fix: prevent /no_think tag from leaking into user message content

The /no_think directive was appended directly to the user's message text,
causing the LLM to interpret it as user input (e.g., referencing it as a
directory path). Now injected as a separate system message after the last
user message. Also adds which, jq, type, and file to shell allowed_commands
(were mistakenly placed in permissions.auto_approve).

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

app/agent/loop.py

@@ -94,24 +94,23 @@ class AgentLoop:
     def _get_messages_with_system_prompt(self) -> list[Message]:
         """Prepend the system prompt to conversation history.
 
-        When thinking is disabled, injects a /no_think tag into the last user
-        message so Qwen 3.x (and similar) chat templates see it regardless of
-        where tool-result messages fall in the history.
+        When thinking is disabled, appends a system-level /no_think directive
+        after the last user message so Qwen 3.x (and similar) chat templates
+        see it, without polluting the user's actual message content.
         """
         system_msg = Message(role="system", content=self._system_prompt)
         history = self._ctx.get_history()
 
         if not self._config.llm.thinking and history:
             history = list(history)
+            # Find last user message and insert a system hint after it
             for i in range(len(history) - 1, -1, -1):
                 if history[i].role == "user":
-                    original = history[i]
-                    history[i] = Message(
-                        role="user",
-                        content=(original.content or "") + " /no_think",
-                        tool_call_id=original.tool_call_id,
-                        name=original.name,
+                    no_think_msg = Message(
+                        role="system",
+                        content="/no_think",
                     )
+                    history.insert(i + 1, no_think_msg)
                     break
 
         return [system_msg] + history

config/config.yaml

@@ -56,6 +56,10 @@ tools:
       - grep
       - find
       - echo
+      - which
+      - jq
+      - type
+      - file
     denied_commands:
       - rm -rf /
       - sudo