added file permissions and fixed a duplicate output bug.

app/services/permissions.py

@@ -0,0 +1,46 @@
+"""Permission gating for tool execution."""
+
+import logging
+
+from rich.prompt import Confirm
+
+from app.models.config import PermissionsConfig
+
+logger = logging.getLogger(__name__)
+
+
+class PermissionDenied(Exception):
+    """Raised when a tool is denied execution by permissions policy."""
+
+
+class PermissionsService:
+    """Check whether a tool is allowed to execute based on config tiers."""
+
+    def __init__(self, config: PermissionsConfig) -> None:
+        self.config = config
+
+    def check(self, tool_name: str, description: str = "") -> bool:
+        """Check if a tool is permitted to run.
+
+        Returns:
+            True if permitted, False if denied.
+        """
+        if tool_name in self.config.deny:
+            logger.info("Tool '%s' is in deny list — blocked", tool_name)
+            return False
+
+        if tool_name in self.config.auto_approve:
+            logger.debug("Tool '%s' is auto-approved", tool_name)
+            return True
+
+        # Explicit prompt_user list or unlisted tools both trigger a prompt
+        return self._prompt_user(tool_name, description)
+
+    def _prompt_user(self, tool_name: str, description: str) -> bool:
+        """Prompt the user for approval via the terminal."""
+        prompt_text = f"Allow tool [bold]{tool_name}[/bold]"
+        if description:
+            prompt_text += f" — {description}"
+        prompt_text += "?"
+
+        return Confirm.ask(prompt_text, default=False)