refactor(cli)!: hard-cut legacy scripts and standardize console runtime

- remove legacy bin/module-*.php and bin/doctor.php entry scripts

- move module/doctor execution into class-based runners under lib/Console

- add stable JSON output for doctor and module:sync

- introduce bin/dev for init/up/down/logs/console/qa workflow

- update DI wiring, phpstan scan config, tests, and docs to new CLI contract

lib/Console/Commands/DoctorCommand.php

@@ -3,9 +3,18 @@
 namespace MintyPHP\Console\Commands;
 
 use MintyPHP\Console\Command;
+use MintyPHP\Console\Runner\Doctor\DoctorRunner;
+use MintyPHP\Console\Runner\Doctor\DoctorRunnerInterface;
 
 final class DoctorCommand extends Command
 {
+    private ?DoctorRunnerInterface $runner;
+
+    public function __construct(?DoctorRunnerInterface $runner = null)
+    {
+        $this->runner = $runner;
+    }
+
     public function name(): string
     {
         return 'doctor';
@@ -16,14 +25,58 @@ final class DoctorCommand extends Command
         return 'Run system health checks';
     }
 
+    public function usage(): string
+    {
+        return <<<'USAGE'
+        Usage: php bin/console doctor [--format=json]
+
+        Options:
+          --format=json    Output stable JSON for automation
+        USAGE;
+    }
+
     public function execute(array $args, array $options): int
     {
-        // doctor.php calls exit() internally — run as subprocess
-        // to avoid terminating the console process.
-        $scriptPath = $this->projectRoot() . '/bin/doctor.php';
-        $command = PHP_BINARY . ' ' . escapeshellarg($scriptPath);
-        passthru($command, $exitCode);
+        $format = strtolower((string) ($options['format'] ?? 'human'));
+        if (!in_array($format, ['human', 'json'], true)) {
+            fwrite(STDERR, "Invalid format '{$format}'. Supported: human, json\n");
+            return 1;
+        }
 
-        return $exitCode;
+        $result = $this->runner()->run();
+
+        if ($format === 'json') {
+            echo json_encode($result, JSON_PRETTY_PRINT | JSON_UNESCAPED_SLASHES) . PHP_EOL;
+            return (int) $result['exit_code'];
+        }
+
+        echo "Minty Doctor Report\n";
+        echo "===================\n";
+        foreach ($result['checks'] as $item) {
+            echo sprintf(
+                "[%s] %s: %s\n",
+                strtoupper($item['status']),
+                $item['name'],
+                $item['message']
+            );
+        }
+        echo sprintf(
+            "\nSummary: ok=%d warn=%d fail=%d\n",
+            $result['ok_count'],
+            $result['warn_count'],
+            $result['fail_count']
+        );
+
+        return (int) $result['exit_code'];
+    }
+
+    private function runner(): DoctorRunnerInterface
+    {
+        if ($this->runner instanceof DoctorRunnerInterface) {
+            return $this->runner;
+        }
+
+        $this->runner = new DoctorRunner();
+        return $this->runner;
     }
 }