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>

config/config.yaml

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