back out bypassPermissions: claude refuses it under root uid

claude-code rejects --dangerously-skip-permissions / defaultMode=
bypassPermissions when running as root, which all hyperhive
containers do. revert to the previous explicit allow-list plumbing
(per-flavor list spliced into permissions.allow + --tools enable
list), keep TodoWrite out of the built-in allow set, and keep the
deny list (TodoWrite, WebFetch, WebSearch, Task) as belt-and-braces
in case anything sneaks past the allow gate.

hive-ag3nt/prompts/claude-settings.json

@@ -1,9 +1,5 @@
 {
   "autoCompactEnabled": false,
   "autoMemoryEnabled": false,
-  "effortLevel": "medium",
-  "permissions": {
-    "defaultMode": "bypassPermissions",
-    "deny": ["WebFetch", "WebSearch", "Task", "TodoWrite"]
-  }
+  "effortLevel": "medium"
 }