseCommand with the correct fully
qualified import Semitexa\Core\Console\Command\BaseCommand so that the
MakePageCommand class extends the actual BaseCommand class (update the use line
in MakePageCommand.php to reference BaseCommand in the Command namespace).


use Semitexa\Core\Attribute\AsCommand;
use Semitexa\Core\Console\Command\BaseCommand;
use Semitexa\Core\Console\BaseCommand;
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⚠️ Potential issue | 🔴 Critical

🧩 Analysis chain

🏁 Script executed:

# First, check the current state of the file
head -20 src/Application/Console/Command/MakeResourceCommand.php

Repository: semitexa/semitexa-dev

Length of output: 871


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# Search for BaseCommand class definition in the codebase
rg "class BaseCommand" --type php

Repository: semitexa/semitexa-dev

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rg "namespace.*Console" --type php -A 2 | head -50

Repository: semitexa/semitexa-dev

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# Check if there's an alias or re-export at Semitexa\Core\Console level
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Repository: semitexa/semitexa-dev

Length of output: 47


🏁 Script executed:

# Check the BaseCommand file to see its actual namespace declaration
cat vendor/semitexa/core/src/Console/Command/BaseCommand.php | head -20

Repository: semitexa/semitexa-dev

Length of output: 527


Restore the BaseCommand import path.

Semitexa\Core\Console\BaseCommand does not match the actual class namespace Semitexa\Core\Console\Command\BaseCommand, so this command will fail to autoload when the file is loaded. Revert to the correct import.

🔧 Suggested fix
-use Semitexa\Core\Console\BaseCommand;
+use Semitexa\Core\Console\Command\BaseCommand;
📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
use Semitexa\Core\Console\BaseCommand;
use Semitexa\Core\Console\Command\BaseCommand;
🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed.

In `@src/Application/Console/Command/MakeResourceCommand.php` at line 8, The
import for BaseCommand is incorrect and causes autoloading to fail; update the
use statement in MakeResourceCommand (the class referencing BaseCommand) to
import Semitexa\Core\Console\Command\BaseCommand instead of
Semitexa\Core\Console\BaseCommand so the class symbol BaseCommand resolves
correctly; confirm the MakeResourceCommand class extends BaseCommand and run a
quick autoload/classmap check to verify resolution.

Comment on lines 24 to 27
private const CHECKS = [
'handlers' => 'semitexa:lint:handlers',
'di' => 'semitexa:lint:di',
'handlers' => 'lint:handlers',
'di' => 'lint:di',
];
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⚠️ Potential issue | 🔴 Critical

🧩 Analysis chain

🏁 Script executed:

#!/bin/bash
set -euo pipefail
rg -n "AsCommand\(name: 'semitexa:lint:(handlers|di)'" vendor src

Repository: semitexa/semitexa-dev

Length of output: 443


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cat -n src/Generation/Verifier/PostWriteLinter.php | head -40

Repository: semitexa/semitexa-dev

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Repository: semitexa/semitexa-dev

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rg -n "CHECKS" src/Generation/Verifier/PostWriteLinter.php -B 2 -A 10

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Repository: semitexa/semitexa-dev

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rg -n "lint:handlers|lint:di|semitexa:lint" src/Generation/Verifier/PostWriteLinter.php

Repository: semitexa/semitexa-dev

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# Check git history to see if this was recently changed
git show 71417a3:src/Generation/Verifier/PostWriteLinter.php | head -40

Repository: semitexa/semitexa-dev

Length of output: 1288


Restore the registered lint command IDs.

Application::find() will not resolve lint:handlers and lint:di; the dependency registers semitexa:lint:handlers and semitexa:lint:di. Both checks will throw CommandNotFoundException and be reported as skipped, making post-write linting ineffective.

🔧 Proposed fix
-        'handlers' => 'lint:handlers',
-        'di'       => 'lint:di',
+        'handlers' => 'semitexa:lint:handlers',
+        'di'       => 'semitexa:lint:di',
📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
private const CHECKS = [
'handlers' => 'semitexa:lint:handlers',
'di' => 'semitexa:lint:di',
'handlers' => 'lint:handlers',
'di' => 'lint:di',
];
private const CHECKS = [
'handlers' => 'semitexa:lint:handlers',
'di' => 'semitexa:lint:di',
];
🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed.

In `@src/Generation/Verifier/PostWriteLinter.php` around lines 24 - 27, The CHECKS
mapping in PostWriteLinter.php uses unregistered command IDs ('lint:handlers'
and 'lint:di') so Application::find() cannot resolve them and they get skipped;
update the CHECKS constant to use the actual registered command IDs
('semitexa:lint:handlers' and 'semitexa:lint:di') so the code in PostWriteLinter
(which looks up these keys to call Application::find and execute the commands)
finds and runs the real lint commands.

Comment on lines 37 to 40
$commands = $this->lintCommandNames($plan);
sort($commands);
$this->assertSame(['semitexa:lint:di', 'semitexa:lint:handlers'], $commands);
$this->assertSame(['lint:di', 'lint:handlers'], $commands);
$this->assertCount(1, $this->targetsOfType($plan, VerificationTarget::TYPE_SYNTAX));
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⚠️ Potential issue | 🔴 Critical

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🏁 Script executed:

#!/bin/bash
set -euo pipefail

echo "Planner / test expectations:"
rg -n -C2 --type=php "'(?:semitexa:)?lint:(handlers|di|responses|scoping|templates)'" src/Ai/Verify/VerificationPlanner.php tests/Unit/Ai/Verify/VerificationPlannerTest.php

echo
echo "Registered command names / aliases:"
rg -n -C2 --type=php "AsCommand\(.*lint:(handlers|di|responses|scoping|templates)|getAliases\s*\("

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set -euo pipefail

echo "=== All lint command class definitions with setAliases or AsCommand attributes ==="
fd -t f 'Lint.*Command\.php$' vendor/semitexa/core/src/Console/Command/ | while read file; do
  echo "=== $file ==="
  head -50 "$file" | cat -n
done

echo
echo "=== LintTemplatesCommand registration ==="
fd -t f 'LintTemplatesCommand\.php$' vendor/semitexa/core/src/Console/Command/
if [ $? -eq 0 ]; then
  fd -t f 'LintTemplatesCommand\.php$' vendor/semitexa/core/src/Console/Command/ -exec head -50 {} \;
else
  echo "LintTemplatesCommand not found in vendor"
fi

echo
echo "=== Searching for any setAliases() calls in the entire codebase ==="
rg -n 'setAliases|->aliases|getAliases\(\)' src/ vendor/semitexa/core/src/ -t php | grep -i lint || echo "No aliases found"

Repository: semitexa/semitexa-dev

Length of output: 11379


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#!/bin/bash
set -euo pipefail

echo "=== BaseCommand class definition ==="
find . -path ./node_modules -prune -o -name "BaseCommand.php" -type f -print | head -5
find . -path ./node_modules -prune -o -name "BaseCommand.php" -type f -print | xargs head -80

echo
echo "=== AsCommand attribute definition ==="
find . -path ./node_modules -prune -o -name "AsCommand.php" -type f -print | head -5
find . -path ./node_modules -prune -o -name "AsCommand.php" -type f -print | xargs cat

echo
echo "=== Checking if VerificationExecutor uses aliases ==="
rg -n -A5 -B5 'Application::find|runLint' src/Ai/Verify/VerificationExecutor.php

Repository: semitexa/semitexa-dev

Length of output: 6406


Revert test assertions to match actual registered command names or add unprefixed aliases.

The test assertions now expect unprefixed command names (lint:di, lint:handlers, etc.), but the actual registered Symfony commands use the semitexa:lint:* prefix. When VerificationExecutor::runLint() calls Application::find($commandName), it will fail to locate unprefixed commands because they are not registered in the container.

Either:

  1. Update test and planner expectations back to semitexa:lint:*, or
  2. Register unprefixed aliases for all five lint commands in their AsCommand attributes or via application bootstrap

Applies to: Lines 39, 52–53, 83–87

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