Add Phase 6: write tools, shell, and edit tools with reasoning-only fix

Implement 6 new agent tools — write_file, make_dir, delete_file,
str_replace, patch_apply, run_command — bringing the agent from
read-only observer to active code modifier. All write/shell operations
are gated through the existing permissions service.

Also fix a bug where qwen3.5 thinking mode produces reasoning tokens
but no content after tool results, causing the agent to silently exit.
The loop now detects reasoning-only responses, retries twice, then
injects a nudge message to break the model out of its thinking loop.

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

app/agent/context.py

@@ -41,6 +41,13 @@ class SessionContext:
         self._message_count += 1
         return message
 
+    def pop_last_message(self) -> Message | None:
+        """Remove and return the last message, or None if history is empty."""
+        if self._history:
+            self._message_count -= 1
+            return self._history.pop()
+        return None
+
     def get_history(self) -> list[Message]:
         """Return a shallow copy of the conversation history."""
         return list(self._history)