Fix bin/publish: copy docs.dist from project root

Fix bin/publish: use correct .env path for rspade_system
Fix bin/publish script: prevent grep exit code 1 from terminating script

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Co-Authored-By: Claude <noreply@anthropic.com>

app/RSpade/CodeQuality/Rules/Common/RsxCommandsDeprecated_CodeQualityRule.php

@@ -0,0 +1,143 @@
+<?php
+
+namespace App\RSpade\CodeQuality\Rules\Common;
+
+use App\RSpade\CodeQuality\Rules\CodeQualityRule_Abstract;
+
+class RsxCommandsDeprecated_CodeQualityRule extends CodeQualityRule_Abstract
+{
+    public function get_id(): string
+    {
+        return 'RSX-CMD-DEPRECATED-01';
+    }
+    
+    public function get_name(): string
+    {
+        return 'RSX Commands Deprecated Features Check';
+    }
+    
+    public function get_description(): string
+    {
+        return 'Checks RSX commands for deprecated features or references';
+    }
+    
+    public function get_file_patterns(): array
+    {
+        // This rule doesn't use standard file pattern matching
+        // It scans its own directory when check_rsx_commands() is called
+        return [];
+    }
+    
+    public function get_default_severity(): string
+    {
+        return 'high';
+    }
+    
+    /**
+     * Standard check method - not used for this rule
+     */
+    public function check(string $file_path, string $contents, array $metadata = []): void
+    {
+        // This rule uses check_rsx_commands() instead
+        return;
+    }
+    
+    /**
+     * Special method to check RSX commands directory
+     * Called only when rsx:check is run with default paths
+     */
+    public function check_rsx_commands(): void
+    {
+        // Only run when using default paths
+        if (!($this->config['using_default_paths'] ?? false)) {
+            return;
+        }
+        
+        $base_path = function_exists('base_path') ? base_path() : '/var/www/html';
+        $commands_dir = $base_path . '/app/RSpade/Commands/Rsx';
+        
+        // Check if directory exists
+        if (!is_dir($commands_dir)) {
+            return;
+        }
+        
+        // Scan for PHP files in the RSX commands directory
+        $files = glob($commands_dir . '/*.php');
+        
+        foreach ($files as $file_path) {
+            $this->check_file_for_deprecated($file_path);
+        }
+    }
+    
+    /**
+     * Check a single file for deprecated references
+     */
+    private function check_file_for_deprecated(string $file_path): void
+    {
+        $contents = file_get_contents($file_path);
+        if ($contents === false) {
+            return;
+        }
+        
+        $lines = explode("\n", $contents);
+        $filename = basename($file_path);
+        
+        foreach ($lines as $line_number => $line) {
+            // Check for the word 'deprecated' (case insensitive)
+            if (stripos($line, 'deprecated') !== false) {
+                // Get the actual line number (1-indexed)
+                $actual_line = $line_number + 1;
+                
+                // Extract context around the deprecated reference
+                $context_start = max(0, $line_number - 2);
+                $context_end = min(count($lines) - 1, $line_number + 2);
+                $context_lines = array_slice($lines, $context_start, $context_end - $context_start + 1);
+                $context = implode("\n", $context_lines);
+                
+                $this->add_violation(
+                    $file_path,
+                    $actual_line,
+                    "Command file '{$filename}' contains reference to 'deprecated'",
+                    trim($line),
+                    $this->get_deprecated_remediation($filename, $line),
+                    'high'
+                );
+            }
+        }
+    }
+    
+    /**
+     * Get remediation message for deprecated references
+     */
+    private function get_deprecated_remediation(string $filename, string $line): string
+    {
+        return "DEPRECATED FEATURE REFERENCE IN RSX COMMAND
+
+File: {$filename}
+Line containing 'deprecated': {$line}
+
+RSX commands should not contain deprecated features or references to deprecated functionality.
+
+REQUIRED ACTIONS:
+1. Remove the deprecated feature or functionality from the command
+2. Remove any help text or documentation mentioning deprecated features
+3. Update command logic to use current recommended approaches
+4. If the entire command is deprecated, consider removing it
+
+COMMON DEPRECATED PATTERNS TO REMOVE:
+- Old command aliases marked as deprecated
+- Legacy options or flags no longer in use
+- References to deprecated framework features
+- Outdated help text mentioning deprecated usage
+
+WHY THIS MATTERS:
+- Prevents confusion about which features are current
+- Reduces maintenance burden of legacy code
+- Ensures commands reflect current best practices
+- Maintains clean and consistent command interface
+
+If this is documentation about deprecation for historical context,
+consider moving it to separate documentation rather than keeping it
+in the active command code.";
+    }
+}