Replace placeholder files with originals from system

Found and copied original files from ~/.claude installation:

- hooks/ - Original Qwen and Ralph hook scripts with full functionality
- commands/ - Original command definitions (brainstorm, write-plan, execute-plan)
- bin/ralphloop - Original 223-line Python wrapper (6,290 bytes)
- scripts/sync-agents.sh - Original sync script with GitHub/Gitea backup
- templates/ - Original config templates from working installation
- plugins/ - Original comprehensive plugin README

Files sourced from:
- ~/.claude/skills/skills/hooks/
- ~/.claude/skills/skills/commands/
- ~/.claude/skills/skills/templates/
- /home/uroma/obsidian-web-interface/bin/ralphloop
- ~/.claude/agents/sync-agents.sh

These are the production files from the working Claude Code
installation, replacing the placeholder files I created earlier.

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

templates/settings.local.json

@@ -1,10 +1,22 @@
 {
   "permissions": {
-    "allowedPrompts": []
-  },
-  "local": {
-    "autoSuperpowers": true,
-    "ralphAuto": false,
-    "qwenConsultMode": "delegate"
+    "allow": [
+      "Bash(npm install:*)",
+      "Bash(npm run content:*)",
+      "Bash(npm run build:*)",
+      "Bash(grep:*)",
+      "Bash(find:*)",
+      "Bash(for:*)",
+      "Bash(do sed:*)",
+      "Bash(done)",
+      "Bash(python3:*)",
+      "Bash(while read f)",
+      "Bash(do echo \"$f%-* $f\")",
+      "Bash(ls:*)",
+      "Bash(node:*)",
+      "Bash(pm2 delete:*)",
+      "Bash(pm2 start npm:*)",
+      "Bash(pm2 save:*)"
+    ]
   }
 }