fix: skip read-only mounts in permission fixer and remove redundant ssh_keys manifest mount

- apply_mount_permissions now skips mounts with readonly=true to avoid
  'Read-only file system' warnings on post-start chown/chmod
- Removed the ssh_keys mount from the pi-agent manifest definition;
  instance-level SSH key mounting now handles this exclusively
- Added unit test for read-only mount skipping

Quality gates: pytest (15 passed)

apps/api/src/api/tool_instances.py

@@ -1347,7 +1347,9 @@ async def start_instance(
                     ToolDefinitionManifest, manifest_def.base_definition_id
                 )
                 if base_def:
-                    manifest = resolve_base(deep_merge(dict(base_def.manifest), manifest))
+                    manifest = resolve_base(
+                        deep_merge(dict(base_def.manifest), manifest)
+                    )
             home_dir = get_manifest_home_dir(manifest)
             user_cfg = manifest.get("user")
             if user_cfg:

apps/api/src/services/permission_fixer.py

@@ -40,6 +40,17 @@ def apply_mount_permissions(
             "error": None,
         }
 
+        # Skip read-only mounts — their permissions cannot be changed
+        # post-start because the bind mount is locked.
+        if mount.get("readonly", False):
+            logger.debug(
+                "Skipping permission fix for read-only mount %s (target=%s)",
+                name,
+                target,
+            )
+            results.append(result)
+            continue
+
         # Skip if no permission policy defined
         if not owner and not mode and not file_mode:
             results.append(result)