docs: consolidate documentation into organized structure

- Move 12 markdown files from root to docs/ subdirectories
- Organize documentation by category:
  • docs/troubleshooting/ (1 file)  - Technical troubleshooting guides
  • docs/deployment/      (4 files) - Deployment and security documentation
  • docs/guides/          (3 files) - Feature-specific guides
  • docs/planning/        (4 files) - Planning and improvement proposals

Root directory cleanup:
- Reduced from 16 to 4 markdown files in root
- Only essential project files remain:
  • CLAUDE.md (AI instructions)
  • README.md (Main project readme)
  • CLEANUP_PLAN.md (Current cleanup plan)
  • SRC_STRUCTURE_IMPROVEMENTS.md (Structure improvements)

This improves:
✅ Documentation discoverability
✅ Logical organization by purpose
✅ Clean root directory
✅ Better maintainability

tests/debug/fix-git-tools-attributes.php

@@ -0,0 +1,18 @@
+<?php
+
+declare(strict_types=1);
+
+$file = __DIR__ . '/../../src/Framework/Mcp/Tools/GitTools.php';
+$content = file_get_contents($file);
+
+// Find and replace all McpTool attributes with inputSchema
+$pattern = '/(#\[McpTool\(\s*name:\s*[\'"]([^\'"]+)[\'"]\s*,\s*description:\s*[\'"]([^\'"]+)[\'"]\s*),\s*inputSchema:\s*\[[^\]]*(?:\[[^\]]*\][^\]]*)*\]\s*\)/s';
+
+$content = preg_replace_callback($pattern, function($matches) {
+    return $matches[1] . ')';
+}, $content);
+
+file_put_contents($file, $content);
+
+echo "Fixed McpTool attributes in GitTools.php\n";
+echo "Removed inputSchema from all attributes\n";